Editorial

3 pages, 176 KiB

Open AccessEditorial

Plant Genomics—Advancing Our Understanding of Plants

by Frank M. You

Int. J. Mol. Sci. 2023, 24(14), 11528; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms241411528 - 16 Jul 2023

Cited by 1 | Viewed by 897

Plant genomics has made significant progress in recent years, enabling researchers to identify genes and genomic regions responsible for plant growth, development, and stress response [...] Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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17 pages, 6176 KiB

Open AccessArticle

Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations

by Aleksandra Skalska, Christoph Stritt, Michele Wyler, Hefin W. Williams, Martin Vickers, Jiwan Han, Metin Tuna, Gulsemin Savas Tuna, Karolina Susek, Martin Swain, Rafał K. Wóycicki, Saurabh Chaudhary, Fiona Corke, John H. Doonan, Anne C. Roulin, Robert Hasterok and Luis A. J. Mur

Int. J. Mol. Sci. 2020, 21(18), 6700; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21186700 - 13 Sep 2020

Cited by 10 | Viewed by 4660

Abstract

Brachypodium distachyon (Brachypodium) is a non-domesticated model grass species that can be used to test if variation in genetic sequence or methylation are linked to environmental differences. To assess this, we collected seeds from 12 sites within five climatically distinct regions of Turkey. [...] Read more.

Brachypodium distachyon (Brachypodium) is a non-domesticated model grass species that can be used to test if variation in genetic sequence or methylation are linked to environmental differences. To assess this, we collected seeds from 12 sites within five climatically distinct regions of Turkey. Seeds from each region were grown under standardized growth conditions in the UK to preserve methylated sequence variation. At six weeks following germination, leaves were sampled and assessed for genomic and DNA methylation variation. In a follow-up experiment, phenomic approaches were used to describe plant growth and drought responses. Genome sequencing and population structure analysis suggested three ancestral clusters across the Mediterranean, two of which were geographically separated in Turkey into coastal and central subpopulations. Phenotypic analyses showed that the coastal subpopulation tended to exhibit relatively delayed flowering and the central, increased drought tolerance as indicated by reduced yellowing. Genome-wide methylation analyses in GpC, CHG and CHH contexts also showed variation which aligned with the separation into coastal and central subpopulations. The climate niche modelling of both subpopulations showed a significant influence from the “Precipitation in the Driest Quarter” on the central subpopulation and “Temperature of the Coldest Month” on the coastal subpopulation. Our work demonstrates genetic diversity and variation in DNA methylation in Turkish accessions of Brachypodium that may be associated with climate variables and the molecular basis of which will feature in ongoing analyses. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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17 pages, 3531 KiB

Open AccessArticle

Identification and Expression Analysis of Hormone Biosynthetic and Metabolism Genes in the 2OGD Family for Identifying Genes That May Be Involved in Tomato Fruit Ripening

by Qiangqiang Ding, Feng Wang, Juan Xue, Xinxin Yang, Junmiao Fan, Hong Chen, Yi Li and Han Wu

Int. J. Mol. Sci. 2020, 21(15), 5344; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21155344 - 28 Jul 2020

Cited by 11 | Viewed by 3192

Abstract

Phytohormones play important roles in modulating tomato fruit development and ripening. The 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily containing several subfamilies involved in hormone biosynthesis and metabolism. In this study, we aimed to identify hormone biosynthesis and metabolism-related to 2OGD proteins in tomato and explored [...] Read more.

Phytohormones play important roles in modulating tomato fruit development and ripening. The 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily containing several subfamilies involved in hormone biosynthesis and metabolism. In this study, we aimed to identify hormone biosynthesis and metabolism-related to 2OGD proteins in tomato and explored their roles in fruit development and ripening. We identified nine 2OGD protein subfamilies involved in hormone biosynthesis and metabolism, including the gibberellin (GA) biosynthetic protein families GA20ox and GA3ox, GA degradation protein families C19-GA2ox and C20-GA2ox, ethylene biosynthetic protein family ACO, auxin degradation protein family DAO, jasmonate hydroxylation protein family JOX, salicylic acid degradation protein family DMR6, and strigolactone biosynthetic protein family LBO. These genes were differentially expressed in different tomato organs. The GA degradation gene SlGA2ox2, and the auxin degradation gene SlDAO1, showed significantly increased expression from the mature-green to the breaker stage during tomato fruit ripening, accompanied by decreased endogenous GA and auxin, indicating that SlGA2ox2 and SlDAO1 were responsible for the reduced GA and auxin concentrations. Additionally, exogenous gibberellin 3 (GA₃) and indole-3-acetic acid (IAA) treatment of mature-green fruits delayed fruit ripening and increased the expression of SlGA2ox2 and SlDAO1, respectively. Therefore, SlGA2ox2 and SlDAO1 are implicated in the degradation of GAs and auxin during tomato fruit ripening. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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20 pages, 2763 KiB

Open AccessArticle

Silencing of TaCKX1 Mediates Expression of Other TaCKX Genes to Increase Yield Parameters in Wheat

by Bartosz Jabłoński, Hanna Ogonowska, Karolina Szala, Andrzej Bajguz, Wacław Orczyk and Anna Nadolska-Orczyk

Int. J. Mol. Sci. 2020, 21(13), 4809; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21134809 - 07 Jul 2020

Cited by 24 | Viewed by 3013

Abstract

TaCKX, Triticum aestivum (cytokinin oxidase/dehydrogenase) family genes influence the development of wheat plants by the specific regulation of cytokinin content in different organs. However, their detailed role is not known. The TaCKX1, highly and specifically expressed in developing spikes and in [...] Read more.

TaCKX, Triticum aestivum (cytokinin oxidase/dehydrogenase) family genes influence the development of wheat plants by the specific regulation of cytokinin content in different organs. However, their detailed role is not known. The TaCKX1, highly and specifically expressed in developing spikes and in seedling roots, was silenced by RNAi-mediated gene silencing via Agrobacterium tumefaciens and the effect of silencing was investigated in 7 DAP (days after pollination) spikes of T₁ and T₂ generations. Various levels of TaCKX1 silencing in both generations influence different models of co-expression with other TaCKX genes and parameters of yield-related traits. Only a high level of silencing in T₂ resulted in strong down-regulation of TaCKX11 (3), up-regulation of TaCKX2.1, 2.2, 5, and 9 (10), and a high yielding phenotype. This phenotype is characterized by a higher spike number, grain number, and grain yield, but lower thousand grain weight (TGW). The content of most of cytokinin forms in 7 DAP spikes of silenced T₂ lines increased from 23% to 76% compared to the non-silenced control. The CKs cross talk with other phytohormones. Each of the tested yield-related traits is regulated by various up- or down-regulated TaCKX genes and phytohormones. The coordinated effect of TaCKX1 silencing on the expression of other TaCKX genes, phytohormone levels in 7 DAP spikes, and yield-related traits in silenced T₂ lines is presented. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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19 pages, 3703 KiB

Open AccessArticle

Evolutionary and Predictive Functional Insights into the Aquaporin Gene Family in the Allotetraploid Plant Nicotiana tabacum

by Jahed Ahmed, Sébastien Mercx, Marc Boutry and François Chaumont

Int. J. Mol. Sci. 2020, 21(13), 4743; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21134743 - 03 Jul 2020

Cited by 10 | Viewed by 4525

Abstract

Aquaporins (AQPs) are a class of integral membrane proteins that facilitate the membrane diffusion of water and other small solutes. Nicotiana tabacum is an important model plant, and its allotetraploid genome has recently been released, providing us with the opportunity to analyze the [...] Read more.

Aquaporins (AQPs) are a class of integral membrane proteins that facilitate the membrane diffusion of water and other small solutes. Nicotiana tabacum is an important model plant, and its allotetraploid genome has recently been released, providing us with the opportunity to analyze the AQP gene family and its evolution. A total of 88 full-length AQP genes were identified in the N. tabacum genome, and the encoding proteins were assigned into five subfamilies: 34 plasma membrane intrinsic proteins (PIPs); 27 tonoplast intrinsic proteins (TIPs); 20 nodulin26-like intrinsic proteins (NIPs); 3 small basic intrinsic proteins (SIPs); 4 uncharacterized X intrinsic proteins (XIPs), including two splice variants. We also analyzed the genomes of two N. tabacum ancestors, Nicotiana tomentosiformis and Nicotiana sylvestris, and identified 49 AQP genes in each species. Functional prediction, based on the substrate specificity-determining positions (SDPs), revealed significant differences in substrate specificity among the AQP subfamilies. Analysis of the organ-specific AQP expression levels in the N. tabacum plant and RNA-seq data of N. tabacum bright yellow-2 suspension cells indicated that many AQPs are simultaneously expressed, but differentially, according to the organs or the cells. Altogether, these data constitute an important resource for future investigations of the molecular, evolutionary, and physiological functions of AQPs in N. tabacum. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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18 pages, 4644 KiB

Open AccessArticle

Gene Expression Analysis and Metabolite Profiling of Silymarin Biosynthesis during Milk Thistle (Silybum marianum (L.) Gaertn.) Fruit Ripening

by Samantha Drouet, Duangjai Tungmunnithum, Éric Lainé and Christophe Hano

Int. J. Mol. Sci. 2020, 21(13), 4730; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21134730 - 02 Jul 2020

Cited by 12 | Viewed by 3753

Abstract

Mature fruits (i.e., achenes) of milk thistle (Silybum marianum (L.) Gaertn., Asteraceae) accumulate high amounts of silymarin (SILM), a complex mixture of bioactive flavonolignans deriving from taxifolin. Their biological activities in relation with human health promotion and disease prevention are well described. [...] Read more.

Mature fruits (i.e., achenes) of milk thistle (Silybum marianum (L.) Gaertn., Asteraceae) accumulate high amounts of silymarin (SILM), a complex mixture of bioactive flavonolignans deriving from taxifolin. Their biological activities in relation with human health promotion and disease prevention are well described. However, the conditions of their biosynthesis in planta are still obscure. To fill this gap, fruit development stages were first precisely defined to study the accumulation kinetics of SILM constituents during fruit ripening. The accumulation profiles of the SILM components during fruit maturation were determined using the LC-MS analysis of these defined developmental phases. The kinetics of phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS) and peroxidase (POX) activities suggest in situ biosynthesis of SILM from l-Phenylalanine during fruit maturation rather than a transport of precursors to the achene. In particular, in contrast to laccase activity, POX activity was associated with the accumulation of silymarin, thus indicating a possible preferential involvement of peroxidase(s) in the oxidative coupling step leading to flavonolignans. Reference genes have been identified, selected and validated to allow accurate gene expression profiling of candidate biosynthetic genes (PAL, CAD, CHS, F3H, F3’H and POX) related to SILM accumulation. Gene expression profiles were correlated with SILM accumulation kinetic and preferential location in pericarp during S. marianum fruit maturation, reaching maximum biosynthesis when desiccation occurs, thus reinforcing the hypothesis of an in situ biosynthesis. This observation led us to consider the involvement of abscisic acid (ABA), a key phytohormone in the control of fruit ripening process. ABA accumulation timing and location during milk thistle fruit ripening appeared in line with a potential regulation of the SLIM accumulation. A possible transcriptional regulation of SILM biosynthesis by ABA was supported by the presence of ABA-responsive cis-acting elements in the promoter regions of the SILM biosynthetic genes studied. These results pave the way for a better understanding of the biosynthetic regulation of SILM during the maturation of S. marianum fruit and offer important insights to better control the production of these medicinally important compounds. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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30 pages, 5761 KiB

Open AccessArticle

Red Chinese Cabbage Transcriptome Analysis Reveals Structural Genes and Multiple Transcription Factors Regulating Reddish Purple Color

by Jana Jeevan Rameneni, Su Ryun Choi, Sushil Satish Chhapekar, Man-Sun Kim, Sonam Singh, So Young Yi, Sang Heon Oh, Hyuna Kim, Chang Yeol Lee, Man-Ho Oh, Jhongchul Lee, Oh Ha Kwon, Sang Un Park, Sun-Ju Kim and Yong Pyo Lim

Int. J. Mol. Sci. 2020, 21(8), 2901; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21082901 - 21 Apr 2020

Cited by 20 | Viewed by 4907

Abstract

Reddish purple Chinese cabbage (RPCC) is a popular variety of Brassica rapa (AA = 20). It is rich in anthocyanins, which have many health benefits. We detected novel anthocyanins including cyanidin 3-(feruloyl) diglucoside-5-(malonoyl) glucoside and pelargonidin 3-(caffeoyl) diglucoside-5-(malonoyl) glucoside in RPCC. Analyses of [...] Read more.

Reddish purple Chinese cabbage (RPCC) is a popular variety of Brassica rapa (AA = 20). It is rich in anthocyanins, which have many health benefits. We detected novel anthocyanins including cyanidin 3-(feruloyl) diglucoside-5-(malonoyl) glucoside and pelargonidin 3-(caffeoyl) diglucoside-5-(malonoyl) glucoside in RPCC. Analyses of transcriptome data revealed 32,395 genes including 3345 differentially expressed genes (DEGs) between 3-week-old RPCC and green Chinese cabbage (GCC). The DEGs included 218 transcription factor (TF) genes and some functionally uncharacterized genes. Sixty DEGs identified from the transcriptome data were analyzed in 3-, 6- and 9-week old seedlings by RT-qPCR, and 35 of them had higher transcript levels in RPCC than in GCC. We detected cis-regulatory motifs of MYB, bHLH, WRKY, bZIP and AP2/ERF TFs in anthocyanin biosynthetic gene promoters. A network analysis revealed that MYB75, MYB90, and MYBL2 strongly interact with anthocyanin biosynthetic genes. Our results show that the late biosynthesis genes BrDFR, BrLDOX, BrUF3GT, BrUGT75c1-1, Br5MAT, BrAT-1, BrAT-2, BrTT19-1, and BrTT19-2 and the regulatory MYB genes BrMYB90, BrMYB75, and BrMYBL2-1 are highly expressed in RPCC, indicative of their important roles in anthocyanin biosynthesis, modification, and accumulation. Finally, we propose a model anthocyanin biosynthesis pathway that includes the unique anthocyanin pigments and genes specific to RPCC. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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14 pages, 3171 KiB

Open AccessArticle

Identification and Characterization of microRNAs in the Developing Seed of Linseed Flax (Linum usitatissimum L.)

by Tianbao Zhang, Zhen Li, Xiaxia Song, Lida Han, Limin Wang, Jianping Zhang, Yan Long and Xinwu Pei

Int. J. Mol. Sci. 2020, 21(8), 2708; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21082708 - 14 Apr 2020

Cited by 13 | Viewed by 2807

Abstract

Seed development plays an important role during the life cycle of plants. Linseed flax is an oil crop and the seed is a key organ for fatty acids synthesis and storage. So it is important to understand the molecular mechanism of fatty acid [...] Read more.

