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Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology

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A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 23934

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Special Issue Editors

Prof. Dr. Jian Zhang

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Guest Editor

1. Department of Biology, University of British Columbia, Okanagan, Kelowna, BC V1V 1V7, Canada
2. Faculty of Agronomy, Jilin Agricultural University, Changchun 131018, China
Interests: digital agriculture; bioinformatics; genomics; plant phenomics; indoor breeding
Special Issues, Collections and Topics in MDPI journals

Dr. Guofei Tan

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Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
Interests: biotechnology; genomics; vegetable biology; germplasm; secondary metabolism; breeding
Special Issues, Collections and Topics in MDPI journals

Dr. Feng Que

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Guest Editor

Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
Interests: growth and development of bamboo plants; hormones in bamboo plants; cell wall development
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Biological diversity is the most important of nature’s gifts, and many elite or superior gene alleles that confer favorable traits remain to be discovered and utilized. With the advancement of “omics” disciplines, plant genetic resources and biodiversity have become more critical for future agricultural and horticultural development. The data mining of these genetic resources to advance domestication has great potential in enhancing the crop vegetable yield and quality through molecular breeding and genetic engineering. A better knowledge of accumulated genomic plant resources for seeds, tubers, bamboo, etc., would help provide a fundamental understanding of the underlying genetics, physiology, biochemistry and metabolism, with the aim of developing improved breeding regimes for future agriculture and horticulture.

The introduction of newly identified germplasm for major crops, improving their important traits such as oil, fiber and bioproduct production and increasing the understanding of the genetic background, genome information, proteome and metabolome of plants.

Second and third generation sequencing, GWAS, transcriptomics, proteomics, metabolomics, and genetic basis of quality and production.

What kind of papers we are soliciting: Crop genomics; genetic improvement; molecular markers; genetic engineering/transformation; organ formation and development and their genetic basis; digital agriculture.

Prof. Dr. Jian Zhang
Dr. Guofei Tan
Dr. Feng Que
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

genetic resources
genomics
biotechnology
genetic transformation
tissue culture

Published Papers (14 papers)

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Research

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14 pages, 5135 KiB

Open AccessArticle

by Xiu-Lai Zhong, Shun-Hua Zhu, Qian Zhao, Qing Luo, Kun Wang, Zhi-Feng Chen and Guo-Fei Tan

Agronomy 2023, 13(8), 2025; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13082025 - 30 Jul 2023

Viewed by 1053

Abstract

4-Coumarate: coenzyme A ligase (4CL; EC 6.2.1.12) is an important enzyme in the phenylpropanoid metabolic pathway that controls the biosynthesis of lignin and flavonoids. In this study, to identify the function of the Ag4CL3 gene of celery, the Ag4CL3 gene was cloned from celery cv. “Nanxuan Liuhe Ziqin”. Sequence analysis results showed that the Ag4CL3 gene contained an open reading frame (ORF) with a length of 1688 bp, and 555 amino acids were encoded. The Ag4CL3 protein was highly conserved among different plant species. Phylogenetic analysis demonstrated that the 4CL proteins from celery and carrot belonged to the same clade. The Ag4CL3 protein was mainly composed of 31.89% α-helixes, 18.02% extended strands, 6.67% β-turns, and 43.42% random coils, and the signal peptide was unfound. A total of 62 phosphorylation sites and a class-I superfamily of adenylate-forming domains were found. As the growth time increased, the plant height and stem thickness also increased, and the petiole lignin content increased and became lignified gradually. The relative expression levels of the Ag4CL3 gene in “Nanxuan Liuhe Ziqin” petioles were higher than those in other tissues, with the highest level occurring 70 d after sowing. The lignin contents in the transgenic Arabidopsis thaliana lines hosting the Ag4CL3 gene were higher than those in the WT. In this study, the overexpression of Ag4CL3 led to the significant upregulation of lignin biosynthesis gene expression in transgenic A. thaliana plants, except for AtPAL, AtCCR, and AtLAC. This study speculates that Ag4CL3 genes are related to lignin synthesis in A. graveolens. Full article

(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology)

