Topic Editors

Prof. Dr. Gianni Barcaccia
Department of Agronomy Food Natural Resources Animals Environment, Campus of Agripolis, University of Padova, 35020 Legnaro, Italy
Dr. Alessandro Vannozzi
Department of Agronomy Food Natural Resources Animals Environment, Campus of Agripolis, University of Padova, 35020 Legnaro, Italy
Dr. Fabio Palumbo
Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, Viale dell’Università 16, 35020 Legnaro, Padova, Italy

Plant Breeding, Genetics and Genomics

Abstract submission deadline
31 October 2022
Manuscript submission deadline
31 December 2022
Viewed by
16186

Topic Information

Dear Colleagues,

Since the release of the first plant genome (Arabidopsis thaliana, 2000), the genomes of nearly two thousand plant species, including several crops, have been sequenced and published. This priceless treasure trove of information finds great application in breeding and genetic improvement. In fact, conventional breeding methods are more and more frequently combined with marker-assisted and genomic selection approaches, genetic engineering and genome editing. The targeted use of molecular markers associated with traits of agronomic interest, including disease resistance and abiotic stress tolerance, has been optimized for precise genotype selection. Vice versa, the application of molecular markers in broad-spectrum analyses covering entire genomes has deeply simplified the development of customized new varieties by reducing development time and costs. Finally, the in-depth knowledge of a genome and the functional characterization of specific genes loci also represent the starting point for genetic engineering and genome editing studies aimed at improving the agronomic performance of next-generation crops.

The Topic Editors encourage you to contribute to this Special Topic with research articles or reviews supporting the concrete advantages and/or the near-future potentials related to the use of genetics and genomics in the selection or constitution of new horticultural varieties.

Prof. Dr. Gianni Barcaccia
Dr. Alessandro Vannozzi
Dr. Fabio Palumbo
Topic Editors

Keywords

  • plant breeding
  • molecular markers
  • SSR
  • SNP
  • genome sequencing
  • crops
  • genome editing
  • marker assisted selection

Participating Journals

Journal Name Impact Factor CiteScore Launched Year First Decision (median) APC
Agriculture
agriculture
2.925 2.5 2011 19.6 Days 1800 CHF Submit
Agronomy
agronomy
3.417 2.6 2011 19.4 Days 2000 CHF Submit
Crops
crops
- - 2021 15.0 days * 1000 CHF Submit
Horticulturae
horticulturae
2.331 3.4 2015 17.3 Days 1600 CHF Submit
Plants
plants
3.935 2.2 2012 13.1 Days 2200 CHF Submit

* Median value for all MDPI journals in the second half of 2021.

Published Papers (38 papers)