Seed development plays an important role during the life cycle of plants. Linseed flax is an oil crop and the seed is a key organ for fatty acids synthesis and storage. So it is important to understand the molecular mechanism of fatty acid biosynthesis during seed development. In this study, four small RNA libraries from early seeds at 5, 10, 20 and 30 days after flowering (DAF) were constructed and used for high-throughput sequencing to identify microRNAs (miRNAs). A total of 235 miRNAs including 114 known conserved miRNAs and 121 novel miRNAs were identified. The expression patterns of these miRNAs in the four libraries were investigated by bioinformatics and quantitative real-time polymerase chain reaction (qPCR) analysis. It was found that several miRNAs, including Lus-miRNA156a was significantly correlated with seed development process. In order to confirm the actual biological function of Lus-miRNA156a, over-expression vector was constructed and transformed to Arabidopsis. The phenotypes of homozygous transgenic lines showed decreasing of oil content and most of the fatty acid content in seeds as well as late flowering time. The results provided a clue that miRNA156a participating the fatty acid biosynthesis pathway and the detailed molecular mechanism of how it regulates the pathway needs to be further investigated. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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29 pages, 7068 KiB

Open AccessArticle

A Tale of Two Families: Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin (Lupinus angustifolius L.)

by Katarzyna B. Czyż, Michał Książkiewicz, Grzegorz Koczyk, Anna Szczepaniak, Jan Podkowiński and Barbara Naganowska

Int. J. Mol. Sci. 2020, 21(7), 2580; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21072580 - 08 Apr 2020

Cited by 4 | Viewed by 3057

Abstract

Narrow-leafed lupin (Lupinus angustifolius L.) has recently been supplied with advanced genomic resources and, as such, has become a well-known model for molecular evolutionary studies within the legume family—a group of plants able to fix nitrogen from the atmosphere. The phylogenetic position [...] Read more.

Narrow-leafed lupin (Lupinus angustifolius L.) has recently been supplied with advanced genomic resources and, as such, has become a well-known model for molecular evolutionary studies within the legume family—a group of plants able to fix nitrogen from the atmosphere. The phylogenetic position of lupins in Papilionoideae and their evolutionary distance to other higher plants facilitates the use of this model species to improve our knowledge on genes involved in nitrogen assimilation and primary metabolism, providing novel contributions to our understanding of the evolutionary history of legumes. In this study, we present a complex characterization of two narrow-leafed lupin gene families—glutamine synthetase (GS) and phosphoenolpyruvate carboxylase (PEPC). We combine a comparative analysis of gene structures and a synteny-based approach with phylogenetic reconstruction and reconciliation of the gene family and species history in order to examine events underlying the extant diversity of both families. Employing the available evidence, we show the impact of duplications on the initial complement of the analyzed gene families within the genistoid clade and posit that the function of duplicates has been largely retained. In terms of a broader perspective, our results concerning GS and PEPC gene families corroborate earlier findings pointing to key whole genome duplication/triplication event(s) affecting the genistoid lineage. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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21 pages, 4008 KiB

Open AccessArticle

Genomic Prediction Accuracy of Seven Breeding Selection Traits Improved by QTL Identification in Flax

by Samuel Lan, Chunfang Zheng, Kyle Hauck, Madison McCausland, Scott D. Duguid, Helen M. Booker, Sylvie Cloutier and Frank M. You

Int. J. Mol. Sci. 2020, 21(5), 1577; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21051577 - 25 Feb 2020

Cited by 17 | Viewed by 3829

Abstract

Molecular markers are one of the major factors affecting genomic prediction accuracy and the cost of genomic selection (GS). Previous studies have indicated that the use of quantitative trait loci (QTL) as markers in GS significantly increases prediction accuracy compared with genome-wide random [...] Read more.

Molecular markers are one of the major factors affecting genomic prediction accuracy and the cost of genomic selection (GS). Previous studies have indicated that the use of quantitative trait loci (QTL) as markers in GS significantly increases prediction accuracy compared with genome-wide random single nucleotide polymorphism (SNP) markers. To optimize the selection of QTL markers in GS, a set of 260 lines from bi-parental populations with 17,277 genome-wide SNPs were used to evaluate the prediction accuracy for seed yield (YLD), days to maturity (DTM), iodine value (IOD), protein (PRO), oil (OIL), linoleic acid (LIO), and linolenic acid (LIN) contents. These seven traits were phenotyped over four years at two locations. Identification of quantitative trait nucleotides (QTNs) for the seven traits was performed using three types of statistical models for genome-wide association study: two SNP-based single-locus (SS), seven SNP-based multi-locus (SM), and one haplotype-block-based multi-locus (BM) models. The identified QTNs were then grouped into QTL based on haplotype blocks. For all seven traits, 133, 355, and 1208 unique QTL were identified by SS, SM, and BM, respectively. A total of 1420 unique QTL were obtained by SS+SM+BM, ranging from 254 (OIL, LIO) to 361 (YLD) for individual traits, whereas a total of 427 unique QTL were achieved by SS+SM, ranging from 56 (YLD) to 128 (LIO). SS models alone did not identify sufficient QTL for GS. The highest prediction accuracies were obtained using single-trait QTL identified by SS+SM+BM for OIL (0.929 ± 0.016), PRO (0.893 ± 0.023), YLD (0.892 ± 0.030), and DTM (0.730 ± 0.062), and by SS+SM for LIN (0.837 ± 0.053), LIO (0.835 ± 0.049), and IOD (0.835 ± 0.041). In terms of the number of QTL markers and prediction accuracy, SS+SM outperformed other models or combinations thereof. The use of all SNPs or QTL of all seven traits significantly reduced the prediction accuracy of traits. The results further validated that QTL outperformed high-density genome-wide random markers, and demonstrated that the combined use of single and multi-locus models can effectively identify a comprehensive set of QTL that improve prediction accuracy, but further studies on detection and removal of redundant or false-positive QTL to maximize prediction accuracy and minimize the number of QTL markers in GS are warranted. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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19 pages, 4530 KiB

Open AccessArticle

Integrated Metabolomic and Transcriptomic Analysis to Characterize Cutin Biosynthesis between Low- and High-Cutin Genotypes of Capsicum chinense Jacq

by Purushothaman Natarajan, Tolulope Abodunrin Akinmoju, Padma Nimmakayala, Carlos Lopez-Ortiz, Marleny Garcia-Lozano, Benjamin J. Thompson, John Stommel and Umesh K. Reddy

Int. J. Mol. Sci. 2020, 21(4), 1397; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21041397 - 19 Feb 2020

Cited by 15 | Viewed by 4220

Abstract

Habanero peppers constantly face biotic and abiotic stresses such as pathogen/pest infections, extreme temperature, drought and UV radiation. In addition, the fruit cutin lipid composition plays an important role in post-harvest water loss rates, which in turn causes shriveling and reduced fruit quality [...] Read more.

Habanero peppers constantly face biotic and abiotic stresses such as pathogen/pest infections, extreme temperature, drought and UV radiation. In addition, the fruit cutin lipid composition plays an important role in post-harvest water loss rates, which in turn causes shriveling and reduced fruit quality and storage. In this study, we integrated metabolome and transcriptome profiling pertaining to cutin in two habanero genotypes: PI 224448 and PI 257145. The fruits were selected by the waxy or glossy phenotype on their surfaces. Metabolomics analysis showed a significant variation in cutin composition, with about 6-fold higher cutin in PI 257145 than PI 224448. It also revealed that 10,16-dihydroxy hexadecanoic acid is the most abundant monomer in PI 257145. Transcriptomic analysis of high-cutin PI 257145 and low-cutin PI 224448 resulted in the identification of 2703 statistically significant differentially expressed genes, including 1693 genes upregulated and 1010 downregulated in high-cutin PI 257145. Genes and transcription factors such as GDSL lipase, glycerol-3 phosphate acyltransferase 6, long-chain acyltransferase 2, cytochrome P450 86A/77A, SHN1, ANL2 and HDG1 highly contributed to the high cutin content in PI 257145. We predicted a putative cutin biosynthetic pathway for habanero peppers based on deep transcriptome analysis. This is the first study of the transcriptome and metabolome pertaining to cutin in habanero peppers. These analyses improve our knowledge of the molecular mechanisms regulating the accumulation of cutin in habanero pepper fruits. These resources can be built on for developing cultivars with high cutin content that show resistance to biotic and abiotic stresses with superior postharvest appearance. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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18 pages, 1207 KiB

Open AccessArticle

Genomic Prediction for Grain Yield and Yield-Related Traits in Chinese Winter Wheat

by Mohsin Ali, Yong Zhang, Awais Rasheed, Jiankang Wang and Luyan Zhang

Int. J. Mol. Sci. 2020, 21(4), 1342; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21041342 - 17 Feb 2020

Cited by 27 | Viewed by 3420

Abstract

Genomic selection (GS) is a strategy to predict the genetic merits of individuals using genome-wide markers. However, GS prediction accuracy is affected by many factors, including missing rate and minor allele frequency (MAF) of genotypic data, GS models, trait features, etc. In this [...] Read more.

Genomic selection (GS) is a strategy to predict the genetic merits of individuals using genome-wide markers. However, GS prediction accuracy is affected by many factors, including missing rate and minor allele frequency (MAF) of genotypic data, GS models, trait features, etc. In this study, we used one wheat population to investigate prediction accuracies of various GS models on yield and yield-related traits from various quality control (QC) scenarios, missing genotype imputation, and genome-wide association studies (GWAS)-derived markers. Missing rate and MAF of single nucleotide polymorphism (SNP) markers were two major factors in QC. Five missing rate levels (0%, 20%, 40%, 60%, and 80%) and three MAF levels (0%, 5%, and 10%) were considered and the five-fold cross validation was used to estimate the prediction accuracy. The results indicated that a moderate missing rate level (20% to 40%) and MAF (5%) threshold provided better prediction accuracy. Under this QC scenario, prediction accuracies were further calculated for imputed and GWAS-derived markers. It was observed that the accuracies of the six traits were related to their heritability and genetic architecture, as well as the GS prediction model. Moore–Penrose generalized inverse (GenInv), ridge regression (RidgeReg), and random forest (RForest) resulted in higher prediction accuracies than other GS models across traits. Imputation of missing genotypic data had marginal effect on prediction accuracy, while GWAS-derived markers improved the prediction accuracy in most cases. These results demonstrate that QC on missing rate and MAF had positive impact on the predictability of GS models. We failed to identify one single combination of QC scenarios that could outperform the others for all traits and GS models. However, the balance between marker number and marker quality is important for the deployment of GS in wheat breeding. GWAS is able to select markers which are mostly related to traits, and therefore can be used to improve the prediction accuracy of GS. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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19 pages, 4023 KiB

Open AccessArticle

Genomics-Enabled Analysis of Puroindoline b2 Genes Identifies New Alleles in Wheat and Related Triticeae Species

by Xiaoyan Li, Yin Li, Xiaofen Yu, Fusheng Sun, Guangxiao Yang and Guangyuan He

Int. J. Mol. Sci. 2020, 21(4), 1304; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21041304 - 14 Feb 2020

Cited by 4 | Viewed by 3052

Abstract

Kernel hardness is a key trait of wheat seeds, largely controlled by two tightly linked genes Puroindoline a and b (Pina and Pinb). Genes homologous to Pinb, namely Pinb2, have been studied. Whether these genes contribute to kernel hardness [...] Read more.

Kernel hardness is a key trait of wheat seeds, largely controlled by two tightly linked genes Puroindoline a and b (Pina and Pinb). Genes homologous to Pinb, namely Pinb2, have been studied. Whether these genes contribute to kernel hardness and other important seed traits remains inconclusive. Using the high-quality bread wheat reference genome, we show that PINB2 are encoded by three homoeologous loci Pinb2 not syntenic to the Hardness locus, with Pinb2-7A locus containing three tandem copies. PINB2 proteins have several features conserved for the Pin/Pinb2 phylogenetic cluster but lack a structural basis of significant impact on kernel hardness. Pinb2 are seed-specifically expressed with varied expression levels between the homoeologous copies and among wheat varieties. Using the high-quality genome information, we developed new Pinb2 allele specific markers and demonstrated their usefulness by 1) identifying new Pinb2 alleles in Triticeae species; and 2) performing an association analysis of Pinb2 with kernel hardness. The association result suggests that Pinb2 genes may have no substantial contribution to kernel hardness. Our results provide new insights into Pinb2 evolution and expression and the new allele-specific markers are useful to further explore Pinb2’s contribution to seed traits in wheat. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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16 pages, 4239 KiB

Open AccessArticle

Genome-Wide Characterization and Expression Profiling of GASA Genes during Different Stages of Seed Development in Grapevine (Vitis vinifera L.) Predict Their Involvement in Seed Development

by Bilal Ahmad, Jin Yao, Songlin Zhang, Xingmei Li, Xiuming Zhang, Vivek Yadav and Xiping Wang

Int. J. Mol. Sci. 2020, 21(3), 1088; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21031088 - 06 Feb 2020

Cited by 33 | Viewed by 4625

Abstract

Members of the plant-specific GASA (gibberellic acid-stimulated Arabidopsis) gene family have multiple potential roles in plant growth and development, particularly in flower induction and seed development. However, limited information is available about the functions of these genes in fruit plants, particularly in grapes. [...] Read more.

Members of the plant-specific GASA (gibberellic acid-stimulated Arabidopsis) gene family have multiple potential roles in plant growth and development, particularly in flower induction and seed development. However, limited information is available about the functions of these genes in fruit plants, particularly in grapes. We identified 14 GASA genes in grapevine (Vitis vinifera L.) and performed comprehensive bioinformatics and expression analyses. In the bioinformatics analysis, the locations of genes on chromosomes, physiochemical properties of proteins, protein structure, and subcellular positions were described. We evaluated GASA proteins in terms of domain structure, exon-intron distribution, motif arrangements, promoter analysis, phylogenetic, and evolutionary history. According to the results, the GASA domain is conserved in all proteins and the proteins are divided into three well-conserved subgroups. Synteny analysis proposed that segmental and tandem duplication have played a role in the expansion of the GASA gene family in grapes, and duplicated gene pairs have negative selection pressure. Most of the proteins were predicted to be in the extracellular region, chloroplasts, and the vacuole. In silico promoter analysis suggested that the GASA genes may influence different hormone signaling pathways and stress-related mechanisms. Additionally, we performed a comparison of the expression between seedless (Thompson seedless) and seeded (Red globe) cultivars in different plant parts, including the ovule during different stages of development. Furthermore, some genes were differentially expressed in different tissues, signifying their role in grapevine growth and development. Several genes (VvGASA2 and 7) showed different expression levels in later phases of seed development in Red globe and Thompson seedless, suggesting their involvement in seed development. Our study presents the first genome-wide identification and expression profiling of grapevine GASA genes and provides the basis for functional characterization of GASA genes in grapes. We surmise that this information may provide new potential resources for the molecular breeding of grapes. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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17 pages, 4850 KiB

Open AccessArticle

Molecular Characterization and Disease Control of Stem Canker on Royal Poinciana (Delonix regia) Caused by Neoscytalidium dimidiatum in the United Arab Emirates

by Seham M. Al Raish, Esam Eldin Saeed, Arjun Sham, Khulood Alblooshi, Khaled A. El-Tarabily and Synan F. AbuQamar

Int. J. Mol. Sci. 2020, 21(3), 1033; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21031033 - 04 Feb 2020

Cited by 16 | Viewed by 7491

Abstract

In the United Arab Emirates (UAE), royal poinciana (Delonix regia) trees suffer from stem canker disease. Symptoms of stem canker can be characterized by branch and leaf dryness, bark lesions, discoloration of xylem tissues, longitudinal wood necrosis and extensive gumming. General [...] Read more.