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18 pages, 6517 KiB

Open AccessArticle

Genome-Wide Identification, Expansion, Evolution, and Expression Analysis Reveals ABCB Genes Important for Secondary Cell Wall Development in Moso Bamboo (Phyllostachys edulis)

by Feng Que, Yaqi Zhu, Qingnan Liu, Qiang Wei and Muthusamy Ramakrishnan

Agronomy 2023, 13(7), 1828; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13071828 - 10 Jul 2023

Cited by 1 | Viewed by 993

Abstract

The ATP-binding cassette subfamily B (ABCB) is an important transporter family, and many members are well known for their auxin transport function. However, reports on the function of the ABCB genes during Moso bamboo development are few. In this study, we identified and characterized 37 PhABCB genes in Moso bamboo and classified them into five subgroups, Ⅰ–Ⅴ. We further observed gene family expansion and gene loss events during the evolution of the PhABCB gene family. It was found that the expansion of the PhABCB family was mainly attributed to the whole-genome duplication and DNA-transposed duplication models. Gene co-expression analysis and quantitative real-time PCR revealed that several PhABCB genes may be involved in the development of the secondary cell wall (SCW) during the rapid growth of Moso bamboo. Through examining their expression in different parts of the bamboo internode where the cell walls exhibited different developmental stages, the roles of eight candidate PhABCBs in the SCW development were further characterized. Of the eight PhABCB genes, PhABCB7, PhABCB11, PhABCB14, and PhABCB21 may be involved in the SCW biogenesis in Moso bamboo. This study provides the basis for discovering the potential role of PhABCB genes in Moso bamboo cell wall development; further studies are needed to elucidate how these PhABCBs function in SCW development by regulating the polar transport of auxin. Full article

(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology)

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14 pages, 4368 KiB

Open AccessArticle

Construction and Functional Evaluation of CRISPR/Cas9 Multiple Knockout Vectors of the FAD2 Gene Family

by Qi Zhang, Lu Liu, Zhifeng Xiao, Yuwei Sun, Yongjing Xi, Tingting Sun, Jiabao Wang and Piwu Wang

Agronomy 2023, 13(7), 1737; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13071737 - 28 Jun 2023

Cited by 1 | Viewed by 1129

Abstract

Soybean oil is a traditional edible oil. Increasing the oleic acid content is an important direction of soybean breeding. The soybean FAD2 family consists of seven genes that regulate how oleic acid is converted into linoleic acid. Five genes of the soybean FAD2 gene family, GmFAD2-1B, GmFAD2-1A, GmFAD2-2B, GmFAD2-2C, and GmFAD2-2D, were taken as target genes in this study. Firstly, a multivalent CRISPR/Cas9 gene-editing vector was constructed to regulate FAD2 gene expression. Multiple knockout vectors were inserted into the soybean varieties JN38, T6098, and T7010 using Agrobacterium-mediated soybean cotyledon transformation. The functional analysis, agronomic character analysis, and comparison of the mutant lines of the offspring of different genotypes indicated that the JN38 mutant was significantly taller in terms of plant height than the receptor JN38. The fatty acid content of the three groups showed the same trend. The fatty acid contents of mutant plants were higher than those of recipient plants, and the linoleic acid contents of mutant plants were lower than those of recipient plants. The best-performing among the three groups was the JN38 mutant, whose oleic acid content increased from 18.58% to 54.07% and whose linoleic acid content decreased from 57.79% to 26.17%. In conclusion, the knockout expression of multiple FAD2 genes increased the soybean oleic acid content and decreased the linoleic acid content in different receptors. Full article

(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology)

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15 pages, 3559 KiB

Open AccessArticle

Using Isoform Sequencing for De Novo Transcriptome Sequencing and the Identification of Genes Related to Drought Tolerance and Agronomic Traits in Tall Fescue (Festuca arundinacea Schreb.)

by Chunyan Yang, Li Zhong, Erling Ou, Fang Tian, Mei Yao, Ming Chen, Xu Yan, Yingzheng Li, Xiaofeng Li, Ruyu He, Jianmei He, Qilin Tang and Degang Zhao

Agronomy 2023, 13(6), 1484; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13061484 - 28 May 2023