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Communication
Evidence That 2n Eggs Explain Partial Hybrids between Medicago sativa and Medicago arborea
Plants 2022, 11(10), 1380; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11101380 - 23 May 2022
Abstract
Selected genotypes of alfalfa (Medicago sativa) produce partial hybrids in sexual crosses with Medicago arborea, as reported in Plants (2013). The hybrids contain mostly alfalfa DNA and traits, but also contain DNA and traits from M. arborea. It was [...] Read more.
Selected genotypes of alfalfa (Medicago sativa) produce partial hybrids in sexual crosses with Medicago arborea, as reported in Plants (2013). The hybrids contain mostly alfalfa DNA and traits, but also contain DNA and traits from M. arborea. It was proposed in 2008 that the partial hybrids could be explained by fertilization of 2n eggs in alfalfa by normal pollen from M. arborea, followed by partial loss of M. arborea chromosomes during embryogenesis. In this paper, we confirm the presence of 2n eggs in the first alfalfa parents that produced hybrids. The test for 2n eggs involved pollinating 4x alfalfa with pollen from 8x alfalfa. The production of 8x progeny in the cross proved that selected alfalfa parents produced 2n eggs. Thus, 2n eggs appear to explain how the partial hybrids (hereafter hybrids) contain mostly alfalfa DNA and traits. However, two of the six alfalfa plants that did not hybridize with M. arborea also had 2n eggs. Thus, although 2n eggs explain the alfalfa content of hybrids, 2n eggs are not the only factor involved in weakening the hybridization barrier, and in transferring genes to alfalfa from M. arborea. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Combining Ability and Heterotic Patterns of Tropical Early-Maturing Maize Inbred Lines under Individual and Combined Heat and Drought Environments
Plants 2022, 11(10), 1365; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11101365 - 20 May 2022
Abstract
Information on combining ability and heterotic patterns of multiple stress-tolerant inbred lines are fundamental prerequisites for devising appropriate breeding strategies for the development of climate-resilient maize hybrids. In the present study, we evaluated 150 single cross hybrids derived from the North Carolina Design [...] Read more.
Information on combining ability and heterotic patterns of multiple stress-tolerant inbred lines are fundamental prerequisites for devising appropriate breeding strategies for the development of climate-resilient maize hybrids. In the present study, we evaluated 150 single cross hybrids derived from the North Carolina Design II (NCD II) along with six commercial checks under terminal drought stress (TDS), heat stress (HS), and combined drought and heat stress (CHDS)conditions. The objectives of the study were to: (i) determine the combining ability of the inbred lines and identify the best testers across the stresses; (ii) classify the inbred lines into heterotic groups (HGs) based on the general combining ability of multiple traits (HGCAMT) and sequencing-based diversity array technology (DArTseq) and (iii) assess the performance and stability of the lines in hybrid combinations. The inbred lines showed significantly (p < 0.01 and p < 0.05) positive and negative general combining ability (GCA) and specific combining ability (SCA) effects for grain yield (GY) and most other measured traits. The inbred line TZEI 135 displayed relatively larger positive GCA effects for GY when mated either as male or female and was identified as the best tester. TZEI 135 × TZEI 182 was identified as the best single-cross tester across environments. Results of the assessment of the relative importance of GCA and SCA effects revealed the predominance of additive gene action over the non-additive. Six HGs of inbreds were identified using the HGCAMT and three, based on the DArTseq marker genetic distance method, were the most efficient. The best hybrids in this study significantly out-yielded the best checks by 21, 46, and 70% under CHDS, HS, and TDS, respectively. These hybrids should be extensively tested in on-farm trials for possible commercialization in sub-Saharan Africa. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Introgression of Resistance to Multiple Pathotypes of Plasmodiophora brassicae from Turnip (Brassica rapa ssp. rapifera) into Spring B. napus Canola
Agronomy 2022, 12(5), 1225; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12051225 - 19 May 2022
Abstract
Clubroot disease resistance has been introgressed from Brassica rapa into canola following different approaches including a B. napus × B. rapa interspecific cross; however, the details of this cross are not available. To extend our knowledge of this cross for the introgression of [...] Read more.
Clubroot disease resistance has been introgressed from Brassica rapa into canola following different approaches including a B. napus × B. rapa interspecific cross; however, the details of this cross are not available. To extend our knowledge of this cross for the introgression of resistance to multiple pathotypes, we crossed a clubroot-resistant turnip with a susceptible canola and backcrossed the F1′s to canola. The backcross population was subjected to pedigree breeding with selection for clubroot resistance and canola-quality traits; selection for resistance to pathotype 3H and 3A was performed in the early and advanced generations, respectively. The advanced generation lines were also evaluated for resistance to 3H, 3A, 2B, and 5x, and for field resistance to clubroot, and agronomic and seed quality traits. Following this, we developed canola lines carrying resistance to multiple pathotypes and nuclear DNA content similar to B. napus. Resistance to 3H showed a weak correlation with other pathotypes whereas resistance to 3A showed a strong positive correlation with 5x indicating that resistance to these pathotypes was under a similar genetic control. Thus, the results demonstrate that resistance to multiple pathotypes can be introgressed from a turnip into a canola even when selection for resistance to single pathotype is performed in early generations. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Characterisation of the Complete Chloroplast Genomes of Seven Hyacinthus orientalis L. Cultivars: Insights into Cultivar Phylogeny
Horticulturae 2022, 8(5), 453; https://0-doi-org.brum.beds.ac.uk/10.3390/horticulturae8050453 - 18 May 2022
Abstract
To improve agricultural performance and obtain potential economic benefits, an understanding of phylogenetic relationships of Hyacinthus cultivars is needed. This study aims to revisit the phylogenetic relationships of Hyacinthus cultivars using complete chloroplast genomes. Nine chloroplast genomes were de novo sequenced, assembled and [...] Read more.
To improve agricultural performance and obtain potential economic benefits, an understanding of phylogenetic relationships of Hyacinthus cultivars is needed. This study aims to revisit the phylogenetic relationships of Hyacinthus cultivars using complete chloroplast genomes. Nine chloroplast genomes were de novo sequenced, assembled and annotated from seven cultivars of Hyacinthus orientalis and two Scilloideae species including Bellevalia paradoxa and Scilla siberica. The chloroplast genomes of Hyacinthus cultivars ranged from 154,458 bp to 154,641 bp, while those of Bellevalia paradoxa and Scilla siberica were 154,020 bp and 154,943 bp, respectively. Each chloroplast genome was annotated with 133 genes, including 87 protein-coding genes, 38 transfer RNA genes and 8 ribosomal RNA genes. Simple sequence repeats AAGC/CTTG and ACTAT/AGTAT were identified only in ‘Eros’, while AAATC/ATTTG were identified in all cultivars except ‘Eros’. Five haplotypes were identified based on 460 variable sites. Combined with six other previously published chloroplast genomes of Scilloideae, a sliding window analysis and a phylogenetic analysis were performed. Divergence hotspots ndhA and trnG-UGC were identified with a nucleotide diversity threshold at 0.04. The phylogenetic positions of Hyacinthus cultivars were different from the previous study using ISSR. Complete chloroplast genomes serve as new evidence in Hyacinthus cultivar phylogeny, contributing to cultivar identification, preservation and breeding. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Phenotypic and Genotypic Characterization and Correlation Analysis of Pea (Pisum sativum L.) Diversity Panel