In the United Arab Emirates (UAE), royal poinciana (Delonix regia) trees suffer from stem canker disease. Symptoms of stem canker can be characterized by branch and leaf dryness, bark lesions, discoloration of xylem tissues, longitudinal wood necrosis and extensive gumming. General dieback signs were also observed leading to complete defoliation of leaves and ultimately death of trees in advanced stages. The fungus, Neoscytalidium dimidiatum DSM 109897, was consistently recovered from diseased royal poinciana tissues; this was confirmed by the molecular, structural and morphological studies. Phylogenetic analyses of the translation elongation factor 1-a (TEF1-α) of N. dimidiatum from the UAE with reference specimens of Botryosphaeriaceae family validated the identity of the pathogen. To manage the disease, the chemical fungicides, Protifert^®, Cidely^® Top and Amistrar^® Top, significantly inhibited mycelial growth and reduced conidial numbers of N. dimidiatum in laboratory and greenhouse experiments. The described “apple bioassay” is an innovative approach that can be useful when performing fungicide treatment studies. Under field conditions, Cidely^® Top proved to be the most effective fungicide against N. dimidiatum among all tested treatments. Our data suggest that the causal agent of stem canker disease on royal poinciana in the UAE is N. dimidiatum. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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20 pages, 17650 KiB

Open AccessArticle

Genome-Wide Identification, Expression Profile and Evolution Analysis of Karyopherin β Gene Family in Solanum tuberosum Group Phureja DM1-3 Reveals Its Roles in Abiotic Stresses

by Ya Xu, Lu Liu, Pan Zhao, Jing Tong, Naiqin Zhong, Hongji Zhang and Ning Liu

Int. J. Mol. Sci. 2020, 21(3), 931; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21030931 - 31 Jan 2020

Cited by 5 | Viewed by 2895

Abstract

In eukaryotic cells, nucleocytoplasmic trafficking of macromolecules is largely mediated by Karyopherin β/Importin (KPNβ or Impβ) nuclear transport factors, and they import and export cargo proteins or RNAs via the nuclear pores across the nuclear envelope, consequently effecting the cellular signal cascades in [...] Read more.

In eukaryotic cells, nucleocytoplasmic trafficking of macromolecules is largely mediated by Karyopherin β/Importin (KPNβ or Impβ) nuclear transport factors, and they import and export cargo proteins or RNAs via the nuclear pores across the nuclear envelope, consequently effecting the cellular signal cascades in response to pathogen attack and environmental cues. Although achievements on understanding the roles of several KPNβs have been obtained from model plant Arabidopsis thaliana, comprehensive analysis of potato KPNβ gene family is yet to be elucidated. In our genome-wide identifications, a total of 13 StKPNβ (Solanum tuberosum KPNβ) genes were found in the genome of the doubled monoploid S. tuberosum Group Phureja DM1-3. Sequence alignment and conserved domain analysis suggested the presence of importin-β N-terminal domain (IBN_N, PF08310) or Exporin1-like domain (XpoI, PF08389) at N-terminus and HEAT motif at the C-terminal portion in most StKPNβs. Phylogenetic analysis indicated that members of StKPNβ could be classified into 16 subgroups in accordance with their homology to human KPNβs, which was also supported by exon-intron structure, consensus motifs, and domain compositions. RNA-Seq analysis and quantitative real-time PCR experiments revealed that, except StKPNβ3d and StKPNβ4, almost all StKPNβs were ubiquitously expressed in all tissues analyzed, whereas transcriptional levels of several StKPNβs were increased upon biotic/abiotic stress or phytohormone treatments, reflecting their potential roles in plant growth, development or stress responses. Furthermore, we demonstrated that silencing of StKPNβ3a, a SA- and H₂O₂-inducible KPNβ genes led to increased susceptibility to environmental challenges, implying its crucial roles in plant adaption to abiotic stresses. Overall, our results provide molecular insights into StKPNβ gene family, which will serve as a strong foundation for further functional characterization and will facilitate potato breeding programs. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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24 pages, 3711 KiB

Open AccessArticle

The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity

by Saura R. Silva, Ana Paula Moraes, Helen A. Penha, Maria H. M. Julião, Douglas S. Domingues, Todd P. Michael, Vitor F. O. Miranda and Alessandro M. Varani

Int. J. Mol. Sci. 2020, 21(1), 3; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21010003 - 18 Dec 2019

Cited by 14 | Viewed by 7086

Abstract

Utricularia belongs to Lentibulariaceae, a widespread family of carnivorous plants that possess ultra-small and highly dynamic nuclear genomes. It has been shown that the Lentibulariaceae genomes have been shaped by transposable elements expansion and loss, and multiple rounds of whole-genome duplications (WGD), making [...] Read more.

Utricularia belongs to Lentibulariaceae, a widespread family of carnivorous plants that possess ultra-small and highly dynamic nuclear genomes. It has been shown that the Lentibulariaceae genomes have been shaped by transposable elements expansion and loss, and multiple rounds of whole-genome duplications (WGD), making the family a platform for evolutionary and comparative genomics studies. To explore the evolution of Utricularia, we estimated the chromosome number and genome size, as well as sequenced the terrestrial bladderwort Utricularia reniformis (2n = 40, 1C = 317.1-Mpb). Here, we report a high quality 304 Mb draft genome, with a scaffold NG50 of 466-Kb, a BUSCO completeness of 87.8%, and 42,582 predicted genes. Compared to the smaller and aquatic U. gibba genome (101 Mb) that has a 32% repetitive sequence, the U. reniformis genome is highly repetitive (56%). The structural differences between the two genomes are the result of distinct fractionation and rearrangements after WGD, and massive proliferation of LTR-retrotransposons. Moreover, GO enrichment analyses suggest an ongoing gene birth–death–innovation process occurring among the tandem duplicated genes, shaping the evolution of carnivory-associated functions. We also identified unique patterns of developmentally related genes that support the terrestrial life-form and body plan of U. reniformis. Collectively, our results provided additional insights into the evolution of the plastic and specialized Lentibulariaceae genomes. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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17 pages, 2807 KiB

Open AccessArticle

Combined De Novo Transcriptome and Metabolome Analysis of Common Bean Response to Fusarium oxysporum f. sp. phaseoli Infection

by Limin Chen, Quancong Wu, Weimin He, Tianjun He, Qianqian Wu and Yeminzi Miao

Int. J. Mol. Sci. 2019, 20(24), 6278; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20246278 - 12 Dec 2019

Cited by 56 | Viewed by 5330

Abstract

Molecular changes elicited by common bean (Phaseolus vulgaris L.) in response to Fusarium oxysproum f. sp. Phaseoli (FOP) remain elusive. We studied the changes in root metabolism during common bean–FOP interactions using a combined de novo transcriptome and metabolome approach. Our results [...] Read more.

Molecular changes elicited by common bean (Phaseolus vulgaris L.) in response to Fusarium oxysproum f. sp. Phaseoli (FOP) remain elusive. We studied the changes in root metabolism during common bean–FOP interactions using a combined de novo transcriptome and metabolome approach. Our results demonstrated alterations of transcript levels and metabolite concentrations in common bean roots 24 h post infection as compared to control. The transcriptome and metabolome responses in common bean roots revealed significant changes in structural defense i.e., cell-wall loosening and weakening characterized by hyper accumulation of cell-wall loosening and degradation related transcripts. The levels of pathogenesis related genes were significantly higher upon FOP inoculation. Interestingly, we found the involvement of glycosylphosphatidylinositol- anchored proteins (GPI-APs) in signal transduction in response to FOP infection. Our results confirmed that hormones have strong role in signaling pathways i.e., salicylic acid, jasmonate, and ethylene pathways. FOP induced energy metabolism and nitrogen mobilization in infected common bean roots as compared to control. Importantly, the flavonoid biosynthesis pathway was the most significantly enriched pathway in response to FOP infection as revealed by the combined transcriptome and metabolome analysis. Overall, the observed modulations in the transcriptome and metabolome flux as outcome of several orchestrated molecular events are determinant of host’s role in common bean–FOP interactions. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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17 pages, 3571 KiB

Open AccessArticle

Molecular Analysis of UV-C Induced Resveratrol Accumulation in Polygonum cuspidatum Leaves

by Zhongyu Liu, Junxiong Xu, Xiang Wu, Yanyan Wang, Yanli Lin, Duanyang Wu, Hongjie Zhang and Jianbing Qin

Int. J. Mol. Sci. 2019, 20(24), 6185; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20246185 - 07 Dec 2019

Cited by 18 | Viewed by 3061

Abstract

Resveratrol is one of the most studied plant secondary metabolites owing to its numerous health benefits. It is accumulated in some plants following biotic and abiotic stress pressures, including UV-C irradiation. Polygonum cuspidatum represents the major natural source of concentrated resveratrol but the [...] Read more.

Resveratrol is one of the most studied plant secondary metabolites owing to its numerous health benefits. It is accumulated in some plants following biotic and abiotic stress pressures, including UV-C irradiation. Polygonum cuspidatum represents the major natural source of concentrated resveratrol but the underlying mechanisms as well as the effects of UV-C irradiation on resveratrol content have not yet been documented. Herein, we found that UV-C irradiation significantly increased by 2.6-fold and 1.6-fold the resveratrol content in irradiated leaf samples followed by a dark incubation for 6 h and 12 h, respectively, compared to the untreated samples. De novo transcriptome sequencing and assembly resulted into 165,013 unigenes with 98 unigenes mapped to the resveratrol biosynthetic pathway. Differential expression analysis showed that P. cuspidatum strongly induced the genes directly involved in the resveratrol synthesis, including phenylalanine ammonia-lyase, cinnamic acid 4-hydroxylase, 4-coumarate-CoA ligase and stilbene synthase (STS) genes, while strongly decreased the chalcone synthase (CHS) genes after exposure to UV-C. Since CHS and STS share the same substrate, P. cuspidatum tends to preferentially divert the substrate to the resveratrol synthesis pathway under UV-C treatment. We identified several members of the MYB, bHLH and ERF families as potential regulators of the resveratrol biosynthesis genes. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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16 pages, 2532 KiB

Open AccessArticle

Pairing and Exchanging between Daypyrum villosum Chromosomes 6V#2 and 6V#4 in the Hybrids of Two Different Wheat Alien Substitution Lines

by Xiaolan Ma, Zhiying Xu, Jing Wang, Haiqiang Chen, Xingguo Ye and Zhishan Lin

Int. J. Mol. Sci. 2019, 20(23), 6063; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20236063 - 01 Dec 2019

Cited by 3 | Viewed by 2442

Abstract

Normal pairing and exchanging is an important basis to evaluate the genetic relationship between homologous chromosomes in a wheat background. The pairing behavior between 6V#2 and 6V#4, two chromosomes from different Dasypyrum villosum accessions, is still not clear. In this study, two wheat [...] Read more.

Normal pairing and exchanging is an important basis to evaluate the genetic relationship between homologous chromosomes in a wheat background. The pairing behavior between 6V#2 and 6V#4, two chromosomes from different Dasypyrum villosum accessions, is still not clear. In this study, two wheat alien substitution lines, 6V#2 (6A) and 6V#4 (6D), were crossed to obtain the F₁ hybrids and F₂ segregating populations, and the testcross populations were obtained by using the F₁ as a parent crossed with wheat variety Wan7107. The chromosomal behavior at meiosis in pollen mother cells (PMCs) of the F₁ hybrids was observed using a genomic in situ hybridization (GISH) technique. Exchange events of two alien chromosomes were investigated in the F₂ populations using nine polymerase chain reaction (PCR) markers located on the 6V short arm. The results showed that the two alien chromosomes could pair with each other to form ring- or rod-shaped bivalent chromosomes in 79.76% of the total PMCs, and most were pulled to two poles evenly at anaphase I. Investigation of the F₂ populations showed that the segregation ratios of seven markers were consistent with the theoretical values 3:1 or 1:2:1, and recombinants among markers were detected. A genetic linkage map of nine PCR markers for 6VS was accordingly constructed based on the exchange frequencies and compared with the physical maps of wheat and barley based on homologous sequences of the markers, which showed that conservation of sequence order compared to 6V was 6H and 6B > 6A > 6D. In the testcross populations with 482 plants, seven showed susceptibility to powdery mildew (PM) and lacked amplification of alien chromosomal bands. Six other plants had amplification of specific bands of both the alien chromosomes at multiple sites, which suggested that the alien chromosomes had abnormal separation behavior in about 1.5% of the PMCs in F₁, which resulted in some gametes containing two alien chromosomes. In addition, three new types of chromosome substitution were developed. This study lays a foundation for alien allelism tests and further assessment of the genetic relationship among 6V#2, 6V#4, and their wheat homoeologous chromosomes. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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30 pages, 7893 KiB

Open AccessArticle

Analysis of Centranthera grandiflora Benth Transcriptome Explores Genes of Catalpol, Acteoside and Azafrin Biosynthesis

by Xiaodong Zhang, Caixia Li, Lianchun Wang, Yahong Fei and Wensheng Qin

Int. J. Mol. Sci. 2019, 20(23), 6034; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20236034 - 29 Nov 2019

Cited by 17 | Viewed by 3669

Abstract

Cardiovascular diseases (CVDs) are a major cause of health loss in the world. Prevention and treatment of this disease by traditional Chinese medicine is a promising method. Centranthera grandiflora Benth is a high-value medicinal herb in the prevention and treatment of CVDs; its [...] Read more.

Cardiovascular diseases (CVDs) are a major cause of health loss in the world. Prevention and treatment of this disease by traditional Chinese medicine is a promising method. Centranthera grandiflora Benth is a high-value medicinal herb in the prevention and treatment of CVDs; its main medicinal components include iridoid glycosides, phenylethanoid glycosides, and azafrin in roots. However, biosynthetic pathways of these components and their regulatory mechanisms are unknown. Furthermore, there are no genomic resources of this herb. In this article, we provide sequence and transcript abundance data for the root, stem, and leaf transcriptome of C. grandiflora Benth obtained by the Illumina Hiseq2000. More than 438 million clean reads were obtained from root, stem, and leaf libraries, which produced 153,198 unigenes. Based on databases annotation, a total of 557, 213, and 161 unigenes were annotated to catalpol, acteoside, and azafrin biosynthetic pathways, respectively. Differentially expressed gene analysis identified 14,875 unigenes differentially enriched between leaf and root with 8,054 upregulated genes and 6,821 downregulated genes. Candidate MYB transcription factors involved in catalpol, acteoside, and azafrin biosynthesis were also predicated. This work is the first transcriptome analysis in C. grandiflora Benth which will aid the deciphering of biosynthesis pathways and regulatory mechanisms of active components. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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14 pages, 2979 KiB

Open AccessArticle

Species Identification of Oaks (Quercus L., Fagaceae) from Gene to Genome

by Xinbo Pang, Hongshan Liu, Suran Wu, Yangchen Yuan, Haijun Li, Junsheng Dong, Zhaohua Liu, Chuanzhi An, Zhihai Su and Bin Li

Int. J. Mol. Sci. 2019, 20(23), 5940; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20235940 - 26 Nov 2019

Cited by 37 | Viewed by 4445

Abstract

Species identification of oaks (Quercus) is always a challenge because many species exhibit variable phenotypes that overlap with other species. Oaks are notorious for interspecific hybridization and introgression, and complex speciation patterns involving incomplete lineage sorting. Therefore, accurately identifying Quercus species [...] Read more.