Cited by 1 | Viewed by 1376

Abstract

Plant height and tillering are the key traits of tall fescue (Festuca arundinacea Schreb.), a perennial turf grass widely used for forage and turf worldwide. It exhibits excellent abiotic stress tolerance. However, the investigation of these traits at the genetic level is limited by the lack of a completely sequenced genome of tall fescue. Here, we generated genome-wide transcriptome data using PacBio isoform sequencing (Iso-Seq) technology. We obtained 73,628 transcripts with an average length of 2410 bp. Among these transcripts, 42,265 (60.09%) were predicted as complete full-length open reading frames. The dataset contained 11,520 simple sequence repeats; 737 bp long non-coding RNAs; and 1599 alternative splicing sites in unigenes. Sixty-three unigenes involved in abscisic acid biosynthesis, catabolism, and signaling pathways were identified. The Illumina-sequencing analysis results, further verified using qRT-PCR, revealed the significant upregulation of nine unigenes under drought stress. Ninety-three unigenes involved in controlling plant height and tillering were also identified, of which FaMAX1 was functionally verified to regulate plant tillering. Our results provide a valuable genetic resource about the complete transcriptome of tall fescue; the identified candidate genes can aid in improving the drought tolerance and agronomic traits in tall fescue and other related plants. Full article

(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology)

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13 pages, 1956 KiB

Open AccessArticle

Composition of Strawberry Flower Volatiles and Their Effects on Behavior of Strawberry Pollinators, Bombus terrestris and Apis mellifera

by Jinjia Liu, Min Chen, Weihua Ma, Lifang Zheng, Bing Zhang, Huiting Zhao and Yusuo Jiang

Agronomy 2023, 13(2), 339; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13020339 - 24 Jan 2023

Cited by 4 | Viewed by 1892

Abstract

Strawberries are popular fruits around the world, and their yield and fruit quality rely on pollination by honey bees and bumblebee colonies. Both bee species have their own advantages in strawberry pollination. This study investigates the characteristic of strawberry (Fragaria × ananassa ‘Red Face’) flower volatiles and their effects on bee pollinators by (1) detecting the volatile compounds of strawberry flowers by polydimethylsiloxane (PDMS) combined gas chromatography-mass spectrometry (GC-MS), (2) determining whether Bombus terrestris or Apis mellifera showed antennae responses to certain compounds of strawberry flower volatiles by an electroantennography test (EAG), and (3) testing whether these compounds could elicit a corresponding behavioral response in bees. The results showed that (1) there were 38 chemical compounds in ‘Red Face’ volatiles with 7 types, most of which were known to be generally emitted by flowers but also have some compounds that have not been reported in strawberry flowers; (2) B. terrestris and A. mellifera had strong EAG responses to several compounds, respectively, especially to ethyl benzoate, (Z)-3-hexenyl propionate, (Z)-3-hexenyl acetate, benzeneacetaldehyde and melonal; and (3) both bee species showed significant avoidance behaviors to four tested compounds, especially the B. terrestris. Flower volatiles of strawberry ‘Red face’ were different from other strawberry varieties that have been reported; some of these electrophysiologically active compounds could cause antennal potential responses in bees, as well as behavioral responses. Our study supports the idea that strawberry flower volatiles are one of the factors influencing bee foraging decisions and provides a reference for formulating more reasonable bee pollination to improve strawberry fruit quality. Full article

(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology)

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15 pages, 2011 KiB

Open AccessArticle

Genetic Diversity and Population Structure in Bread Wheat Germplasm from Türkiye Using iPBS-Retrotransposons-Based Markers

by Kamil Haliloğlu, Aras Türkoğlu, Ali Öztürk, Gniewko Niedbała, Mohsen Niazian, Tomasz Wojciechowski and Magdalena Piekutowska

Agronomy 2023, 13(1), 255; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13010255 - 14 Jan 2023