Plants 2022, 11(10), 1321; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11101321 - 16 May 2022
Abstract
Phenotypic and genotypic characterization were performed to assess heritability, variability, and seed yield stability of pea genotypes used in breeding to increase the pea production area. A European pea diversity panel, including genotypes from North America, Asia, and Australia consisting of varieties, breeding [...] Read more.
Phenotypic and genotypic characterization were performed to assess heritability, variability, and seed yield stability of pea genotypes used in breeding to increase the pea production area. A European pea diversity panel, including genotypes from North America, Asia, and Australia consisting of varieties, breeding lines, pea, and landraces was examined in 2019 and 2020 in Serbia and Belgium using augmented block design. The highest heritability was for thousand seed weight; the highest coefficient of variation was for seed yield. The highest positive correlation was between number of seeds per plant and number of pods per plant; the highest negative correlation was between seed yield and protein content. Hierarchical clustering separated pea germplasm based on use and type. Different Principal component analysis grouping of landraces, breeding lines, and varieties, as well as forage types and garden and dry peas, confirms that there was an apparent decrease in similarity between the genotypes, which can be explained by their different purposes. Pea breeding should be focused on traits with consistent heritability and a positive effect on seed yield when selecting high-yielding genotypes, and on allowing for more widespread use of pea in various agricultural production systems. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Extensive Sampling Provides New Insights into Phylogenetic Relationships between Wild and Domesticated Zanthoxylum Species in China
Horticulturae 2022, 8(5), 440; https://0-doi-org.brum.beds.ac.uk/10.3390/horticulturae8050440 - 14 May 2022
Abstract
Zanthoxylum, belonging to the Rutaceae family, is widely distributed in tropical and subtropical regions. The genus has high economic value as spices, oils, medicinal plants, and culinary applications. Zanthoxylum has a long history of domestication and cultivation in China. However, the phylogenetic [...] Read more.
Zanthoxylum, belonging to the Rutaceae family, is widely distributed in tropical and subtropical regions. The genus has high economic value as spices, oils, medicinal plants, and culinary applications. Zanthoxylum has a long history of domestication and cultivation in China. However, the phylogenetic relationships and origin of wild and cultivated Zanthoxylum species in China remain largely unknown. Moreover, there is still no clear molecular phylogenetic system for Zanthoxylum species. Herein, 373 Zanthoxylum samples were collected from all presently known provenances of Zanthoxylum in China. In this study, four chloroplast DNA (cpDNA) markers (matK, ndhH, psbB, rbcL) were used to comprehensively analyze the genetic diversity, relatedness, and geographical origin of Chinese Zanthoxylum species. The results were as follows: (1) The aligned length of the four pairs of cpDNA sequences was 3836 bp, and 68 haplotypes were identified according to 219 variable polymorphic sites, including 90 singleton variable sites, 129 parsimony informative sites, 3 Indels (insertions and deletions). (2) Phylogenetic tree and haplotype network strongly supported the division of Zanthoxylum species consistent with the taxonomic recognition of five species: Z. bungeanum, Z. piasezkii, Z. piperitum, Z. armatum, and Z. micranthum. (3) Divergence time estimation suggested that Zanthoxylum genus originated from the Late Eocene, and most Zanthoxylum species diverged after the Middle Miocene. (4) Haplotype 16 (H16) was at the bottom of the phylogenetic tree, had higher haplotype diversity (Hd) and nucleotide polymorphism (Pi) than other haplotypes, and was located in the center of the network figure. Therefore, we deduced that the cultivated Zanthoxylum species may originate in Zhouqu County, Gansu Province, China. Meanwhile, our research provided a scientific basis for the identification and breeding programs of Chinese Zanthoxylum species. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Identification, Characterization and Comparison of the Genome-Scale UTR Introns from Six Citrus Species
Horticulturae 2022, 8(5), 434; https://0-doi-org.brum.beds.ac.uk/10.3390/horticulturae8050434 - 13 May 2022
Abstract
Ever since their discovery, introns within the coding sequence (CDS) of transcripts have been paid great attention. However, the introns located in the untranslated regions (UTRs) are often ignored. Here, we identified, characterized and compared the UTR introns (UIs) from six citrus species. [...] Read more.
Ever since their discovery, introns within the coding sequence (CDS) of transcripts have been paid great attention. However, the introns located in the untranslated regions (UTRs) are often ignored. Here, we identified, characterized and compared the UTR introns (UIs) from six citrus species. Results showed that the average intron number of UTRs is greatly lower than that of CDSs. Among all six citrus species, the number and density of 5′UTR introns (5UIs) are higher than those of 3′UTR introns (3UIs). The UI densities varied greatly among different citrus species. There are 11 and 9 types of splice site (SS) pairs for the UIs of C. sinensis and C. medica, respectively. However, the UIs of the other four citrus species all own only three kinds of SS pairs. The ‘GT-AG’, accounting for more than 95% of both 5UIs and 3UIs SS pairs for all the six species, is the most popular type. Moreover, 81 5UIs and 26 3UIs were identified as common UIs among the six citrus species, and the transcripts containing these common UIs were mostly involved in gene expression or gene expression regulation. Our study revealed that the UIs’ length, abundance, density and SS pair types varied among different citrus species and that many UI-containing genes play important roles in gene expression regulation. Our findings have great implications for future citrus UI function research. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Overexpression of CgbHLH001, a Positive Regulator to Adversity, Enhances the Photosynthetic Capacity of Maize Seedlings under Drought Stress
Agronomy 2022, 12(5), 1149; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12051149 - 10 May 2022
Abstract
Drought is a major environmental factor limiting crop productivity. Photosynthesis is very sensitive to drought. Basic helix-loop-helix (bHLH) transcription factors (TFs) are important in response to abiotic stress. However, their functions remain unclear. Herein, we generated CgbHLH001 (a TF gene from halophyte Chenopodium [...] Read more.