Species identification of oaks (Quercus) is always a challenge because many species exhibit variable phenotypes that overlap with other species. Oaks are notorious for interspecific hybridization and introgression, and complex speciation patterns involving incomplete lineage sorting. Therefore, accurately identifying Quercus species barcodes has been unsuccessful. In this study, we used chloroplast genome sequence data to identify molecular markers for oak species identification. Using next generation sequencing methods, we sequenced 14 chloroplast genomes of Quercus species in this study and added 10 additional chloroplast genome sequences from GenBank to develop a DNA barcode for oaks. Chloroplast genome sequence divergence was low. We identified four mutation hotspots as candidate Quercus DNA barcodes; two intergenic regions (matK-trnK-rps16 and trnR-atpA) were located in the large single copy region, and two coding regions (ndhF and ycf1b) were located in the small single copy region. The standard plant DNA barcode (rbcL and matK) had lower variability than that of the newly identified markers. Our data provide complete chloroplast genome sequences that improve the phylogenetic resolution and species level discrimination of Quercus. This study demonstrates that the complete chloroplast genome can substantially increase species discriminatory power and resolve phylogenetic relationships in plants. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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17 pages, 3879 KiB

Open AccessArticle

Genome-Wide Analysis of the YABBY Transcription Factor Family in Pineapple and Functional Identification of AcYABBY4 Involvement in Salt Stress

by Zeyun Li, Gang Li, Mingxing Cai, Samaranayaka V.G.N. Priyadarshani, Mohammad Aslam, Qiao Zhou, Xiaoyi Huang, Xiaomei Wang, Yeqiang Liu and Yuan Qin

Int. J. Mol. Sci. 2019, 20(23), 5863; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20235863 - 22 Nov 2019

Cited by 33 | Viewed by 4103

Abstract

The plant-specific transcription factor gene family, YABBY, belongs to the subfamily of zinc finger protein superfamily and plays an essential regulatory role in lateral organ development. In this study, nine YABBY genes were identified in the pineapple genome. Seven of them were located [...] Read more.

The plant-specific transcription factor gene family, YABBY, belongs to the subfamily of zinc finger protein superfamily and plays an essential regulatory role in lateral organ development. In this study, nine YABBY genes were identified in the pineapple genome. Seven of them were located on seven different chromosomes and the remaining two were located on scaffold 1235. Through protein structure prediction and protein multiple sequence alignment, we found that AcYABBY3, AcYABBY5 and AcYABBY7 lack a C2 structure in their N-terminal C2C2 zinc finger protein structure. Analysis of the cis-acting element indicated that all the seven pineapple YABBY genes contain multiple MYB and MYC elements. Further, the expression patterns analysis using the RNA-seq data of different pineapple tissues indicated that different AcYABBYs are preferentially expressed in various tissues. RT-qPCR showed that the expression of AcYABBY2, AcYABBY3, AcYABBY6 and AcYABBY7 were highly sensitive to abiotic stresses. Subcellular localization in pineapple protoplasts, tobacco leaves and Arabidopsis roots showed that all the seven pineapple YABBY proteins were nucleus localized. Overexpression of AcYABBY4 in Arabidopsis resulted in short root under NaCl treatment, indicating a negative regulatory role of AcYABBY4 in plant resistance to salt stress. This study provides valuable information for the classification of pineapple AcYABBY genes and established a basis for further research on the functions of AcYABBY proteins in plant development and environmental stress response. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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16 pages, 3191 KiB

Open AccessArticle

Exploring the Molecular Mechanism underlying the Stable Purple-Red Leaf Phenotype in Lagerstroemia indica cv. Ebony Embers

by Zhongquan Qiao, Sisi Liu, Huijie Zeng, Yongxin Li, Xiangying Wang, Yi Chen, Xiaoming Wang and Neng Cai

Int. J. Mol. Sci. 2019, 20(22), 5636; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20225636 - 11 Nov 2019

Cited by 21 | Viewed by 2982

Abstract

Lagerstroemia indica is an important ornamental tree worldwide. The development of cultivars with colorful leaves and increased ornamental value represents one of the current main research topics. We investigated the anthocyanin profiles in two contrasting cultivars for leaf color phenotypes and explored the [...] Read more.

Lagerstroemia indica is an important ornamental tree worldwide. The development of cultivars with colorful leaves and increased ornamental value represents one of the current main research topics. We investigated the anthocyanin profiles in two contrasting cultivars for leaf color phenotypes and explored the underlying molecular basis. Both cultivars display purple-red young leaves (Stage 1), and when the leaves mature (Stage 2), they turn green in HD (Lagerstroemia Dynamite) but remain unchanged in ZD (Lagerstroemia Ebony Embers). Seven different anthocyanins were detected, and globally, the leaves of ZD contained higher levels of anthocyanins than those of HD at the two stages with the most pronounced difference observed at Stage 2. Transcriptome sequencing revealed that in contrast to HD, ZD tends to keep a higher activity level of key genes involved in the flavonoid–anthocyanin biosynthesis pathways throughout the leaf developmental stages in order to maintain the synthesis, accumulation, and modification of anthocyanins. By applying gene co-expression analysis, we detected 19 key MYB regulators were co-expressed with the flavonoid–anthocyanin biosynthetic genes and were found strongly down-regulated in HD. This study lays the foundation for the artificial manipulation of the anthocyanin biosynthesis in order to create new L. indica cultivars with colorful leaves and increased ornamental value. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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14 pages, 3259 KiB

Open AccessArticle

Engineered Artificial MicroRNA Precursors Facilitate Cloning and Gene Silencing in Arabidopsis and Rice

by Dandan Zhang, Nannan Zhang, Wenzhong Shen and Jian-Feng Li

Int. J. Mol. Sci. 2019, 20(22), 5620; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20225620 - 10 Nov 2019

Cited by 10 | Viewed by 3288

Abstract

Plant genome sequences are presently deciphered at a staggering speed, due to the rapid advancement of high-throughput sequencing technologies. However, functional genomics significantly lag behind due to technical obstacles related to functional redundancy and mutant lethality. Artificial microRNA (amiRNA) technology is a specific, [...] Read more.

Plant genome sequences are presently deciphered at a staggering speed, due to the rapid advancement of high-throughput sequencing technologies. However, functional genomics significantly lag behind due to technical obstacles related to functional redundancy and mutant lethality. Artificial microRNA (amiRNA) technology is a specific, reversible, and multiplex gene silencing tool that has been frequently used in generating constitutive or conditional mutants for gene functional interrogation. The routine approach to construct amiRNA precursors involves multiple polymerase chain reactions (PCRs) that can increase both time and labor expenses, as well as the chance to introduce sequence errors. Here, we report a simplified method to clone and express amiRNAs in Arabidopsis and rice based on the engineered Arabidopsis miR319a or rice miR528 precursor, which harbor restriction sites to facilitate one-step cloning of a single PCR product. Stem-loop reverse-transcriptase quantitative PCR (RT-qPCR) and functional assays validated that amiRNAs can be accurately processed from these modified precursors and work efficiently in plant protoplasts. In addition, Arabidopsis transgenic plants overexpressing the modified miR319a precursor or its derived amiRNA could exhibit strong gene silencing phenotypes, as expected. The simplified amiRNA cloning strategy will be broadly useful for functional genomic studies in Arabidopsis and rice, and maybe other dicotyledon and monocotyledon species as well. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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19 pages, 3376 KiB

Open AccessArticle

Comparatively Barcoded Chromosomes of Brachypodium Perennials Tell the Story of Their Karyotype Structure and Evolution

by Joanna Lusinska, Alexander Betekhtin, Diana Lopez-Alvarez, Pilar Catalan, Glyn Jenkins, Elzbieta Wolny and Robert Hasterok

Int. J. Mol. Sci. 2019, 20(22), 5557; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20225557 - 07 Nov 2019

Cited by 12 | Viewed by 2943

Abstract

The Brachypodium genus is an informative model system for studying grass karyotype organization. Previous studies of a limited number of species and reference chromosomes have not provided a comprehensive picture of the enigmatic phylogenetic relationships in the genus. Comparative chromosome barcoding, which enables [...] Read more.

The Brachypodium genus is an informative model system for studying grass karyotype organization. Previous studies of a limited number of species and reference chromosomes have not provided a comprehensive picture of the enigmatic phylogenetic relationships in the genus. Comparative chromosome barcoding, which enables the reconstruction of the evolutionary history of individual chromosomes and their segments, allowed us to infer the relationships between putative ancestral karyotypes of extinct species and extant karyotypes of current species. We used over 80 chromosome-specific BAC (bacterial artificial chromosome) clones derived from five reference chromosomes of B. distachyon as probes against the karyotypes of twelve accessions representing five diploid and polyploid Brachypodium perennials. The results showed that descending dysploidy is common in Brachypodium and occurs primarily via nested chromosome fusions. Brachypodium distachyon was rejected as a putative ancestor for allotetraploid perennials and B. stacei for B. mexicanum. We propose two alternative models of perennial polyploid evolution involving either the incorporation of a putative x = 5 ancestral karyotype with different descending dysploidy patterns compared to B. distachyon chromosomes or hybridization of two x = 9 ancestors followed by genome doubling and descending dysploidy. Details of the karyotype structure and evolution in several Brachypodium perennials are revealed for the first time. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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14 pages, 3760 KiB

Open AccessArticle

Identification of Rice Large Grain Gene GW2 by Whole-Genome Sequencing of a Large Grain-Isogenic Line Integrated with Japonica Native Gene and Its Linkage Relationship with the Co-integrated Semidwarf Gene d60 on Chromosome 2

by Motonori Tomita, Shiho Yazawa and Yoshimasa Uenishi

Int. J. Mol. Sci. 2019, 20(21), 5442; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20215442 - 31 Oct 2019

Cited by 3 | Viewed by 3294

Abstract

Genetic analysis of “InochinoIchi,” an exceptionally large grain rice variety, was conducted through five continuous backcrosses with Koshihikari as a recurrent parent using the large grain F₃ plant in Koshihikari × Inochinoichi as a nonrecurrent parent. Thorough the F₂ and all [...] Read more.

Genetic analysis of “InochinoIchi,” an exceptionally large grain rice variety, was conducted through five continuous backcrosses with Koshihikari as a recurrent parent using the large grain F₃ plant in Koshihikari × Inochinoichi as a nonrecurrent parent. Thorough the F₂ and all BCnF₂ generations, large, medium, and small grain segregated in a 1:2:1 ratio, indicating that the large grain is controlled by a single allele. Mapping by using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers with small grain homozygous segregants in the F₂ of Nipponbare × Inochinoichi, revealed linkage with around 7.7 Mb markers from the distal end of the short arm of chromosome 2. Whole-genome sequencing on a large grain isogenic Koshihikari (BC₄F₂) using next-generation sequencing (NGS) identified a single nucleotide deletion in GW2 gene, which is located 8.1 Mb from the end of chromosome 2, encoding a RING protein with E3 ubiquitin ligase activity. The GW2-integrated isogenic Koshihikari showed a 34% increase in thousand kernel weight compared to Koshihikari, while retaining a taste score of 80. We further developed a large grain/semi-dwarf isogenic Koshihikari integrated with GW2 and the semidwarfing gene d60, which was found to be localized on chromosome 2. The combined genotype secured high yielding while providing robustness to withstand climate change, which can contribute to the New Green Revolution. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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15 pages, 3473 KiB

Open AccessArticle

Haplotype Networking of GWAS Hits for Citrulline Variation Associated with the Domestication of Watermelon

by Vijay Joshi, Suhas Shinde, Padma Nimmakayala, Venkata Lakshmi Abburi, Suresh Babu Alaparthi, Carlos Lopez-Ortiz, Amnon Levi, Girish Panicker and Umesh K. Reddy

Int. J. Mol. Sci. 2019, 20(21), 5392; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20215392 - 29 Oct 2019

Cited by 5 | Viewed by 4067

Abstract

Watermelon is a good source of citrulline, a non-protein amino acid. Citrulline has several therapeutic and clinical implications as it produces nitric oxide via arginine. In plants, citrulline plays a pivotal role in nitrogen transport and osmoprotection. The purpose of this study was [...] Read more.

Watermelon is a good source of citrulline, a non-protein amino acid. Citrulline has several therapeutic and clinical implications as it produces nitric oxide via arginine. In plants, citrulline plays a pivotal role in nitrogen transport and osmoprotection. The purpose of this study was to identify single nucleotide polymorphism (SNP) markers associated with citrulline metabolism using a genome-wide association study (GWAS) and understand the role of citrulline in watermelon domestication. A watermelon collection consisting of 187 wild, landraces, and cultivated accessions was used to estimate citrulline content. An association analysis involved a total of 12,125 SNPs with a minor allele frequency (MAF)>0.05 in understanding the population structure and phylogeny in light of citrulline accumulation. Wild egusi types and landraces contained low to medium citrulline content, whereas cultivars had higher content, which suggests that obtaining higher content of citrulline is a domesticated trait. GWAS analysis identified candidate genes (ferrochelatase and acetolactate synthase) showing a significant association of SNPs with citrulline content. Haplotype networking indicated positive selection from wild to domesticated watermelon. To our knowledge, this is the first study showing genetic regulation of citrulline variation in plants by using a GWAS strategy. These results provide new insights into the citrulline metabolism in plants and the possibility of incorporating high citrulline as a trait in watermelon breeding programs. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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25 pages, 5334 KiB

Open AccessArticle

Gene Expression Profiling Reveals Enhanced Defense Responses in an Invasive Weed Compared to Its Native Congener During Pathogenesis

by Bharani Manoharan, Shan-Shan Qi, Vignesh Dhandapani, Qi Chen, Susan Rutherford, Justin SH Wan, Sridharan Jegadeesan, Hong-Yu Yang, Qin Li, Jian Li, Zhi-Cong Dai and Dao-Lin Du

Int. J. Mol. Sci. 2019, 20(19), 4916; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20194916 - 03 Oct 2019

Cited by 4 | Viewed by 4228

Abstract

Invasive plants are a huge burden on the environment, and modify local ecosystems by affecting the indigenous biodiversity. Invasive plants are generally less affected by pathogens, although the underlying molecular mechanisms responsible for their enhanced resistance are unknown. We investigated expression profiles of [...] Read more.