Cited by 11 | Viewed by 2270

Abstract

This study investigated the genetic diversity and population structure of 63 genotypes from Turkish bread wheat germplasm using iPBS-retrotransposons primers. The thirty-four iPBS primers produced a total of 1231 polymorphic bands, ranging from 8 (iPBS-2375) to 60 (iPBS-2381) alleles per marker, with an average number of 36.00 alleles. The polymorphism information content (PIC) per marker varied between 0.048 (iPBS 2087) and 0.303 (iPBS 2382), with an average of 0.175. The numbers of effective alleles (ne), genetic diversity of Nei (h), and Shannon’s information index (I) value were calculated as 1.157, 0.95, and 0.144, respectively. The greatest genetic distance (0.164) was between Eastern Anatolia Agricultural Research Institute genotypes and Çukurova Agricultural Research Institute genotypes. The unweighted pair-group method with arithmetic mean (UPGMA) dendrogram placed the 63 wheat genotypes into three clusters. The percentage of genetic diversity explained by each of the three main coordinates of the basic coordinate analysis was determined to be 44.58, 12.08, and 3.44, respectively. AMOVA (Analysis of Molecular Variance) showed that the variation within populations was 99% and that between populations was 1%. The result of genetic structure analysis suggests that the greatest value of K was calculated as 3. The F-statistic (Fst) value was determined as 0.4005, 0.2374, and 0.3773 in the first to third subpopulations, respectively. Likewise, the expected heterozygosity values (He) were determined as 0.2203, 0.2599, and 0.2155 in the first, second, and third subpopulations, respectively. According to the information obtained in the study, the most genetically distant genotypes were the G1 (Aksel 2000) and G63 (Karasu 90) genotypes. This study provided a deep insight into genetic variations in Turkish bread wheat germplasm using the iPBS-retrotransposons marker system. Full article

(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology)

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12 pages, 3326 KiB

Open AccessArticle

Comparative Physiological Analysis of Lignification, Anthocyanin Metabolism and Correlated Gene Expression in Red Toona sinensis Buds during Cold Storage

by Qian Zhao, Xiu-Lai Zhong, Xia Cai, Shun-Hua Zhu, Ping-Hong Meng, Jian Zhang and Guo-Fei Tan

Agronomy 2023, 13(1), 119; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13010119 - 30 Dec 2022

Cited by 2 | Viewed by 1289

Abstract

The characteristics of anthocyanin and lignin are important parameters in evaluating the quality of red Toona sinensis buds. Red T. sinensis buds are prone to senescence during postharvest storage, which subsequently affects their quality and sales. However, the mechanism of senescence in red T. sinensis buds under low-temperature conditions remains unclear. In this study, red T. sinensis buds were stored at 4 °C, and their anthocyanin and lignin contents as well as the enzyme activities of PAL (phenylalanine ammonia lyase), 4CL (4-coumarate-CoA ligase), CAD (cinnamyl alcohol dehydrogenase) and POD (peroxidase) were determined at 0, 1, 2 and 3 d after handing. Meanwhile, the cellular structure of postharvest red T. sinensis buds was observed by microscopy. The relative expression of lignin-related and anthocyanin-related genes was analyzed using qRT-PCR. The results show that the anthocyanin content of the leaves was higher than that of the petioles. After 3 d of storage, the anthocyanin content of the leaves was 4.66 times that of the petioles. Moreover, the lignin content of the red T. sinensis buds gradually increased. Compared with 0 d, the lignin content of the leaves and petioles increased by 331.8 and 94.14 mg·g⁻¹, respectively. The enzyme activities of PAL, 4CL, CAD and POD increased during cold storage. The intercellular space and the arrangement of the palisade tissue and sponge tissue in the mesophyll of red T. sinensis buds became smaller and closer, respectively. The secondary cell wall of xylem cells thickened, the number of xylem cells increased, and the arrangement number of the xylem cells became closed in the leaf vein and petioles during red T. sinensis bud storage. The expression levels of anthocyanin-related (Except for TsCHS and TsANS) and lignin-related genes increased during red T. sinensis bud storage and are highly consistent with the accumulation patterns of anthocyanins and lignin. This study may serve as a reference for exploring the molecular mechanisms of senescence, regulating the quality and cultivating new varieties of red T. sinensis buds that have low lignin content but high anthocyanin content after harvest. Full article

(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology)