Drought is a major environmental factor limiting crop productivity. Photosynthesis is very sensitive to drought. Basic helix-loop-helix (bHLH) transcription factors (TFs) are important in response to abiotic stress. However, their functions remain unclear. Herein, we generated CgbHLH001 (a TF gene from halophyte Chenopodium glaucum)-overexpressed (OE) and ZmbHLH-RNA interference (Ri) maize lines to investigate their photosynthesis-associated indexes under drought conditions. The photosynthetic capacity was increased in OE lines under drought stress compared with that in non-transgenic (NT) and Ri plants. A greater root biomass, higher root/shoot ratio, and a relatively lower leaf area reduction ratio was also observed in OE plants. Compared to NT and Ri plants, OE lines showed a higher chlorophyll content and net photosynthetic rate and better chlorophyll fluorescence parameters under drought conditions. Fructose and glucose contents were also significantly elevated in OE lines. Moreover, under stressful conditions, CgbHLH001 overexpression increased the expression of genes related to photosynthesis. Transcriptomic data showed that many differentially expressed genes were enriched in the photosynthetic system in OE and Ri plants under drought conditions and were prone to being upregulated under drought stress in OE plants. Therefore, our results suggest that CgbHLH001 improves photosynthetic efficiency under drought stress and confers drought tolerance in maize seedlings. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
High-Density Linkage Mapping and Identification of Quantitative Trait Loci Associated with Powdery Mildew Resistance in Flowering Dogwood (Cornus florida)
Horticulturae 2022, 8(5), 405; https://0-doi-org.brum.beds.ac.uk/10.3390/horticulturae8050405 - 05 May 2022
Abstract
Flowering dogwood (Cornus florida L.) is a popular, spring-blooming ornamental tree native to the eastern United States. The species is in general very susceptible to powdery mildew caused by Erysiphe pulchra, which disfigures leaves, decreases growth, and negatively affects flowering. Breeding [...] Read more.
Flowering dogwood (Cornus florida L.) is a popular, spring-blooming ornamental tree native to the eastern United States. The species is in general very susceptible to powdery mildew caused by Erysiphe pulchra, which disfigures leaves, decreases growth, and negatively affects flowering. Breeding for resistance has been recognized as an ideal strategy for controlling the disease in C. florida, but efforts have been hindered by the rarity of PM resistance in available germplasm and knowledge of its genetic control. In this study, we mapped quantitative trait loci (QTL) associated with PM resistance/tolerance in two full sibling populations segregating for PM response: Rutgers H4AR15P25 (P25) × Rutgers H4AR15R28 (P28) (n = 195) and Rutgers H4AR15R25 × Rutgers H4AR15P35 (P35) (n = 83). High-density genetic linkage maps were constructed for the mapping populations using double digest restriction-site associated DNA sequencing-derived single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs). The P25 × P28 map consisted of 2265 markers, spanning 1520 cM and 11 linkage groups (LGs) with an average marker spacing of 0.69 cM. The P25 × P35 map was constructed with 1788 markers, spanning 1256 cM and 11 LGs, with an average marker spacing of 0.72 cM. The maps had 604 markers in common and exhibited excellent collinearity. Through multiple QTL model mapping, one major QTL (LOD = 11.36 and R2 = 58.9%) was identified in P25 × P35. Furthermore, a minor QTL (LOD = 3.30 and R2 = 7.8%) was detected in P25 × P28. Due to their proximity onLG3, these QTL may be designating the same locus or tightly linked loci. The negative additive effects of both QTL signify that the PM susceptible male parents were contributing susceptibility alleles to the progeny. This is the first report of QTL associated with PM response on LG3 in C. florida and lays the groundwork for the development of marker-assisted selection for PM resistance in C. florida breeding programs. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Utilization of Intra-Cultivar Variation for Grain Yield and Protein Content within Durum Wheat Cultivars
Agriculture 2022, 12(5), 661; https://0-doi-org.brum.beds.ac.uk/10.3390/agriculture12050661 - 03 May 2022
Abstract
This study assessed the variations in grain yield (GY) and protein content (PC) within two commercial durum wheat cultivars (Svevo and Maestrale) and evaluated their responses to intra-cultivar selection for both traits. We investigated whether the variations are exploitable and could result in [...] Read more.
This study assessed the variations in grain yield (GY) and protein content (PC) within two commercial durum wheat cultivars (Svevo and Maestrale) and evaluated their responses to intra-cultivar selection for both traits. We investigated whether the variations are exploitable and could result in concurrent GY and PC upgrading. The experiments were conducted in the IPBGR, Thessaloniki, Greece (2018–2020). The first year included two identical honeycomb design trials under ultra-low plant density (ULD) where the divergent selection was applied based on single plant yield and protein content. In the second year, progeny evaluation under typical crop density (TCD) for GY and PC occurred in a randomized complete block (RCB) and with three replications for each cultivar selected line. This revealed considerable variation within already improved commercial cultivars. Single-plant selection for GY and PC simultaneously resulted in: (a) one high-yielding line that significantly outperformed the original cultivar Svevo while maintaining high PC, and (b) two high-grain PC lines that outperformed the original cultivar Maestrale significantly while maintaining high GY. ULD allowed efficient selection for GY and PC simultaneously within narrow gene pools by maximizing phenotypic expression and differentiation among individual plants. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Accelerated Genetic Gains in Early-Maturing Maize Hybrids following Three Periods of Genetic Enhancement for Grain Yield under Low and High Soil-Nitrogen Environments
Plants 2022, 11(9), 1208; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11091208 - 29 Apr 2022
Abstract
Maize (Zea mays L.) is an important staple, as well as cash crop, in sub-Saharan Africa (SSA). However, its production is severely constrained by low soil nitrogen (low N). Fifty-four early-maturing hybrids developed during three breeding periods, (2008–2010, 2011–2013 and 2014–2016) were [...] Read more.
Maize (Zea mays L.) is an important staple, as well as cash crop, in sub-Saharan Africa (SSA). However, its production is severely constrained by low soil nitrogen (low N). Fifty-four early-maturing hybrids developed during three breeding periods, (2008–2010, 2011–2013 and 2014–2016) were evaluated under low (30 kg ha−1) and high (120 kg ha−1) soil nitrogen (N) in Ile-Ife and Mokwa, Nigeria, from 2017 to 2019. The study was designed to (i) determine the genetic gains in grain yield of the early-maturing maize hybrids developed during the three breeding periods, (ii) determine the relationship between grain yield and other agronomic traits and (iii) identify the highest-yielding and most stable hybrids under low- and high-N environments. The 54 hybrids were evaluated using a 6 × 9 lattice design with three replications. Mean squares for hybrids were significant for measured traits under low- and high-N environments, except the mean squares for stalk lodging and EPP under low N. Annual genetic gains in grain yield were 75 kg ha−1 year−1 (2.91%) and 55 kg ha−1 year−1 (1.33%) under low- and high-N environments, respectively, indicating that substantial gains were achieved in the genetic enhancement of the early-maturing hybrids. The hybrids TZdEI 314 × TZdEI 105, TZdEI 378 × TZdEI 173, ENT 12 × TZEI 48 and TZdEI 352 × TZdEI 315 were identified as the highest-yielding and most stable across test environments and should be tested extensively on farms and commercialized in SSA. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Comparative Analyses of Chloroplast Genomes Provide Comprehensive Insights into the Adaptive Evolution of Paphiopedilum (Orchidaceae)