Invasive plants are a huge burden on the environment, and modify local ecosystems by affecting the indigenous biodiversity. Invasive plants are generally less affected by pathogens, although the underlying molecular mechanisms responsible for their enhanced resistance are unknown. We investigated expression profiles of three defense hormones (salicylic acid, jasmonic acid, and ethylene) and their associated genes in the invasive weed, Alternanthera philoxeroides, and its native congener, A. sessilis, after inoculation with Rhizoctonia solani. Pathogenicity tests showed significantly slower disease progression in A. philoxeroides compared to A. sessilis. Expression analyses revealed jasmonic acid (JA) and ethylene (ET) expressions were differentially regulated between A. philoxeroides and A. sessilis, with the former having prominent antagonistic cross-talk between salicylic acid (SA) and JA, and the latter showing weak or no cross-talk during disease development. We also found that JA levels decreased and SA levels increased during disease development in A. philoxeroides. Variations in hormonal gene expression between the invasive and native species (including interspecific differences in the strength of antagonistic cross-talk) were identified during R. solani pathogenesis. Thus, plant hormones and their cross-talk signaling may improve the resistance of invasive A. philoxeroides to pathogens, which has implications for other invasive species during the invasion process. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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20 pages, 4239 KiB

Open AccessArticle

Protective Role of Leaf Variegation in Pittosporum tobira under Low Temperature: Insights into the Physio-Biochemical and Molecular Mechanisms

by Zhilu Zhang, Zhonghua Liu, Haina Song, Minghui Chen and Shiping Cheng

Int. J. Mol. Sci. 2019, 20(19), 4857; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20194857 - 30 Sep 2019

Cited by 4 | Viewed by 4237

Abstract

Leaf variegation has been demonstrated to have adaptive functions such as cold tolerance. Pittosporum tobira is an ornamental plant with natural leaf variegated cultivars grown in temperate regions. Herein, we investigated the role of leaf variegation in low temperature responses by comparing variegated [...] Read more.

Leaf variegation has been demonstrated to have adaptive functions such as cold tolerance. Pittosporum tobira is an ornamental plant with natural leaf variegated cultivars grown in temperate regions. Herein, we investigated the role of leaf variegation in low temperature responses by comparing variegated “Variegatum” and non-variegated “Green Pittosporum” cultivars. We found that leaf variegation is associated with impaired chloroplast development in the yellow sector, reduced chlorophyll content, strong accumulation of carotenoids and high levels of ROS. However, the photosynthetic efficiency was not obviously impaired in the variegated leaves. Also, leaf variegation plays low temperature protective function since “Variegatum” displayed strong and efficient ROS-scavenging enzymatic systems to buffer cold (10 °C)-induced damages. Transcriptome analysis under cold conditions revealed 309 differentially expressed genes between both cultivars. Distinctly, the strong cold response observed in “Variegatum” was essentially attributed to the up-regulation of HSP70/90 genes involved in cellular homeostasis; up-regulation of POD genes responsible for cell detoxification and up-regulation of FAD2 genes and subsequent down-regulation of GDSL genes leading to high accumulation of polyunsaturated fatty acids for cell membrane fluidity. Overall, our results indicated that leaf variegation is associated with changes in physiological, biochemical and molecular components playing low temperature protective function in P. tobira. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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19 pages, 3921 KiB

Open AccessArticle

Genomic Organization of the B3-Domain Transcription Factor Family in Grapevine (Vitis vinifera L.) and Expression during Seed Development in Seedless and Seeded Cultivars

by Bilal Ahmad, Songlin Zhang, Jin Yao, Mati Ur Rahman, Muhammad Hanif, Yanxun Zhu and Xiping Wang

Int. J. Mol. Sci. 2019, 20(18), 4553; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20184553 - 14 Sep 2019

Cited by 33 | Viewed by 3486

Abstract

Members of the plant-specific B3-domain transcription factor family have important and varied functions, especially with respect to vegetative and reproductive growth. Although B3 genes have been studied in many other plants, there is limited information on the genomic organization and expression of B3 [...] Read more.

Members of the plant-specific B3-domain transcription factor family have important and varied functions, especially with respect to vegetative and reproductive growth. Although B3 genes have been studied in many other plants, there is limited information on the genomic organization and expression of B3 genes in grapevine (Vitis vinifera L.). In this study, we identified 50 B3 genes in the grapevine genome and analyzed these genes in terms of chromosomal location and syntenic relationships, intron–exon organization, and promoter cis-element content. We also analyzed the presumed proteins in terms of domain structure and phylogenetic relationships. Based on the results, we classified these genes into five subfamilies. The syntenic relationships suggest that approximately half of the genes resulted from genome duplication, contributing to the expansion of the B3 family in grapevine. The analysis of cis-element composition suggested that most of these genes may function in response to hormones, light, and stress. We also analyzed expression of members of the B3 family in various structures of grapevine plants, including the seed during seed development. Many B3 genes were expressed preferentially in one or more structures of the developed plant, suggesting specific roles in growth and development. Furthermore, several of the genes were expressed differentially in early developing seeds from representative seeded and seedless cultivars, suggesting a role in seed development or abortion. The results of this study provide a foundation for functional analysis of B3 genes and new resources for future molecular breeding of grapevine. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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18 pages, 4056 KiB

Open AccessArticle

Differential Regulation of Anthocyanins in Green and Purple Turnips Revealed by Combined De Novo Transcriptome and Metabolome Analysis

by Hongmei Zhuang, Qian Lou, Huifang Liu, Hongwei Han, Qiang Wang, Zhonghua Tang, Yanming Ma and Hao Wang

Int. J. Mol. Sci. 2019, 20(18), 4387; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20184387 - 06 Sep 2019

Cited by 62 | Viewed by 4895

Abstract

Purple turnip Brassica rapa ssp. rapa is highly appreciated by consumers but the metabolites and molecular mechanisms underlying the root skin pigmentation remain open to study. Herein, we analyzed the anthocyanin composition in purple turnip (PT) and green turnip (GT) at five developmental [...] Read more.

Purple turnip Brassica rapa ssp. rapa is highly appreciated by consumers but the metabolites and molecular mechanisms underlying the root skin pigmentation remain open to study. Herein, we analyzed the anthocyanin composition in purple turnip (PT) and green turnip (GT) at five developmental stages. A total of 21 anthocyanins were detected and classified into the six major anthocynanin aglycones. Distinctly, PT contains 20 times higher levels of anthocyanins than GT, which explain the difference in the root skin pigmentation. We further sequenced the transcriptomes and analyzed the differentially expressed genes between the two turnips. We found that PT essentially diverts dihydroflavonols to the biosynthesis of anthocyanins over flavonols biosynthesis by strongly down-regulating one flavonol synthase gene, while strikingly up-regulating dihydroflavonol 4-reductase (DFR), anthocyanidin synthase and UDP-glucose: flavonoid-3-O-glucosyltransferase genes as compared to GT. Moreover, a nonsense mutation identified in the coding sequence of the DFR gene may lead to a nonfunctional protein, adding another hurdle to the accumulation of anthocyanin in GT. We also uncovered several key members of MYB, bHLH and WRKY families as the putative main drivers of transcriptional changes between the two turnips. Overall, this study provides new tools for modifying anthocyanin content and improving turnip nutritional quality. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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19 pages, 3444 KiB

Open AccessArticle

Transcriptome Profiling Provides Insight into the Genes in Carotenoid Biosynthesis during the Mesocarp and Seed Developmental Stages of Avocado (Persea americana)

by Yu Ge, Zhihao Cheng, Xiongyuan Si, Weihong Ma, Lin Tan, Xiaoping Zang, Bin Wu, Zining Xu, Nan Wang, Zhaoxi Zhou, Xinge Lin, Xiangshu Dong and Rulin Zhan

Int. J. Mol. Sci. 2019, 20(17), 4117; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20174117 - 23 Aug 2019

Cited by 17 | Viewed by 3468

Abstract

Avocado (Persea americana Mill.) is an economically important crop because of its high nutritional value. However, the absence of a sequenced avocado reference genome has hindered investigations of secondary metabolism. For next-generation high-throughput transcriptome sequencing, we obtained 365,615,152 and 348,623,402 clean reads [...] Read more.

Avocado (Persea americana Mill.) is an economically important crop because of its high nutritional value. However, the absence of a sequenced avocado reference genome has hindered investigations of secondary metabolism. For next-generation high-throughput transcriptome sequencing, we obtained 365,615,152 and 348,623,402 clean reads as well as 109.13 and 104.10 Gb of sequencing data for avocado mesocarp and seed, respectively, during five developmental stages. High-quality reads were assembled into 100,837 unigenes with an average length of 847.40 bp (N50 = 1725 bp). Additionally, 16,903 differentially expressed genes (DEGs) were detected, 17 of which were related to carotenoid biosynthesis. The expression levels of most of these 17 DEGs were higher in the mesocarp than in the seed during five developmental stages. In this study, the avocado mesocarp and seed transcriptome were also sequenced using single-molecule long-read sequencing to acquired 25.79 and 17.67 Gb clean data, respectively. We identified 233,014 and 238,219 consensus isoforms in avocado mesocarp and seed, respectively. Furthermore, 104 and 59 isoforms were found to correspond to the putative 11 carotenoid biosynthetic-related genes in the avocado mesocarp and seed, respectively. The isoform numbers of 10 out of the putative 11 genes involved in the carotenoid biosynthetic pathway were higher in the mesocarp than those in the seed. Besides, alpha- and beta-carotene contents in the avocado mesocarp and seed during five developmental stages were also measured, and they were higher in the mesocarp than in the seed, which validated the results of transcriptome profiling. Gene expression changes and the associated variations in gene dosage could influence carotenoid biosynthesis. These results will help to further elucidate carotenoid biosynthesis in avocado. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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18 pages, 2101 KiB

Open AccessArticle

Transgenerational Perpetuation of CHS Gene Expression and DNA Methylation Status Induced by Short Oligodeoxynucleotides in Flax (Linum usitatissimum)

by Magdalena Dzialo, Jan Szopa, Agata Hnitecka and Magdalena Zuk

Int. J. Mol. Sci. 2019, 20(16), 3983; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20163983 - 16 Aug 2019

Cited by 4 | Viewed by 2832

Abstract

Over two decades ago, short oligodeoxynucleotides (ODNs) were proven to be an effective and rapid technique for analysis of gene function without interference in the plant genome. Our previous research has shown the successful regulation of chalcone synthase (CHS) gene expression in flax [...] Read more.

Over two decades ago, short oligodeoxynucleotides (ODNs) were proven to be an effective and rapid technique for analysis of gene function without interference in the plant genome. Our previous research has shown the successful regulation of chalcone synthase (CHS) gene expression in flax by ODN technology. The CHS gene encodes a pivotal enzyme in flavonoid biosynthesis. The manipulation of its transcript level was the result of the specific methylation status developed after treatment with ODNs. In further analysis of the application of oligodeoxynucleotides in plants, we will focus on maintaining the methylation status induced originally by ODNs homologous to the regulatory regions of the CHS gene in flax. This article reports the latest investigation applied to stabilization and inheritance of the epigenetic marks induced by plants’ treatment with ODNs. The methylation status was analyzed in the particular CCGG motifs located in the CHS gene sequence. Individual plants were able to maintain alterations induced by ODNs. In order to confirm the impact of methylation marks on the nucleosome rearrangement, chromatin accessibility assay was performed. The perpetuation of targeted plant modulation induced by ODNs exhibits strong potential for improving crops and intensified application for medicine, nutrition and industry. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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13 pages, 3021 KiB

Open AccessArticle

Agrobacterium-Mediated Gene Transient Overexpression and Tobacco Rattle Virus (TRV)-Based Gene Silencing in Cassava

by Hongqiu Zeng, Yanwei Xie, Guoyin Liu, Yunxie Wei, Wei Hu and Haitao Shi

Int. J. Mol. Sci. 2019, 20(16), 3976; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20163976 - 15 Aug 2019

Cited by 40 | Viewed by 7143

Abstract

Agrobacterium-mediated transient expression and virus-induced gene silencing (VIGS) are very useful in functional genomics in plants. However, whether these methods are effective in cassava (Manihot esculenta), one of the most important tropical crops, remains elusive. In this study, we used [...] Read more.

Agrobacterium-mediated transient expression and virus-induced gene silencing (VIGS) are very useful in functional genomics in plants. However, whether these methods are effective in cassava (Manihot esculenta), one of the most important tropical crops, remains elusive. In this study, we used green fluorescent protein (GFP) and β-glucuronidase (GUS) as reporter genes in a transient expression assay. GFP or GUS could be detected in the infiltrated leaves at 2 days postinfiltration (dpi) and were evidenced by visual GFP and GUS assays, reverse-transcription PCR, and Western blot. In addition, phytoene desaturase (PDS) was used to show the silencing effect in a VIGS system. Both Agrobacterium GV3101 and AGL-1 with tobacco rattle virus (TRV)-MePDS-infiltrated distal leaves showed an albino phenotype at 20 dpi; in particular, the AGL-1-infiltrated plants showed an obvious albino area in the most distal leaves. Moreover, the silencing effect was validated by molecular identification. Notably, compared with the obvious cassava mosaic disease symptom infiltrated by African-cassava-mosaic-virus-based VIGS systems in previous studies, TRV-based VIGS-system-infiltrated cassava plants did not show obvious virus-induced disease symptoms, suggesting a significant advantage. Taken together, these methods could promote functional genomics in cassava. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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19 pages, 3037 KiB

Open AccessArticle

Depicting the Core Transcriptome Modulating Multiple Abiotic Stresses Responses in Sesame (Sesamum indicum L.)

by Komivi Dossa, Marie A. Mmadi, Rong Zhou, Tianyuan Zhang, Ruqi Su, Yujuan Zhang, Linhai Wang, Jun You and Xiurong Zhang

Int. J. Mol. Sci. 2019, 20(16), 3930; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20163930 - 13 Aug 2019

Cited by 46 | Viewed by 4683

Abstract

Sesame is a source of a healthy vegetable oil, attracting a growing interest worldwide. Abiotic stresses have devastating effects on sesame yield; hence, studies have been performed to understand sesame molecular responses to abiotic stresses, but the core abiotic stress-responsive genes (CARG) that [...] Read more.