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14 pages, 3415 KiB

Open AccessArticle

Community Composition Specificities of Cyanobacteria in Paddy Soil under Different Ecological Conditions

by Jian Song, Xu He, Shuwen Wang, Xue Yang, Lei Wu, Siyuan Li, Dongchao Wang, Meiying Yang and Zhihai Wu

Agronomy 2022, 12(12), 3090; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12123090 - 6 Dec 2022

Cited by 3 | Viewed by 2023

Abstract

In order to explore the distribution of cyanobacteria in paddy soil under different ecological conditions, the composition, diversity, and environmental drivers of soil cyanobacteria communities in rice fields from six regions of Jilin Province (China) were investigated. The results showed that the 16S amplicon high-throughput sequence detected the existence of cyanobacteria of 16 phyla, 33 orders, 60 families, and 113 genera in the soil of rice fields in Jilin Province. The dominant cyanobacteria populations in Jilin Province paddy soils comprised Cyanobium_PCC-6307, Synechocystis_PCC-6803, Planktothrix_NIVA-CYA_15, and Nodosilinea_PCC-7104. Each soil sample included a significant proportion of nitrogen-fixing filamentous cyanobacteria Anabaena and Nostoc according to microscopic analysis. The structural properties and diversity of cyanobacteria communities differed by geography, with soil pH and SOC being the main environmental drivers of cyanobacteria community structure. The alkaline soils S1, S2, and S5 displayed greater diversity than the acidic soils S3, S4, and S6, with S5 displaying the greatest cyanobacteria diversity. This research has crucial implications for developing and utilizing local cyanobacteria resources. Full article

(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology)

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18 pages, 4662 KiB

Open AccessArticle

Complete Chloroplast Genome Sequence of a New Variety of Brasenia schreberi: Genome Characteristics, Comparative Analysis, and Phylogenetic Relationships

by Yue Sun, Mengyao Li, Junying Ma, Maolin He and Yangxia Zheng

Agronomy 2022, 12(12), 2972; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12122972 - 26 Nov 2022

Cited by 1 | Viewed by 1289

Abstract

This study sequenced and assembled the chloroplast (cp) genome of Brasenia schreberi cv. ‘Mahu Chuncai’, a novel variety of B. schreberi rich in nutrients with distinctive characteristics, unlike other varieties in China. The cpDNA genome of ‘Mahu Chuncai’ has a typical quadripartite structure, with a full length of 158,973 bp, including 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic analysis revealed that all species can be divided into three main clades. Results from inverted repeats (IR) boundary analysis revealed substantial differences between Brasenia and Cabomba species. The cpDNA genome of B. schreberi identified was strongly related to Brasenia species but appeared to be a distant relative of Cabomba aquatica more than other species in Cabombaceae. In contrast with the species from Cabombaceae, ‘Mahu Chuncai’ was a close relative of B. schreberi MN315507.1, which was a distant relative of C. aquatica MG720559.1. Furthermore, we found four potential molecular markers, i.e., ycf1 in the IR region, psbT in the LSC region, and ndhF and rps15 in the SSC region. Collectively, our findings confirm the phylogenetic evolution and cultivation origin of B. schreberi. We identified genetic characteristics and nucleotide diversity hotspots, which provides a theoretical basis for additional research on variety identification, germplasm resources, and molecular breeding of the precious vegetable. Full article

(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology)

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18 pages, 2197 KiB

Open AccessArticle

Physio-Biochemical Responses of Three Aquilegia Species Seedlings to Salt Stress

by Lifei Chen, Yuan Meng, Dawei Jiang, Fengrui Yang and Yunwei Zhou

Agronomy 2022, 12(11), 2841; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12112841 - 14 Nov 2022