Horticulturae 2022, 8(5), 391; https://0-doi-org.brum.beds.ac.uk/10.3390/horticulturae8050391 - 28 Apr 2022
Abstract
An elucidation of how the selection pressures caused by habitat environments affect plant plastid genomes and lead to the adaptive evolution of plants, is a very intense area of research in evolutionary biology. The genus Paphiopedilum is a predominant group of orchids that [...] Read more.
An elucidation of how the selection pressures caused by habitat environments affect plant plastid genomes and lead to the adaptive evolution of plants, is a very intense area of research in evolutionary biology. The genus Paphiopedilum is a predominant group of orchids that includes over 66 species with high horticultural and ornamental value. However, owing to the destructive exploitation and habitat deterioration of wild germplasm resources of Paphiopedilum, it needs more molecular genetic resources and studies on this genus. The chloroplast is cytoplasmically inherited and often used in evolutionary studies. Thus, for this study, we newly sequenced, assembled and annotated five chloroplast genomes of the Paphiopedilum species. The size of these genomes ranged from 155,886 bp (P. henryanum) to 160,503 bp (P. ‘GZSLKY’ Youyou) and they contained 121–122 genes, which consisted of 76 protein coding genes, eight ribosomal RNAs, and 37–38 transfer RNAs. Combined with the other 14 Paphiopedilum species, the characteristics of the repeat sequences, divergent hotspot regions, and the condo usage bias were evaluated and identified, respectively. The gene transfer analysis showed that some fragments of the ndh and ycf gene families were shared by both the chloroplast and nucleus. Although the genomic structure and gene content was conserved, there was a significant boundary shift caused by the inverted repeat (IR) expansion and small single copy (SSC) contraction. The lower GC content and loss of ndh genes could be the result of adaptive evolutionary responses to its unique habitats. The genes under positive selection, including accD, matK, psbM, rpl20, rps12, ycf1, and ycf2 might be regarded as potential candidate genes for further study, which significantly contribute to the adaptive evolution of Paphiopedilum. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Morphoanatomy and Histochemistry of Septal Nectaries Related to Female Fertility in Banana Plants of the ‘Cavendish’ Subgroup
Plants 2022, 11(9), 1177; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11091177 - 27 Apr 2022
Abstract
The objective of this study was to gain a deeper understanding of the morphoanatomical and histochemical structures that compose the nectary of pistillate flowers (female), which are involved in the female fertility of banana plants belonging to the ‘Cavendish’ subgroup. The diploid Calcutta [...] Read more.
The objective of this study was to gain a deeper understanding of the morphoanatomical and histochemical structures that compose the nectary of pistillate flowers (female), which are involved in the female fertility of banana plants belonging to the ‘Cavendish’ subgroup. The diploid Calcutta 4 and the Grand Naine cultivar were used for the assessment. Five stages of floral development were proposed. Pistillate flower nectaries were subjected to morphological characterization, morphoanatomy, and histochemical tests (phenolic compounds, proteins, and lipids). Morphoanatomical analysis revealed a greater presence of narrow nectariferous ducts and more developed pluristratified papillae in Calcutta 4. In contrast, Grand Naine displayed cell disintegration in nectariferous ducts and pluristratified papillae, absent transmitting tissue, and greater amounts of vascular bundles at anthesis. However, Calcutta 4 displayed no changes in the nectariferous duct at any of the stages. An association was found between phenolic compounds and lipids in vacuoles adjacent to the vascular bundles, with greater amounts found in Grand Naine. The localization of phenolic compounds may suggest that these compounds play a role in nectar secretion or the oxidation of the nectary region, ultimately limiting the growth and passage of the pollen tube and preventing ovule fertilization. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Marker-Assisted Improvement of Bread Wheat Variety HD2967 for Leaf and Stripe Rust Resistance
Plants 2022, 11(9), 1152; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11091152 - 24 Apr 2022
Abstract
The mega wheat variety HD2967 was improved for leaf and stripe rust resistance by marker-assisted backcross breeding. After its release in 2011, HD2967 became susceptible to stripe rust and moderately susceptible to leaf rust. The leaf rust resistance gene LrTrk was transferred into [...] Read more.
The mega wheat variety HD2967 was improved for leaf and stripe rust resistance by marker-assisted backcross breeding. After its release in 2011, HD2967 became susceptible to stripe rust and moderately susceptible to leaf rust. The leaf rust resistance gene LrTrk was transferred into HD2967 from the durum wheat genotype Trinakria. Then, HD2967 was crossed with Trinakria to produce F1 plant foreground selection for LrTrk and background selection for the recurrent parent genotype was carried out in BC1F1, BC2F1 and BC2F2 generations. Foreground selection was carried out with the linked marker Xgwm234, while polymorphic SSR markers between parents were used for background selection. Background selection resulted in the rapid recovery of the recurrent parent genome. A morphological evaluation of 6 near isogenic lines (NILs)—2 resistant to leaf and stripe rust, and 4 resistant to leaf rust only—showed no significant differences in yields among NILs and the recurrent parent HD2967. All of the 6 NILs showed the presence of 2NS/2AS translocation, carrying the linked genes Lr37/Sr38/Yr17 present in HD2967 and the targeted leaf rust resistance gene LrTrk. Two NILs also showed additional resistance to stripe rust. Therefore, these NILs with rust resistance and an at par yielding ability of H2967 can replace the susceptible cultivar HD2967 to reduce yield losses due to disease. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
PpMYB39 Activates PpDFR to Modulate Anthocyanin Biosynthesis during Peach Fruit Maturation
Horticulturae 2022, 8(4), 332; https://0-doi-org.brum.beds.ac.uk/10.3390/horticulturae8040332 - 14 Apr 2022
Abstract
Anthocyanins are a class of water-soluble flavonoids widely present in fruits and vegetables responsible for the red flesh formation of peach fruit. Previously, several genes of the MYB family have been reported as transcriptional regulators of the anthocyanin biosynthetic pathway of structural genes [...] Read more.