Sesame is a source of a healthy vegetable oil, attracting a growing interest worldwide. Abiotic stresses have devastating effects on sesame yield; hence, studies have been performed to understand sesame molecular responses to abiotic stresses, but the core abiotic stress-responsive genes (CARG) that the plant reuses in response to an array of environmental stresses are unknown. We performed a meta-analysis of 72 RNA-Seq datasets from drought, waterlogging, salt and osmotic stresses and identified 543 genes constantly and differentially expressed in response to all stresses, representing the sesame CARG. Weighted gene co-expression network analysis of the CARG revealed three functional modules controlled by key transcription factors. Except for salt stress, the modules were positively correlated with the abiotic stresses. Network topology of the modules showed several hub genes predicted to play prominent functions. As proof of concept, we generated over-expressing Arabidopsis lines with hub and non-hub genes. Transgenic plants performed better under drought, waterlogging, and osmotic stresses than the wild-type plants but did not tolerate the salt treatment. As expected, the hub gene was significantly more potent than the non-hub gene. Overall, we discovered several novel candidate genes, which will fuel investigations on plant responses to multiple abiotic stresses. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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17 pages, 3946 KiB

Open AccessArticle

Intergeneric Relationships within the Family Salicaceae s.l. Based on Plastid Phylogenomics

by Meng-Meng Li, De-Yan Wang, Lei Zhang, Ming-Hui Kang, Zhi-Qiang Lu, Ren-Bin Zhu, Xing-Xing Mao, Zhen-Xiang Xi and Tao Ma

Int. J. Mol. Sci. 2019, 20(15), 3788; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20153788 - 02 Aug 2019

Cited by 18 | Viewed by 3453

Abstract

Many Salicaceae s.l. plants are recognized for their important role in the production of products such as wood, oils, and medicines, and as a model organism in life studies. However, the difference in plastid sequence, phylogenetic relationships, and lineage diversification of the family [...] Read more.

Many Salicaceae s.l. plants are recognized for their important role in the production of products such as wood, oils, and medicines, and as a model organism in life studies. However, the difference in plastid sequence, phylogenetic relationships, and lineage diversification of the family Salicaceae s.l. remain poorly understood. In this study, we compare 24 species representing 18 genera of the family. Simple sequence repeats (SSRs) are considered effective molecular markers for plant species identification and population genetics. Among them, a total of 1798 SSRs were identified, among which mononucleotide repeat was the most common with 1455 accounts representing 80.92% of the total. Most of the SSRs are located in the non-coding region. We also identified five other types of repeats, including 1750 tandems, 434 forward, 407 palindromic, 86 reverse, and 30 complementary repeats. The species in Salicaceae s.l. have a conserved plastid genome. Each plastome presented a typical quadripartite structure and varied in size due to the expansion and contraction of the inverted repeat (IR) boundary, lacking major structural variations, but we identified six divergence hotspot regions. We obtained phylogenetic relationships of 18 genera in Salicaceae s.l. and the 24 species formed a highly supported lineage. Casearia was identified as the basal clade. The divergence time between Salicaceae s.l. and the outgroup was estimated as ~93 Mya; Salix, and Populus diverged around 34 Mya, consistent with the previously reported time. Our research will contribute to a better understanding of the phylogenetic relationships among the members of the Salicaceae s.l. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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18 pages, 5924 KiB

Open AccessArticle

Gene-Wide Analysis of Aquaporin Gene Family in Malus domestica and Heterologous Expression of the Gene MpPIP2;1 Confers Drought and Salinity Tolerance in Arabidposis thaliana

by Haili Liu, Leilei Yang, Miaomiao Xin, Fengwang Ma and Jingying Liu

Int. J. Mol. Sci. 2019, 20(15), 3710; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20153710 - 29 Jul 2019

Cited by 21 | Viewed by 3456

Abstract

The aquaporins (AQPs) are a family of integral membrane proteins involved in the transcellular membrane transport of water and other small molecules. A scan of the apple (Malus domestica) genome revealed the presence of 42 genes encoding putative AQPs. Based on [...] Read more.

The aquaporins (AQPs) are a family of integral membrane proteins involved in the transcellular membrane transport of water and other small molecules. A scan of the apple (Malus domestica) genome revealed the presence of 42 genes encoding putative AQPs. Based on a phylogenetic analysis of the deduced peptide sequences of the AQPs generated by Arabidopsis thaliana, poplar (Populus trichocarpa), and rubber (Hevea brasiliensis), the apple AQPs were each assigned membership of the five established AQP subfamilies, namely the PIPs (eleven members), the TIPs (thirteen members), the NIPs (eleven members), the SIPs (five members), and the XIPs (two members). The apple AQPs included asparagine-proline-alanine (NPA) motifs, an aromatic/arginine (ar/R) selectivity filter, and the Froger’s positions. The heterologous expression of MpPIP2;1 in A. thaliana was shown to enhance the level of tolerance exhibited against both drought and salinity. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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21 pages, 2783 KiB

Open AccessArticle

NB-LRRs Not Responding Consecutively to Fusarium oxysporum Proliferation Caused Replant Disease Formation of Rehmannia glutinosa

by Aiguo Chen, Li Gu, Na Xu, Fajie Feng, Dexin Chen, Chuyun Yang, Bao Zhang, Mingjie Li and Zhongyi Zhang

Int. J. Mol. Sci. 2019, 20(13), 3203; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20133203 - 29 Jun 2019

Cited by 9 | Viewed by 2886

Abstract

Consecutive monoculture practice facilitates enrichment of rhizosphere pathogenic microorganisms and eventually leads to the emergence of replant disease. However, little is known about the interaction relationship among pathogens enriched in rhizosphere soils, Nucleotide binding-leucine-rich repeats (NB-LRR) receptors that specifically recognize pathogens in effector-triggered [...] Read more.

Consecutive monoculture practice facilitates enrichment of rhizosphere pathogenic microorganisms and eventually leads to the emergence of replant disease. However, little is known about the interaction relationship among pathogens enriched in rhizosphere soils, Nucleotide binding-leucine-rich repeats (NB-LRR) receptors that specifically recognize pathogens in effector-triggered immunity (ETI) and physiological indicators under replant disease stress in Rehmannia glutinosa. In this study, a controlled experiment was performed using different kinds of soils from sites never planted R. glutinosa (NP), replanted R. glutinosa (TP) and mixed by different ration of TP soils (1/3TP and 2/3TP), respectively. As a result, different levels of TP significantly promoted the proliferation of Fusarium oxysporum f.sp. R. glutinosa (FO). Simultaneously, a comparison between FO numbers and NB-LRR expressions indicated that NB-LRRs were not consecutively responsive to the FO proliferation at transcriptional levels. Further analysis found that NB-LRRs responded to FO invasion with a typical phenomenon of “promotion in low concentration and suppression in high concentration”, and 6 NB-LRRs were identified as candidates for responding R. glutinosa replant disease. Furthermore, four critical hormones of salicylic acid (SA), jasmonic acid (JA), ethylene (ET) and abscisic acid (ABA) had higher levels in 1/3TP, 2/3TP and TP than those in NP. Additionally, increasing extents of SA contents have significantly negative trends with FO changes, which implied that SA might be inhibited by FO in replanted R. glutinosa. Concomitantly, the physiological indexes reacted alters of cellular process regulated by NB-LRR were affected by complex replant disease stresses and exhibited strong fluctuations, leading to the death of R. glutinosa. These findings provide important insights and clues into further revealing the mechanism of R. glutinosa replant disease. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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17 pages, 2446 KiB

Open AccessArticle

Genome-Wide Identification and Expression Profiling of the Polygalacturonase (PG) and Pectin Methylesterase (PME) Genes in Grapevine (Vitis vinifera L.)

by Nadeem Khan, Fizza Fatima, Muhammad Salman Haider, Hamna Shazadee, Zhongjie Liu, Ting Zheng and Jinggui Fang

Int. J. Mol. Sci. 2019, 20(13), 3180; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20133180 - 28 Jun 2019

Cited by 35 | Viewed by 4418

Abstract

In pectin regulation, polygalacturonases (PGs) and pectin methylesterases (PMEs) are critical components in the transformation, disassembly network, and remodeling of plant primary cell walls. In the current study, we identified 36 PG and 47 PME genes using the available genomic resources of grapevine. [...] Read more.

In pectin regulation, polygalacturonases (PGs) and pectin methylesterases (PMEs) are critical components in the transformation, disassembly network, and remodeling of plant primary cell walls. In the current study, we identified 36 PG and 47 PME genes using the available genomic resources of grapevine. Herein, we provide a comprehensive overview of PGs and PMEs, including phylogenetic and collinearity relationships, motif and gene structure compositions, gene duplications, principal component analysis, and expression profiling during developmental stages. Phylogenetic analysis of PGs and PMEs revealed similar domain composition patterns with Arabidopsis. The collinearity analysis showed high conservation and gene duplications with purifying selection. The type of duplications also varied in terms of gene numbers in PGs (10 dispersed, 1 proximal, 12 tandem, and 13 segmental, respectively) and PMEs (23 dispersed, 1 proximal, 16 tandem, and 7 segmental, respectively). The tissue-specific response of PG and PME genes based on the reported transcriptomic data exhibited diverged expression patterns in various organs during different developmental stages. Among PGs, VvPG8, VvPG10, VvPG13, VvPG17, VvPG18, VvPG19, VvPG20, VvPG22, and VvPG23 showed tissue- or organ-specific expression in majority of the tissues during development. Similarly, in PMEs, VvPME3, VvPME4, VvPME5, VvPME6, VvPME19, VvPME21, VvPME23, VvPME29, VvPME31, and VvPME32 suggested high tissue-specific response. The gene ontology (GO), Kyoto Encyclopedia of Genes and Genomics (KEGG) enrichment, and cis-elements prediction analysis also suggested the putative functions of PGs and PMEs in plant development, such as pectin and carbohydrate metabolism, and stress activities. Moreover, qRT-PCR validation of 32 PG and PME genes revealed their role in various organs of grapevines (i.e., root, stem, tendril, inflorescence, flesh, skins, and leaves). Therefore, these findings will lead to novel insights and encourage cutting-edge research on functional characterization of PGs and PMEs in fruit crop species. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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23 pages, 3692 KiB

Open AccessArticle

Genome-Wide Analysis of the MADS-Box Transcription Factor Family in Solanum lycopersicum

by Yunshu Wang, Jianling Zhang, Zongli Hu, Xuhu Guo, Shibing Tian and Guoping Chen

Int. J. Mol. Sci. 2019, 20(12), 2961; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20122961 - 18 Jun 2019

Cited by 69 | Viewed by 7496

Abstract

MADS-box family genes encode transcription factors that are involved in multiple developmental processes in plants, especially in floral organ specification, fruit development, and ripening. However, a comprehensive analysis of tomato MADS-box family genes, which is an important model plant to study flower fruit [...] Read more.

MADS-box family genes encode transcription factors that are involved in multiple developmental processes in plants, especially in floral organ specification, fruit development, and ripening. However, a comprehensive analysis of tomato MADS-box family genes, which is an important model plant to study flower fruit development and ripening, remains obscure. To gain insight into the MADS-box genes in tomato, 131 tomato MADS-box genes were identified. These genes could be divided into five groups (Mα, Mβ, Mγ, Mδ, and MIKC) and were found to be located on all 12 chromosomes. We further analyzed the phylogenetic relationships among Arabidopsis and tomato, as well as the protein motif structure and exon–intron organization, to better understand the tomato MADS-box gene family. Additionally, owing to the role of MADS-box genes in floral organ identification and fruit development, the constitutive expression patterns of MADS-box genes at different stages in tomato development were identified. We analyzed 15 tomato MADS-box genes involved in floral organ identification and five tomato MADS-box genes related to fruit development by qRT-PCR. Collectively, our study provides a comprehensive and systematic analysis of the tomato MADS-box genes and would be valuable for the further functional characterization of some important members of the MADS-box gene family. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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17 pages, 2814 KiB

Open AccessArticle

The Complete Chloroplast Genomes of Punica granatum and a Comparison with Other Species in Lythraceae

by Ming Yan, Xueqing Zhao, Jianqing Zhou, Yan Huo, Yu Ding and Zhaohe Yuan

Int. J. Mol. Sci. 2019, 20(12), 2886; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20122886 - 13 Jun 2019

Cited by 38 | Viewed by 4593

Abstract

Pomegranates (Punica granatum L.) are one of the most popular fruit trees cultivated in arid and semi-arid tropics and subtropics. In this study, we determined and characterized three complete chloroplast (cp) genomes of P. granatum cultivars with different phenotypes using the genome [...] Read more.

Pomegranates (Punica granatum L.) are one of the most popular fruit trees cultivated in arid and semi-arid tropics and subtropics. In this study, we determined and characterized three complete chloroplast (cp) genomes of P. granatum cultivars with different phenotypes using the genome skimming approach. The complete cp genomes of three pomegranate cultivars displayed the typical quadripartite structure of angiosperms, and their length ranged from 156,638 to 156,639 bp. They encoded 113 unique genes and 17 are duplicated in the inverted regions. We analyzed the sequence diversity of pomegranate cp genomes coupled with two previous reports. The results showed that the sequence diversity is extremely low and no informative sites were detected, which suggests that cp genome sequences may be not be suitable for investigating the genetic diversity of pomegranate genotypes. Further, we analyzed the codon usage pattern and identified the potential RNA editing sites. A comparative cp genome analysis with other species within Lythraceae revealed that the gene content and organization are highly conserved. Based on a site-specific model, 11 genes with positively selected sites were detected, and most of them were photosynthesis-related genes and genetic system-related genes. Together with previously released cp genomes of the order Myrtales, we determined the taxonomic position of P. granatum based on the complete chloroplast genomes. Phylogenetic analysis suggested that P. granatum form a single clade with other species from Lythraceae with a high support value. The complete cp genomes provides valuable information for understanding the phylogenetic position of P. gramatum in the order Myrtales. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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14 pages, 2494 KiB

Open AccessArticle

Isolation and Characterization of CsWRKY7, a Subgroup IId WRKY Transcription Factor from Camellia sinensis, Linked to Development in Arabidopsis

by Wei Chen, Wan-Jun Hao, Yan-Xia Xu, Chao Zheng, De-Jiang Ni, Ming-Zhe Yao and Liang Chen

Int. J. Mol. Sci. 2019, 20(11), 2815; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20112815 - 09 Jun 2019

Cited by 16 | Viewed by 3536

Abstract

WRKY transcription factors (TFs) containing one or two WRKY domains are a class of plant TFs that respond to diverse abiotic stresses and are associated with developmental processes. However, little has been known about the function of WRKY gene in tea plant. In [...] Read more.