Cited by 4 | Viewed by 1599

Abstract

Road deicing salts are widely used during winter in northern China, which makes it essential to choose proper salt-tolerant plant species in urban landscapes. Columbine (Aquilegia) is a herb with high ornamental and commercial values. This study evaluated three Aquilegia species (A. oxysepala, A. parviflora, and A. viridiflora) for salt tolerance by monitoring their germination state under different electrical conductivity (EC) of 0.1 dS·m⁻¹ (distilled water), 1.0 dS·m⁻¹, 2.0 dS·m⁻¹, 3.0 dS·m⁻¹, 4.0 dS·m⁻¹, 5.0 dS·m⁻¹, 6.0 dS·m⁻¹, physio-biochemical responses to different EC of 0.3 dS·m⁻¹ (tap water), 5.0 dS·m⁻¹, and 10.0 dS·m⁻¹. The germination and growth parameters, visual scores, dry weight, leaf stomatal conductance, photosynthetic rate, and chlorophyll contents of three species decreased under salt stress, which was opposite to the changes of electrolyte leakage, malondialdehyde, proline, and soluble sugar contents. Superoxide dismutase and peroxidase activity trend differently among species. These results showed that the germination threshold of three species was 6.0 dS·m⁻¹. A. oxysepala was the most salt-tolerant species, with a tolerance threshold of soil conductivity in 2.83 dS·m⁻¹, followed by A. viridiflora and A. parviflora. Therefore, A. oxysepala is suitable for planting as a ground cover in urban areas where deicing salt is applied. Full article

(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology)

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12 pages, 4008 KiB

Open AccessArticle

The Lobed-Leaf Phenotype in Brassica juncea Is Associated with the BjLMI1 Locus as Evidenced Using GradedPool-Seq

by Wen-Yuan Fu, Jiu-Cui Teng, Bing Tang, Qing-Qing Wang, Wei Yang, Lian Tao, Zheng-Jie Wan, Kang-Yun Wu, Guo-Fei Tan and Ying Deng

Agronomy 2022, 12(11), 2696; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12112696 - 30 Oct 2022

Viewed by 1325

Abstract

The shape of the leaf is the primary phenotype which determines the commercial value of leaf mustard (Brassica juncea). However, there arefew reports on the lobed-leaf gene of B. juncea, and the molecular regulatory mechanisms underlying leaf margin formation are unknown. In this study, an F₂ population derived from ‘MN001’ and ‘MU056’ was constructed. Genetic analysis revealed that the lobed-leaf trait is controlled by a major gene, and lobed leavesare dominant compared to round leaves. The GradedPool-Seq analysis combined with the re-sequencing results of parents identified a major interval on chromosome 10 of B. juncea’s genome A. The BjLMI1 gene (BjuA040054) was confirmed to be a candidate gene by gene ontology (GO) analysis, and it is homologous with LMI1 and encodes HD-Zip protein ATHB-51. A base substitution was observed in the conserved domain, and a 63 bp fragment deletion was found in the exon region between the two parents in the CDs region. The expression of BjLMI1 was significantly higher in the lobed-leaf parent than in the round-leaf parent. These findings provide insights into the molecular mechanism underlying leaf margin formation and will be valuable in the development of an ideal leaf shape in B. juncea. Full article

(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology)

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16 pages, 6808 KiB

Open AccessArticle

Modification of Gene Expression, DNA Methylation and Small RNAs Expression in Rice Plants under In Vitro Culture

by Ningning Wang, Yanan Yu, Di Zhang, Zhibin Zhang, Zhenhui Wang, Hongwei Xun, Guo Li, Bao Liu and Jian Zhang

Agronomy 2022, 12(7), 1675; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12071675 - 14 Jul 2022

Cited by 2 | Viewed by 2047

Abstract

Tissue culture is an important experimental technique widely used for plant transformation and can induce somaclonal variation that is shown to be associated with genetic and epigenetic changes. However, the molecular basis of somaclonal variation and plant cell response to tissue culture has yet to be fully understood. In this study, we investigated gene expression, DNA methylation, and small RNA changes in regenerated lines (RL) compared with the wild-type progenitor plants (WT) of rice cv. Hitomebore. Using microarray, we identified many genes that were differentially expressed in the shoot-tip tissue and showed that TEs were generally activated in RL. Methylation Sensitive Amplification Polymorphism (MSAP) analysis of 5′CCGG sites combined with bisulfite sequencing detected a generally reduced DNA methylation in the RL lines. Small RNA sequencing analysis detected widespread changes in small RNA accumulation between RL and WT. In particular, repeat and TE-associated 24-nt size class of small RNAs, the inducer of RNA-directed DNA methylation, was in general down-regulated in RL, consistent with reduced CHG and CHH methylation at some of the differentially methylated TE loci. A large number of differentially expressed miRNAs were identified in RL and WT lines, including known and novel miRNAs. The expression of some of these miRNAs exhibited inverse correlation with the predicted target genes, suggesting a regulatory function. The RL plants looked similar to WT plants under normal conditions but showed significant phenotypic alterations under abiotic stress conditions. The widespread changes in DNA methylation, small RNA accumulation and gene expression in regenerated plants supports the role of epigenetic changes in tissue culture-induced somaclonal variation. Full article