Anthocyanins are a class of water-soluble flavonoids widely present in fruits and vegetables responsible for the red flesh formation of peach fruit. Previously, several genes of the MYB family have been reported as transcriptional regulators of the anthocyanin biosynthetic pathway of structural genes in plants. In this study, through comparative transcriptome analysis of the white and red flesh peach cultivars of Harrow Blood and Asama Hakuto, a predicted transcription factor of the R2R3MYB family, PpMYB39, was identified to be associated with anthocyanin biosynthesis in peach fruit. In red-fleshed peach cultivars, the maximum amount of anthocyanin accumulated 95 days after full bloom (DAFB), at full maturity near ripening. Our results showed that, at this stage, PpMYB39 had the highest expression level among the 13 differentially expressed genes (DEGs) found in both red- and white-fleshed fruits, as well as a high correlation with total anthocyanin content throughout fruit development. Moreover, the expression analysis of the structural genes of the anthocyanin biosynthetic pathway in peach fruit revealed that Prunus persica Dihydroflavonol-4-reductase (PpDFR) was co-expressed and up-regulated with PpMYB39 at 95 DAFB, suggesting its possible role as a transcriptional activator of MYB39. This was further confirmed by a yeast one-hybrid assay and a dual luciferase reporter assay. Our results will be helpful in the breeding of peach cultivars and the identification and significance of color in peaches and related fruit species, in addition to providing an understanding of color formation in peach fruit for future research. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Evolutionary History and Functional Diversification of the JmjC Domain-Containing Histone Demethylase Gene Family in Plants
Plants 2022, 11(8), 1041; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11081041 - 12 Apr 2022
Abstract
Histone demethylases containing JumonjiC (JmjC) domains regulate gene transcription and chromatin structure by changing the methylation status of lysine residues and play an important role in plant growth and development. In this study, a total of 332 JmjC family genes were [...] Read more.
Histone demethylases containing JumonjiC (JmjC) domains regulate gene transcription and chromatin structure by changing the methylation status of lysine residues and play an important role in plant growth and development. In this study, a total of 332 JmjC family genes were identified from 21 different plant species. The evolutionary analysis results showed that the JmjC gene was detected in each species, that is, the gene has already appeared in algae. The phylogenetic analysis showed that the KDM3/JHDM2 subfamily genes may have appeared when plants transitioned from water to land, but were lost in lycophytes (Selaginella moellendorffii). During the evolutionary process, some subfamily genes may have been lost in individual species. According to the analysis of the conserved domains, all of the plant JmjC genes contained a typical JmjC domain, which was highly conserved during plant evolution. The analysis of cis-acting elements showed that the promoter region of the JmjC gene was rich in phytohormones and biotic and abiotic stress-related elements. The transcriptome data analysis and protein interaction analyses showed that JmjC genes play an important role in plant growth and development. The results clarified the evolutionary history of JmjC family genes in plants and lay the foundation for the analysis of the biological functions of JmjC family genes. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Enhancing Genomic Prediction Models for Forecasting Days to Maturity in Soybean Genotypes Using Site-Specific and Cumulative Photoperiod Data
Agriculture 2022, 12(4), 545; https://0-doi-org.brum.beds.ac.uk/10.3390/agriculture12040545 - 11 Apr 2022
Abstract
Genomic selection (GS) has revolutionized breeding strategies by predicting the rank performance of post-harvest traits via implementing genomic prediction (GP) models. However, predicting pre-harvest traits in unobserved environments might produce serious biases. In soybean, days to maturity (DTM) represents a crucial stage with [...] Read more.
Genomic selection (GS) has revolutionized breeding strategies by predicting the rank performance of post-harvest traits via implementing genomic prediction (GP) models. However, predicting pre-harvest traits in unobserved environments might produce serious biases. In soybean, days to maturity (DTM) represents a crucial stage with a significant impact on yield potential; thus, genotypes must be carefully selected to ensure latitudinal adaptation in this photoperiod-sensitive crop species. This research assessed the use of daylength for predicting DTM in unobserved environments (CV00). A soybean dataset comprising 367 genotypes spanning nine families of the Soybean Nested Association Mapping Panel (SoyNAM) and tested in 11 environments (year-by-location combinations) was considered in this study. The proposed method (CB) returned a root-mean-square error (RMSE) of 5.2 days, a Pearson correlation (PC) of 0.66, and the predicted vs. observed difference in the environmental means (PODEM) ranged from −3.3 to 4.5 days; however, in the absence of daylength data, the conventional GP implementation produced an RMSE of 9 days, a PC of 0.66, and a PODEM range from −14.7 to 7.9 days. These results highlight the importance of dissecting phenotypic variability (G × E) based on photoperiod data and non-predictable environmental stimuli for improving the predictive ability and accuracy of DTM in soybeans. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Genetic Variation in Flowering Traits of Tasmanian Leptospermum scoparium and Association with Provenance Home Site Climatic Factors
Plants 2022, 11(8), 1029; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11081029 - 10 Apr 2022
Abstract
Leptospermum scoparium is emerging as an economically important plant for the commercial production of mānuka honey and essential oils, both exhibiting unique antibacterial attributes. To support its domestication this is the first quantitative genetic study of variation for L. scoparium traits. It utilised [...] Read more.
Leptospermum scoparium is emerging as an economically important plant for the commercial production of mānuka honey and essential oils, both exhibiting unique antibacterial attributes. To support its domestication this is the first quantitative genetic study of variation for L. scoparium traits. It utilised plants from 200 open-pollinated families derived from 40 native populations, from across the species range in Tasmania, grown in a common garden field trial. The traits studied were survival, growth, and the flowering traits precocity, the timing of seasonal peak flowering, flowering duration, and flowering intensity. Significant genetic variation was evident at the population level for all traits studied and at the family level for three traits—growth, flowering precocity, and time to peak flowering. These three traits had moderate to high narrow-sense heritability estimates ranging from 0.27 to 0.69. For six of the traits studied, population differences were associated with climate attributes at the locations where seed was collected, suggesting adaptation to the local climate may have contributed to the observed population differentiation. Population level geographical trends suggest that genotypes to focus on for domestication originate from the eastern half of Tasmania for precociousness and the western half of Tasmania for earlier time to peak flowering and extended flowering duration. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Detection of QTLs for Plant Height Architecture Traits in Rice (Oryza sativa L.) by Association Mapping and the RSTEP-LRT Method
Plants 2022, 11(7), 999; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11070999 - 06 Apr 2022
Abstract
Plant height (PH) and its component traits are critical determinants of lodging resistance and strongly influence yield in rice. The genetic architecture of PH and its component traits were mined in two mapping populations. In the natural population composed of 504 accessions, a [...] Read more.