WRKY transcription factors (TFs) containing one or two WRKY domains are a class of plant TFs that respond to diverse abiotic stresses and are associated with developmental processes. However, little has been known about the function of WRKY gene in tea plant. In this study, a subgroup IId WRKY gene CsWRKY7 was isolated from Camellia sinensis, which displayed amino acid sequence homology with Arabidopsis AtWRKY7 and AtWRKY15. Subcellular localization prediction indicated that CsWRKY7 localized to nucleus. Cis-acting elements detected in the promotor region of CsWRKY7 are mainly involved in plant response to environmental stress and growth. Consistently, expression analysis showed that CsWRKY7 transcripts responded to NaCl, mannitol, PEG, and diverse hormones treatments. Additionally, CsWRKY7 exhibited a higher accumulation both in old leaves and roots compared to bud. Seed germination and root growth assay indicated that overexpressed CsWRKY7 in transgenic Arabidopsis was not sensitive to NaCl, mannitol, PEG, and low concentration of ABA treatments. CsWRKY7 overexpressing Arabidopsis showed a late-flowering phenotype under normal conditions compared to wild type. Furthermore, gene expression analysis showed that the transcription levels of the flowering time integrator gene FLOWERING LOCUS T (FT) and the floral meristem identity genes APETALA1 (AP1) and LEAFY (LFY) were lower in WRKY7-OE than in the WT. Taken together, these findings indicate that CsWRKY7 TF may participate in plant growth. This study provides a potential strategy to breed late-blooming tea cultivar. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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18 pages, 2658 KiB

Open AccessArticle

Genome-Wide Analysis of TCP Family Genes in Zea mays L. Identified a Role for ZmTCP42 in Drought Tolerance

by Shuangcheng Ding, Zhenzhen Cai, Hewei Du and Hongwei Wang

Int. J. Mol. Sci. 2019, 20(11), 2762; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20112762 - 05 Jun 2019

Cited by 58 | Viewed by 5507

Abstract

The Teosinte-branched 1/Cycloidea/Proliferating (TCP) plant-specific transcription factors (TFs) have been demonstrated to play a fundamental role in plant development and organ patterning. However, it remains unknown whether or not the TCP gene family plays a role in conferring a tolerance to drought stress [...] Read more.

The Teosinte-branched 1/Cycloidea/Proliferating (TCP) plant-specific transcription factors (TFs) have been demonstrated to play a fundamental role in plant development and organ patterning. However, it remains unknown whether or not the TCP gene family plays a role in conferring a tolerance to drought stress in maize, which is a major constraint to maize production. In this study, we identified 46 ZmTCP genes in the maize genome and systematically analyzed their phylogenetic relationships and synteny with rice, sorghum, and Arabidopsis TCP genes. Expression analysis of the 46 ZmTCP genes in different tissues and under drought conditions, suggests their involvement in maize response to drought stress. Importantly, genetic variations in ZmTCP32 and ZmTCP42 are significantly associated with drought tolerance at the seedling stage. RT-qPCR results suggest that ZmTCP32 and ZmTCP42 RNA levels are both induced by ABA, drought, and polyethylene glycol treatments. Based on the significant association between the genetic variation of ZmTCP42 and drought tolerance, and the inducible expression of ZmTCP42 by drought stress, we selected ZmTCP42, to investigate its function in drought response. We found that overexpression of ZmTCP42 in Arabidopsis led to a hypersensitivity to ABA in seed germination and enhanced drought tolerance, validating its function in drought tolerance. These results suggested that ZmTCP42 functions as an important TCP TF in maize, which plays a positive role in drought tolerance. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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17 pages, 3692 KiB

Open AccessArticle

The Class III Peroxidase (POD) Gene Family in Cassava: Identification, Phylogeny, Duplication, and Expression

by Chunlai Wu, Xupo Ding, Zehong Ding, Weiwei Tie, Yan Yan, Yu Wang, Hai Yang and Wei Hu

Int. J. Mol. Sci. 2019, 20(11), 2730; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20112730 - 03 Jun 2019

Cited by 39 | Viewed by 5066

Abstract

The class III peroxidase (POD) enzymes participate in plant development, hormone signaling, and stress responses. However, little is known about the POD family in cassava. Here, we identified 91 cassava POD genes (MePODs) and classified them into six subgroups using phylogenetic [...] Read more.

The class III peroxidase (POD) enzymes participate in plant development, hormone signaling, and stress responses. However, little is known about the POD family in cassava. Here, we identified 91 cassava POD genes (MePODs) and classified them into six subgroups using phylogenetic analysis. Conserved motif analysis demonstrated that all MePOD proteins have typical peroxidase domains, and gene structure analysis showed that MePOD genes have between one and nine exons. Duplication pattern analysis suggests that tandem duplication has played a role in MePOD gene expansion. Comprehensive transcriptomic analysis revealed that MePOD genes in cassava are involved in the drought response and postharvest physiological deterioration. Several MePODs underwent transcriptional changes after various stresses and related signaling treatments were applied. In sum, we characterized the POD family in cassava and uncovered the transcriptional control of POD genes in response to various stresses and postharvest physiological deterioration conditions. These results can be used to identify potential target genes for improving the stress tolerance of cassava crops. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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22 pages, 4395 KiB

Open AccessArticle

Salt Tolerance Improvement in Rice through Efficient SNP Marker-Assisted Selection Coupled with Speed-Breeding

by Md Masud Rana, Takeshi Takamatsu, Marouane Baslam, Kentaro Kaneko, Kimiko Itoh, Naoki Harada, Toshie Sugiyama, Takayuki Ohnishi, Tetsu Kinoshita, Hiroki Takagi and Toshiaki Mitsui

Int. J. Mol. Sci. 2019, 20(10), 2585; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20102585 - 26 May 2019

Cited by 80 | Viewed by 10605

Abstract

Salinity critically limits rice metabolism, growth, and productivity worldwide. Improvement of the salt resistance of locally grown high-yielding cultivars is a slow process. The objective of this study was to develop a new salt-tolerant rice germplasm using speed-breeding. Here, we precisely introgressed the [...] Read more.

Salinity critically limits rice metabolism, growth, and productivity worldwide. Improvement of the salt resistance of locally grown high-yielding cultivars is a slow process. The objective of this study was to develop a new salt-tolerant rice germplasm using speed-breeding. Here, we precisely introgressed the hst1 gene, transferring salinity tolerance from “Kaijin” into high-yielding “Yukinko-mai” (WT) rice through single nucleotide polymorphism (SNP) marker-assisted selection. Using a biotron speed-breeding technique, we developed a BC₃F₃ population, named “YNU31-2-4”, in six generations and 17 months. High-resolution genotyping by whole-genome sequencing revealed that the BC₃F₂ genome had 93.5% similarity to the WT and fixed only 2.7% of donor parent alleles. Functional annotation of BC₃F₂ variants along with field assessment data indicated that “YNU31-2-4” plants carrying the hst1 gene had similar agronomic traits to the WT under normal growth condition. “YNU31-2-4” seedlings subjected to salt stress (125 mM NaCl) had a significantly higher survival rate and increased shoot and root biomasses than the WT. At the tissue level, quantitative and electron probe microanalyzer studies indicated that “YNU31-2-4” seedlings avoided Na⁺ accumulation in shoots under salt stress. The “YNU31-2-4” plants showed an improved phenotype with significantly higher net CO₂ assimilation and lower yield decline than WT under salt stress at the reproductive stage. “YNU31-2-4” is a potential candidate for a new rice cultivar that is highly tolerant to salt stress at the seedling and reproductive stages, and which might maintain yields under a changing global climate. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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18 pages, 4258 KiB

Open AccessArticle

Comparative Analysis of Calcium-Dependent Protein Kinase in Cucurbitaceae and Expression Studies in Watermelon

by Chunhua Wei, Ruimin Zhang, Xiaozhen Yang, Chunyu Zhu, Hao Li, Yong Zhang, Jianxiang Ma, Jianqiang Yang and Xian Zhang

Int. J. Mol. Sci. 2019, 20(10), 2527; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20102527 - 23 May 2019

Cited by 17 | Viewed by 3500

Abstract

Both the calcium-dependent protein kinases (CDPKs) and CDPK-related kinases (CRKs) play numerous roles in plant growth, development, and stress response. Despite genome-wide identification of both families in Cucumis, comparative evolutionary and functional analysis of both CDPKs and CRKs in Cucurbitaceae remain unclear. [...] Read more.

Both the calcium-dependent protein kinases (CDPKs) and CDPK-related kinases (CRKs) play numerous roles in plant growth, development, and stress response. Despite genome-wide identification of both families in Cucumis, comparative evolutionary and functional analysis of both CDPKs and CRKs in Cucurbitaceae remain unclear. In this study, we identified 128 CDPK and 56 CRK genes in total in six Cucurbitaceae species (C. lanatus, C. sativus, C. moschata, C. maxima, C. pepo, and L. siceraria). Dot plot analysis indicated that self-duplication of conserved domains contributed to the structural variations of two CDPKs (CpCDPK19 and CpCDPK27) in C. pepo. Using watermelon genome as reference, an integrated map containing 25 loci (16 CDPK and nine CRK loci) was obtained, 16 of which (12 CDPK and four CRK) were shared by all seven Cucurbitaceae species. Combined with exon-intron organizations, topological analyses indicated an ancient origination of groups CDPK IV and CRK. Moreover, the evolutionary scenario of seven modern Cucurbitaceae species could also be reflected on the phylogenetic trees. Expression patterns of ClCDPKs and ClCRKs were studied under different abiotic stresses. Some valuable genes were uncovered for future gene function exploration. For instance, both ClCDPK6 and its ortholog CsCDPK14 in cucumber could be induced by salinity, while ClCDPK6 and ClCDPK16, as well as their orthologs in Cucumis, maintained high expression levels in male flowers. Collectively, these results provide insights into the evolutionary history of two gene families in Cucurbitaceae, and indicate a subset of candidate genes for functional characterizations in the future. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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16 pages, 4704 KiB

Open AccessArticle

Genome-Wide Characterization, Evolution, and Expression Profiling of VQ Gene Family in Response to Phytohormone Treatments and Abiotic Stress in Eucalyptus grandis

by Huifang Yan, Yujiao Wang, Bing Hu, Zhenfei Qiu, Bingshan Zeng and Chunjie Fan

Int. J. Mol. Sci. 2019, 20(7), 1765; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20071765 - 10 Apr 2019

Cited by 16 | Viewed by 3292

Abstract

VQ genes play important roles in plant development, growth, and stress responses. However, little information regarding the functions of VQ genes is available for Eucalyptus grandis. In our study, genome-wide characterization and identification of VQ genes were performed in E. grandis. [...] Read more.

VQ genes play important roles in plant development, growth, and stress responses. However, little information regarding the functions of VQ genes is available for Eucalyptus grandis. In our study, genome-wide characterization and identification of VQ genes were performed in E. grandis. Results showed that 27 VQ genes, which divided into seven sub-families (I–VII), were found, and all but two VQ genes showed no intron by gene structure and conserved motif analysis. To further identify the function of EgrVQ proteins, gene expression analyses were also developed under hormone treatments (brassinosteroids, methyl jasmonate, salicylic acid, and abscisic acid) and abiotic conditions (salt stress, cold 4 °C, and heat 42 °C). The results of a quantitative real-time PCR analysis indicated that the EgrVQs were variously expressed under different hormone treatments and abiotic stressors. Our study provides a comprehensive overview of VQ genes in E. grandis, which will be beneficial in the molecular breeding of E. grandis to promote its resistance to abiotic stressors; the results also provide a basis from which to conduct further investigation into the functions of VQ genes in E. grandis. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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17 pages, 2374 KiB

Open AccessArticle

Genome-Wide Analysis of Glycoside Hydrolase Family 1 β-glucosidase Genes in Brassica rapa and Their Potential Role in Pollen Development

by Xiangshu Dong, Yuan Jiang and Yoonkang Hur

Int. J. Mol. Sci. 2019, 20(7), 1663; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20071663 - 03 Apr 2019

Cited by 22 | Viewed by 4675

Abstract

Glycoside hydrolase family 1 (GH1) β-glucosidases (BGLUs) are encoded by a large number of genes, and are involved in many developmental processes and stress responses in plants. Due to their importance in plant growth and development, genome-wide analyses have been conducted in model [...] Read more.

Glycoside hydrolase family 1 (GH1) β-glucosidases (BGLUs) are encoded by a large number of genes, and are involved in many developmental processes and stress responses in plants. Due to their importance in plant growth and development, genome-wide analyses have been conducted in model plants (Arabidopsis and rice) and maize, but not in Brassica species, which are important vegetable crops. In this study, we systematically analyzed B. rapa BGLUs (BrBGLUs), and demonstrated the involvement of several genes in pollen development. Sixty-four BrBGLUs were identified in Brassica databases, which were anchored onto 10 chromosomes, with 10 tandem duplications. Phylogenetic analysis revealed that 64 genes were classified into 10 subgroups, and each subgroup had relatively conserved intron/exon structures. Clustering with Arabidopsis BGLUs (AtBGLUs) facilitated the identification of several important subgroups for flavonoid metabolism, the production of glucosinolates, the regulation of abscisic acid (ABA) levels, and other defense-related compounds. At least six BrBGLUs might be involved in pollen development. The expression of BrBGLU10/AtBGLU20, the analysis of co-expressed genes, and the examination of knocked down Arabidopsis plants strongly suggests that BrBGLU10/AtBGLU20 has an indispensable function in pollen development. The results that are obtained from this study may provide valuable information for the further understanding of β-glucosidase function and Brassica breeding, for nutraceuticals-rich Brassica crops. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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19 pages, 3700 KiB

Open AccessArticle

Genome-Wide Analysis of Multiple Organellar RNA Editing Factor Family in Poplar Reveals Evolution and Roles in Drought Stress

by Dongli Wang, Sen Meng, Wanlong Su, Yu Bao, Yingying Lu, Weilun Yin, Chao Liu and Xinli Xia

Int. J. Mol. Sci. 2019, 20(6), 1425; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20061425 - 21 Mar 2019

Cited by 20 | Viewed by 3480

Abstract

Poplar (Populus) is one of the most important woody plants worldwide. Drought, a primary abiotic stress, seriously affects poplar growth and development. Multiple organellar RNA editing factor (MORF) genes—pivotal factors in the RNA editosome in Arabidopsis thaliana—are indispensable for the [...] Read more.

Poplar (Populus) is one of the most important woody plants worldwide. Drought, a primary abiotic stress, seriously affects poplar growth and development. Multiple organellar RNA editing factor (MORF) genes—pivotal factors in the RNA editosome in Arabidopsis thaliana—are indispensable for the regulation of various physiological processes, including organelle C-to-U RNA editing and plasmid development, as well as in the response to stresses. Although the poplar genome sequence has been released, little is known about MORF genes in poplar, especially those involved in the response to drought stress at the genome-wide level. In this study, we identified nine MORF genes in the Populus genome. Based on the structural features of MORF proteins and the topology of the phylogenetic tree, the P. trichocarpa (Ptr) MORF family members were classified into six groups (Groups I–VI). A microsynteny analysis indicated that two (22.2%) PtrMORF genes were tandemly duplicated and seven genes (77.8%) were segmentally duplicated. Based on the d_N/d_S ratios, purifying selection likely played a major role in the evolution of this family and contributed to functional divergence among PtrMORF genes. Moreover, analysis of qRT-PCR data revealed that PtrMORFs exhibited tissue- and treatment-specific expression patterns. PtrMORF genes in all group were involved in the stress response. These results provide a solid foundation for further analyses of the functions and molecular evolution of MORF genes in poplar, and, in particular, for improving the drought resistance of poplar by genetics manipulation. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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18 pages, 13743 KiB

Open AccessArticle

Identification and Expression Profiling of Protein Phosphatases (PP2C) Gene Family in Gossypium hirsutum L.

by Hamna Shazadee, Nadeem Khan, Jingjing Wang, Chencan Wang, Jianguo Zeng, Zhongyi Huang and Xinyu Wang

Int. J. Mol. Sci. 2019, 20(6), 1395; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20061395 - 20 Mar 2019

Cited by 34 | Viewed by 6642

Abstract

The protein phosphatase (PP2C) gene family, known to participate in cellular processes, is one of the momentous and conserved plant-specific gene families that regulate signal transduction in eukaryotic organisms. Recently, PP2Cs were identified in Arabidopsis and various other crop species, but [...] Read more.