(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology)

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Review

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18 pages, 1225 KiB

Open AccessReview

Comprehensive Assessment of Houttuynia cordata Thunb., an Important Medicinal Plant and Vegetable

by Qing Luo, Ping-Hong Meng, Da-Wei Jiang, Zhong-Ming Han, Zhen-Hui Wang, Guo-Fei Tan and Jian Zhang

Agronomy 2022, 12(10), 2582; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12102582 - 20 Oct 2022

Cited by 5 | Viewed by 2683

Abstract

Houttuynia cordata Thunb., called Yuxingcao in Chinese, is an important medicinal plant and vegetable consumed in the southern regions of China. This review aims to summarize studies on the phyto-physiological chemistry, cytology, molecular biology, and genomics of H. cordata. Studies on the physiology and biochemistry of H. cordata have grown over the past few decades. Phenotypic and agronomic traits, tissue culture, elemental analysis, photosynthetic studies, bioactive compound identification, and antioxidant research have been reported. Molecular biological studies, such as those of molecular markers, microRNAs, DNA variations, protein variations, and transcriptomes have also advanced. Recent studies have focused on the rDNA and chloroplast genome of this plant. This review could serve as a basis to perform the genetic breeding, genomic advance, and cultivation of this valuable diversified plant resource for medicinal applications and vegetable production. Full article

(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology)

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Other

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11 pages, 1078 KiB

Open AccessBrief Report

Evaluation of In Vitro Morphogenic Response of Triticum urartu, a Donor of A^u Genome of Modern Wheat

by Dmitry Miroshnichenko, Tatiana Sidorova and Sergey Dolgov

Agronomy 2022, 12(12), 3123; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12123123 - 9 Dec 2022

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Abstract

Triticum urartu Thum. ex Gandil. is a wild diploid wheat species (2n = 2x = 14) that is an A^u genome donor of modern polyploid cultivars of durum and bread wheat. In the last decade, this relict species has attracted breeders as donors of various agronomically important characteristics to broaden the genetic diversity of cultivated wheat. In addition, T. urartu can be considered as a model species for studying the evolution, biology and genomics of wheat without the cross-influence of homologous sub-genomes. Various genetic engineering technologies, including transgenesis and genome editing, may be applied to facilitate the functional characterization of genes located in A chromosomes. Such biotechnological techniques are still required for the efficient tissue culture systems to allow easy plant regeneration. The objective of our study was to assess the abilities of in vitro plant regeneration from zygotic immature embryo-derived tissues of spring and winter types of T. urartu. Three synthetic auxins, 2,4-D, Dicamba and Picloram, at four concentrations were studied to stimulate morphogenic responses in spring T. urartu. The induction medium supplemented with 4 mg·L⁻¹ Dicamba stimulated the highest frequency of regenerable callus production (65.8%), promoting the generation of 5.7 plants. Although the presence of 2 mg·L⁻¹ 2,4-D was less effective in stimulating regenerable callus formation (53.2%) than Dicamba, it allowed the regeneration of more plants from one regenerable callus (9.3 plants). These two treatments also successfully initiated morphogenesis in winter assertions; however, their regenerative capacity was generally lower. The frequency of regenerable callus production was accession-dependent and fluctuated within 31.3 to 49.2%, with a formation of an average 2.2–5.8 plants per callus. The relatively simple and fast regeneration system described in this study could be further used as the basis for regenerating transgenic plants of T. urartu. Full article

(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology)

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Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology

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