Plant height (PH) and its component traits are critical determinants of lodging resistance and strongly influence yield in rice. The genetic architecture of PH and its component traits were mined in two mapping populations. In the natural population composed of 504 accessions, a total of forty simple sequence repeat (SSR) markers associated with PH and its component traits were detected across two environments via association mapping. Allele RM305-210 bp on chromosome 5 for PH had the largest phenotypic effect value (PEV) (−51.42 cm) with a reducing effect. Allele RM3533-220 bp on chromosome 9 for panicle length and allele RM264-120 bp on chromosome 8 for the length of upper first elongated internode (1IN) showed the highest positive PEV. Among the elongated internodes with negative effects being desirable, the allele RM348-130 bp showed the largest PEV (−7.48 cm) for the length of upper second elongated internode. In the chromosome segment substitution line population consisting of 53 lines, a total of nine QTLs were detected across two environments, with the phenotypic variance explained (PVE) ranging 10.07–28.42%. Among the detected QTLs, q1IN-7 explained the largest PVE (28.42%) for the 1IN, with an additive of 5.31 cm. The favorable allele RM257-125 bp on chromosome 9 for the 1IN increasing was detected in both populations. The favorable alleles provided here could be used to shape PH architecture against lodging. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Molecular Characterization of Prunus Cultivars from Romania by Microsatellite Markers
Horticulturae 2022, 8(4), 291; https://0-doi-org.brum.beds.ac.uk/10.3390/horticulturae8040291 - 30 Mar 2022
Abstract
In Romania, Prunus species have great economic and social importance. With the introduction of new cultivars arises the need to preserve and characterize the local Prunus germplasm. Thus, a set of 24 polymorphic SSRs were selected for the overall characterization, including 10 peach, [...] Read more.
In Romania, Prunus species have great economic and social importance. With the introduction of new cultivars arises the need to preserve and characterize the local Prunus germplasm. Thus, a set of 24 polymorphic SSRs were selected for the overall characterization, including 10 peach, 11 apricot and 5 nectarine cultivars. The average number of alleles per locus (Na = 1.958), in addition to overall observed (Ho = 0.299) and expected heterozygosity (He = 0.286) were lower or comparable to those reported in similar studies, probably explained by the smaller number of analyzed cultivars restricted to a smaller geographic area. Among 26 genotypes a total of 101 alleles were identified, of which 46 alleles were in peach, 55 in apricot and 40 in nectarine, respectively. Six alleles from six loci (CPPCT-030, Pchgms-003, Pchgms-004, Pchgms-010, UDP97-401, UDP98-405) were common to all taxonomic groups. The most informative loci were BPPCT-025, Pchgms-021 and UDP96-001 in peach; BPPCT-025, BPPCT-001 and UDP96-001 in nectarine; and BPPCT-002, BPPCT-025, Pchgms-004, Pchgms-020 and Pchgms-021 in apricot. Clustering and genetic similarity analysis indicated that the degree of interspecific divergence in peach and nectarine cultivars was less than that in peach and apricot. These results will be useful to prevent confusion between cultivars, to improve breeding strategies and to benefit the management of Prunus cultivars bred in Romania. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Genome-Wide Association Analyses Reveal Candidate Genes Controlling Harvest Index and Related Agronomic Traits in Brassica napus L.
Agronomy 2022, 12(4), 814; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12040814 - 27 Mar 2022
Abstract
Harvest index (HI) is a complex and vital agronomic trait that is closely related to the economic benefits of rapeseed. In this study, we measured the HI and 13 HI-related agronomic traits of 104 core breeding lines of rapeseed during 3 years and [...] Read more.
Harvest index (HI) is a complex and vital agronomic trait that is closely related to the economic benefits of rapeseed. In this study, we measured the HI and 13 HI-related agronomic traits of 104 core breeding lines of rapeseed during 3 years and sequenced the populations using the Bnapus50K array. The phenotypic analyses showed the complex connections among HI and other traits. A total of 212 significant SNPs related to the traits and 22 stable SNPs were identified. Four SNPs, A01_1783685 (PH and SYP), C06_26638717 (PH and NSS), C03_4731660 (MIL and MINS), and C09_36899682 (PH and BYP), were identified as potential pleiotropic loci. Compared to previous reports, 49 consensus loci were obtained that were related to PH, TSW, NSP, BAI, NSS, SL, BN, MINS, SYP, and BYP. Twelve stable SNPs were detected as promising novel loci related to BN (A05_19368584 and A05_19764389), SL (A06_23598999, A06_23608274, and C07_38735522), PH (C04_47349279, C04_47585236, and C09_36899680), MINS (C05_6251826), NSS (C06_22559430 and C06_22570315), and HI (C05_6554451). In addition, 39 putative genes were identified in the candidate intervals. This study provides novel insights into the genetic mechanisms of HI and HI-related traits, and lays a foundation for molecular marker development and casual gene cloning to improve the harvest index of rapeseed. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Stocky1, a Novel Gene Involved in Maize Seedling Development and Cuticle Integrity
Plants 2022, 11(7), 847; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11070847 - 23 Mar 2022
Abstract
The cuticle is the plant’s outermost layer that covers the surfaces of aerial parts. This structure is composed of a variety of aliphatic molecules and is well-known for its protective role against biotic and abiotic stresses in plants. Mutants with a permeable cuticle [...] Read more.
The cuticle is the plant’s outermost layer that covers the surfaces of aerial parts. This structure is composed of a variety of aliphatic molecules and is well-known for its protective role against biotic and abiotic stresses in plants. Mutants with a permeable cuticle show developmental defects such as organ fusions and altered seed germination and viability. In this study, we identified a novel maize mutant, stocky1, with unique features: lethal at the seedling stage, and showing a severely dwarfed phenotype, due to a defective cuticle. For the first time, the mutant was tentatively mapped to chromosome 5, bin 5.04. The mutant phenotype investigated in this work has the potential to contribute to the elucidation of the role of the cuticle during plant development. The possibility of controlling this trait is of relevance in the context of climate change, as it may contribute to tolerance to abiotic stresses. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Thaumatin-like Protein (TLP) Genes in Garlic (Allium sativum L.): Genome-Wide Identification, Characterization, and Expression in Response to Fusarium proliferatum Infection
Plants 2022, 11(6), 748; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11060748 - 11 Mar 2022
Abstract
Plant antifungal proteins include the pathogenesis-related (PR)-5 family of fungi- and other stress-responsive thaumatin-like proteins (TLPs). However, the information on the TLPs of garlic (Allium sativum L.), which is often infected with soil Fusarium fungi, is very limited. In the present study, [...] Read more.