The protein phosphatase (PP2C) gene family, known to participate in cellular processes, is one of the momentous and conserved plant-specific gene families that regulate signal transduction in eukaryotic organisms. Recently, PP2Cs were identified in Arabidopsis and various other crop species, but analysis of PP2C in cotton is yet to be reported. In the current research, we found 87 (Gossypium arboreum), 147 (Gossypium barbadense), 181 (Gossypium hirsutum), and 99 (Gossypium raimondii) PP2C-encoding genes in total from the cotton genome. Herein, we provide a comprehensive analysis of the PP2C gene family in cotton, such as gene structure organization, gene duplications, expression profiling, chromosomal mapping, protein motif organization, and phylogenetic relationships of each species. Phylogenetic analysis further categorized PP2C genes into 12 subgroups based on conserved domain composition analysis. Moreover, we observed a strong signature of purifying selection among duplicated pairs (i.e., segmental and dispersed) of Gossypium hirsutum. We also observed the tissue-specific response of GhPP2C genes in organ and fiber development by comparing the RNA-sequence (RNA-seq) data reported on different organs. The qRT-PCR validation of 30 GhPP2C genes suggested their critical role in cotton by exposure to heat, cold, drought, and salt stress treatments. Hence, our findings provide an overview of the PP2C gene family in cotton based on various bioinformatic tools that demonstrated their critical role in organ and fiber development, and abiotic stress tolerance, thereby contributing to the genetic improvement of cotton for the resistant cultivar. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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17 pages, 2920 KiB

Open AccessArticle

Genome-Wide Analysis of LIM Family Genes in Foxtail Millet (Setaria italica L.) and Characterization of the Role of SiWLIM2b in Drought Tolerance

by Rui Yang, Ming Chen, Jian-Chang Sun, Yue Yu, Dong-Hong Min, Jun Chen, Zhao-Shi Xu, Yong-Bin Zhou, You-Zhi Ma and Xiao-Hong Zhang

Int. J. Mol. Sci. 2019, 20(6), 1303; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20061303 - 15 Mar 2019

Cited by 31 | Viewed by 4662

Abstract

LIM proteins have been found to play important roles in many life activities, including the regulation of gene expression, construction of the cytoskeleton, signal transduction and metabolic regulation. Because of their important roles in many aspects of plant development, LIM genes have been [...] Read more.

LIM proteins have been found to play important roles in many life activities, including the regulation of gene expression, construction of the cytoskeleton, signal transduction and metabolic regulation. Because of their important roles in many aspects of plant development, LIM genes have been studied in many plant species. However, the LIM gene family has not yet been characterized in foxtail millet. In this study, we analyzed the whole genome of foxtail millet and identified 10 LIM genes. All LIM gene promoters contain MYB and MYC cis-acting elements that are related to drought stress. Based on the presence of multiple abiotic stress-related cis-elements in the promoter of SiWLIM2b, we chose this gene for further study. We analyzed SiWLIM2b expression under abiotic stress and hormone treatments using qRT-PCR. We found that SiWLIM2b was induced by various abiotic stresses and hormones. Under drought conditions, transgenic rice of SiWLIM2b-overexpression had a higher survival rate, higher relative water content and less cell damage than wild type (WT) rice. These results indicate that overexpression of the foxtail millet SiWLIM2b gene enhances drought tolerance in transgenic rice, and the SiWLIM2b gene can potentially be used for molecular breeding of crops with increased resistance to abiotic stress. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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17 pages, 4785 KiB

Open AccessArticle

Genome-Wide Identification, Expression Profile, and Alternative Splicing Analysis of the Brassinosteroid-Signaling Kinase (BSK) Family Genes in Arabidopsis

by Zhiyong Li, Jinyu Shen and Jiansheng Liang

Int. J. Mol. Sci. 2019, 20(5), 1138; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20051138 - 06 Mar 2019

Cited by 22 | Viewed by 5357

Abstract

Brassinosteroids (BRs) are steroid hormones essential for different biological processes, ranging from growth to environmental adaptation in plants. The plant brassinosteroid-signaling kinase (BSK) proteins belong to a family of receptor-like cytoplasmic kinases, which have been reported to play an important role in BR [...] Read more.

Brassinosteroids (BRs) are steroid hormones essential for different biological processes, ranging from growth to environmental adaptation in plants. The plant brassinosteroid-signaling kinase (BSK) proteins belong to a family of receptor-like cytoplasmic kinases, which have been reported to play an important role in BR signal transduction. However, the knowledge of BSK genes in plants is still quite limited. In the present study, a total of 143 BSK proteins were identified by a genome-wide search in 17 plant species. A phylogenetic analysis showed that the BSK gene originated in embryophytes, with no BSK found in green algae, and these BSK genes were divided into six groups by comparison with orthologs/paralogs. A further study using comparative analyses of gene structure, expression patterns and alternative splicing of BSK genes in Arabidopsis revealed that all BSK proteins shared similar protein structure with some exception and post-translation modifications including sumolyation and ubiquitination. An expression profile analysis showed that most Arabidopsis BSK genes were constitutively expressed in different tissues; of these, several BSK genes were significantly expressed in response to some hormones or abiotic stresses. Furthermore, reverse transcription-polymerase chain reaction (RT-PCR) assays showed that BSK5, BSK7, and BSK9 underwent alternative splicing in specific stress induced and tissue-dependent patterns. Collectively, these results lay the foundation for further functional analyses of these genes in plants. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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23 pages, 6291 KiB

Open AccessArticle

Complete Chloroplast Genomes and Comparative Analysis of Sequences Evolution among Seven Aristolochia (Aristolochiaceae) Medicinal Species

by Xiaoqin Li, Yunjuan Zuo, Xinxin Zhu, Shuai Liao and Jinshuang Ma

Int. J. Mol. Sci. 2019, 20(5), 1045; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20051045 - 28 Feb 2019

Cited by 46 | Viewed by 4583

Abstract

Aristolochiaceae, comprising about 600 species, is a unique plant family containing aristolochic acids (AAs). In this study, we sequenced seven species of Aristolochia, and retrieved eleven chloroplast (cp) genomes published for comparative genomics analysis and phylogenetic constructions. The results show that the [...] Read more.

Aristolochiaceae, comprising about 600 species, is a unique plant family containing aristolochic acids (AAs). In this study, we sequenced seven species of Aristolochia, and retrieved eleven chloroplast (cp) genomes published for comparative genomics analysis and phylogenetic constructions. The results show that the cp genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The cp genomes range from 159,308 bp to 160,520 bp in length and have a similar GC content of 38.5%–38.9%. A total number of 113 genes were identified, including 79 protein-coding genes, 30 tRNAs and four rRNAs. Although genomic structure and size were highly conserved, the IR-SC boundary regions were variable between these seven cp genomes. The trnH-GUG genes, are one of major differences between the plastomes of the two subgenera Siphisia and Aristolochia. We analyzed the features of nucleotide substitutions, distribution of repeat sequences and simple sequences repeats (SSRs), positive selections in the cp genomes, and identified 16 hotspot regions for genomes divergence that could be utilized as potential markers for phylogeny reconstruction. Phylogenetic relationships of the family Aristolochiaceae inferred from the 18 cp genome sequences were consistent and robust, using maximum parsimony (MP), maximum likelihood (ML), and Bayesian analysis (BI) methods. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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Review

Jump to: Editorial, Research

30 pages, 2085 KiB

Open AccessReview

RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism

by Isiaka Ibrahim Muhammad, Sze Ling Kong, Siti Nor Akmar Abdullah and Umaiyal Munusamy

Int. J. Mol. Sci. 2020, 21(1), 167; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21010167 - 25 Dec 2019

Cited by 18 | Viewed by 10611

Abstract

The availability of data produced from various sequencing platforms offer the possibility to answer complex questions in plant research. However, drawbacks can arise when there are gaps in the information generated, and complementary platforms are essential to obtain more comprehensive data sets relating [...] Read more.

The availability of data produced from various sequencing platforms offer the possibility to answer complex questions in plant research. However, drawbacks can arise when there are gaps in the information generated, and complementary platforms are essential to obtain more comprehensive data sets relating to specific biological process, such as responses to environmental perturbations in plant systems. The investigation of transcriptional regulation raises different challenges, particularly in associating differentially expressed transcription factors with their downstream responsive genes. In this paper, we discuss the integration of transcriptional factor studies through RNA sequencing (RNA-seq) and Chromatin Immunoprecipitation sequencing (ChIP-seq). We show how the data from ChIP-seq can strengthen information generated from RNA-seq in elucidating gene regulatory mechanisms. In particular, we discuss how integration of ChIP-seq and RNA-seq data can help to unravel transcriptional regulatory networks. This review discusses recent advances in methods for studying transcriptional regulation using these two methods. It also provides guidelines for making choices in selecting specific protocols in RNA-seq pipelines for genome-wide analysis to achieve more detailed characterization of specific transcription regulatory pathways via ChIP-seq. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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24 pages, 1311 KiB

Open AccessReview

Insights on Calcium-Dependent Protein Kinases (CPKs) Signaling for Abiotic Stress Tolerance in Plants

by Rana Muhammad Atif, Luqman Shahid, Muhammad Waqas, Babar Ali, Muhammad Abdul Rehman Rashid, Farrukh Azeem, Muhammad Amjad Nawaz, Shabir Hussain Wani and Gyuhwa Chung

Int. J. Mol. Sci. 2019, 20(21), 5298; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20215298 - 24 Oct 2019

Cited by 76 | Viewed by 7531

Abstract

Abiotic stresses are the major limiting factors influencing the growth and productivity of plants species. To combat these stresses, plants can modify numerous physiological, biochemical, and molecular processes through cellular and subcellular signaling pathways. Calcium-dependent protein kinases (CDPKs or CPKs) are the unique [...] Read more.

Abiotic stresses are the major limiting factors influencing the growth and productivity of plants species. To combat these stresses, plants can modify numerous physiological, biochemical, and molecular processes through cellular and subcellular signaling pathways. Calcium-dependent protein kinases (CDPKs or CPKs) are the unique and key calcium-binding proteins, which act as a sensor for the increase and decrease in the calcium (Ca) concentrations. These Ca flux signals are decrypted and interpreted into the phosphorylation events, which are crucial for signal transduction processes. Several functional and expression studies of different CPKs and their encoding genes validated their versatile role for abiotic stress tolerance in plants. CPKs are indispensable for modulating abiotic stress tolerance through activation and regulation of several genes, transcription factors, enzymes, and ion channels. CPKs have been involved in supporting plant adaptation under drought, salinity, and heat and cold stress environments. Diverse functions of plant CPKs have been reported against various abiotic stresses in numerous research studies. In this review, we have described the evaluated functions of plant CPKs against various abiotic stresses and their role in stress response signaling pathways. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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44 pages, 3081 KiB

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Modern Trends in Plant Genome Editing: An Inclusive Review of the CRISPR/Cas9 Toolbox

by Ali Razzaq, Fozia Saleem, Mehak Kanwal, Ghulam Mustafa, Sumaira Yousaf, Hafiz Muhammad Imran Arshad, Muhammad Khalid Hameed, Muhammad Sarwar Khan and Faiz Ahmad Joyia

Int. J. Mol. Sci. 2019, 20(16), 4045; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20164045 - 19 Aug 2019

Cited by 126 | Viewed by 17351

Abstract

Increasing agricultural productivity via modern breeding strategies is of prime interest to attain global food security. An array of biotic and abiotic stressors affect productivity as well as the quality of crop plants, and it is a primary need to develop crops with [...] Read more.

Increasing agricultural productivity via modern breeding strategies is of prime interest to attain global food security. An array of biotic and abiotic stressors affect productivity as well as the quality of crop plants, and it is a primary need to develop crops with improved adaptability, high productivity, and resilience against these biotic/abiotic stressors. Conventional approaches to genetic engineering involve tedious procedures. State-of-the-art OMICS approaches reinforced with next-generation sequencing and the latest developments in genome editing tools have paved the way for targeted mutagenesis, opening new horizons for precise genome engineering. Various genome editing tools such as transcription activator-like effector nucleases (TALENs), zinc-finger nucleases (ZFNs), and meganucleases (MNs) have enabled plant scientists to manipulate desired genes in crop plants. However, these approaches are expensive and laborious involving complex procedures for successful editing. Conversely, CRISPR/Cas9 is an entrancing, easy-to-design, cost-effective, and versatile tool for precise and efficient plant genome editing. In recent years, the CRISPR/Cas9 system has emerged as a powerful tool for targeted mutagenesis, including single base substitution, multiplex gene editing, gene knockouts, and regulation of gene transcription in plants. Thus, CRISPR/Cas9-based genome editing has demonstrated great potential for crop improvement but regulation of genome-edited crops is still in its infancy. Here, we extensively reviewed the availability of CRISPR/Cas9 genome editing tools for plant biotechnologists to target desired genes and its vast applications in crop breeding research. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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Open AccessReview

Genetic and Molecular Control of Floral Organ Identity in Cereals

by Zulfiqar Ali, Qasim Raza, Rana Muhammad Atif, Usman Aslam, Muhammad Ajmal and Gyuhwa Chung

Int. J. Mol. Sci. 2019, 20(11), 2743; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20112743 - 04 Jun 2019

Cited by 28 | Viewed by 6833

Abstract

Grasses represent a major family of monocots comprising mostly cereals. When compared to their eudicot counterparts, cereals show a remarkable morphological diversity. Understanding the molecular basis of floral organ identity and inflorescence development is crucial to gain insight into the grain development for [...] Read more.

Grasses represent a major family of monocots comprising mostly cereals. When compared to their eudicot counterparts, cereals show a remarkable morphological diversity. Understanding the molecular basis of floral organ identity and inflorescence development is crucial to gain insight into the grain development for yield improvement purposes in cereals, however, the exact genetic mechanism of floral organogenesis remains elusive due to their complex inflorescence architecture. Extensive molecular analyses of Arabidopsis and other plant genera and species have established the ABCDE floral organ identity model. According to this model, hierarchical combinatorial activities of A, B, C, D, and E classes of homeotic genes regulate the identity of different floral organs with partial conservation and partial diversification between eudicots and cereals. Here, we review the developmental role of A, B, C, D, and E gene classes and explore the recent advances in understanding the floral development and subsequent organ specification in major cereals with reference to model plants. Furthermore, we discuss the evolutionary relationships among known floral organ identity genes. This comparative overview of floral developmental genes and associated regulatory factors, within and between species, will provide a thorough understanding of underlying complex genetic and molecular control of flower development and floral organ identity, which can be helpful to devise innovative strategies for grain yield improvement in cereals. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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