Plant antifungal proteins include the pathogenesis-related (PR)-5 family of fungi- and other stress-responsive thaumatin-like proteins (TLPs). However, the information on the TLPs of garlic (Allium sativum L.), which is often infected with soil Fusarium fungi, is very limited. In the present study, we identified 32 TLP homologs in the A. sativum cv. Ershuizao genome, which may function in the defense against Fusarium attack. The promoters of A. sativumTLP (AsTLP) genes contained cis-acting elements associated with hormone signaling and response to various types of stress, including those caused by fungal pathogens and their elicitors. The expression of AsTLP genes in Fusarium-resistant and -susceptible garlic cultivars was differently regulated by F. proliferatum infection. Thus, in the roots the mRNA levels of AsTLP7–9 and 21 genes were increased in resistant and decreased in susceptible A. sativum cultivars, suggesting the involvement of these genes in the garlic response to F. proliferatum attack. Our results provide insights into the role of TLPs in garlic and may be useful for breeding programs to increase the resistance of Allium crops to Fusarium infections. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Review
Interactions of Gibberellins with Phytohormones and Their Role in Stress Responses
Horticulturae 2022, 8(3), 241; https://0-doi-org.brum.beds.ac.uk/10.3390/horticulturae8030241 - 10 Mar 2022
Abstract
Gibberellins are amongst the main plant growth regulators. Discovered over a century ago, the interest in gibberellins research is growing due to their current and potential applications in crop production and their role in the responses to environmental stresses. In the present review, [...] Read more.
Gibberellins are amongst the main plant growth regulators. Discovered over a century ago, the interest in gibberellins research is growing due to their current and potential applications in crop production and their role in the responses to environmental stresses. In the present review, the current knowledge on gibberellins’ homeostasis and modes of action is outlined. Besides this, the complex interrelations between gibberellins and other plant growth regulators are also described, providing an intricate network of interactions that ultimately drives towards precise and specific gene expression. Thus, genes and proteins identified as being involved in gibberellin responses in model and non-model species are highlighted. Furthermore, the molecular mechanisms governing the gibberellins’ relation to stress responses are also depicted. This review aims to provide a comprehensive picture of the state-of-the-art of the current perceptions of the interactions of gibberellins with other phytohormones, and their responses to plant stresses, thus allowing for the identification of the specific mechanisms involved. This knowledge will help us to improve our understanding of gibberellins’ biology, and might help increase the biotechnological toolbox needed to refine plant resilience, particularly under a climate change scenario. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Comparison between Germinated Seed and Isolated Microspore EMS Mutagenesis in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)
Horticulturae 2022, 8(3), 232; https://0-doi-org.brum.beds.ac.uk/10.3390/horticulturae8030232 - 08 Mar 2022
Abstract
Mutagenesis is an important tool for breeding and genomic research. In this study, the germinated seeds and isolated microspores of a double haploid line ‘FT’ were treated with EMS, respectively, with the aim of comparing the effects of the two approaches on generating [...] Read more.
Mutagenesis is an important tool for breeding and genomic research. In this study, the germinated seeds and isolated microspores of a double haploid line ‘FT’ were treated with EMS, respectively, with the aim of comparing the effects of the two approaches on generating mutants in Chinese cabbage. For microspore EMS mutagenesis, the isolated microspores were treated with 0.12% EMS for 20 min, a total of 1268 plantlets were obtained, and 15 M1 mutants were screened with a mutation frequency of 1.2%. For seed EMS mutagenesis, 7800 germinated seeds were treated with 0.8% EMS for 12 h, and a total of 701 M2 mutants were screened, with a mutation frequency of 18.78%. In total, 716 mutants with heritable morphological variation including leaf color, leaf shape, leafy head, bolting, and fertility, were obtained from the EMS mutagenesis experiments. Homozygous mutant plants could be screened from M1 lines by microspore mutagenesis, and M2 lines by seed mutagenesis. The mutation frequency was higher in seed mutagenesis than in microspore mutagenesis. Based on these results, we propose that seed EMS mutagenesis is more suitable to generate a large-scale mutant library, and the microspore EMS mutagenesis is conducive to rapidly obtaining homozygous mutants. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Metabolic Profiling of Sugars and Organic Acids, and Expression Analyses of Metabolism-Associated Genes in Two Yellow-Peel Pitaya Species
Plants 2022, 11(5), 694; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11050694 - 04 Mar 2022
Abstract
Sugar and organic acids are important factors determining pitaya fruit quality. However, changes in sugars and acids, and expressions of metabolism-associated genes during fruit maturation of yellow-peel pitayas are not well-documented. In this study, metabolic and expression analyses in pulps of different fruit [...] Read more.
Sugar and organic acids are important factors determining pitaya fruit quality. However, changes in sugars and acids, and expressions of metabolism-associated genes during fruit maturation of yellow-peel pitayas are not well-documented. In this study, metabolic and expression analyses in pulps of different fruit developmental stages of ‘Wucihuanglong’ (‘WCHL’, Hylocereus undatus) and ‘Youcihuanglong’ pitaya (‘YCHL’, Hylocereus megalanthus) were used to explore the sugar and organic acid metabolic process. Total phenols and flavonoids were mainly accumulated at S1 in pitaya pulps. Ascorbic acid contents of ‘WCHL’ pitaya were higher than that of ‘YCHL’ pitaya during fruit maturation. Starch was mainly accumulated at early fruit development stages while soluble sugars were rich in late stages. Sucrose, fructose, and glucose were the main sugar components of ‘YCHL’ pitaya while glucose was dominant in ‘WCHL’ pitaya. Malic and citric acids were the main organic acids in ‘WCHL’ and ‘YCHL’ pitayas, respectively. Based on the transcriptome analyses, 118 genes involved in pitaya sugar and organic acid metabolism were obtained. Results from the correlation analyses between the expression profiling of candidate genes and the contents of sugar and organic acid showed that 51 genes had a significant correlation relationship and probably perform key role in pitaya sugar and organic acid metabolism processes. The finding of the present study provides new information for quality regulation of pitayas. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Development and Cross-Species Transferability of Novel Genomic-SSR Markers and Their Utility in Hybrid Identification and Trait Association Analysis in Chinese Cherry
Horticulturae 2022, 8(3), 222; https://0-doi-org.brum.beds.ac.uk/10.3390/horticulturae8030222 - 03 Mar 2022
Abstract
Chinese cherry (Cerasus pseudocerasus (Lindl.) G.Don) is an economically important tetraploid fruiting cherry species native to China. Simple sequence repeats (SSRs)—due to their codominance, polymorphism, and stability—have been widely applied in genetic identification and trait-association analysis. In this study, using comparative genomics [...] Read more.
Chinese cherry (Cerasus pseudocerasus (Lindl.) G.Don) is an economically important tetraploid fruiting cherry species native to China. Simple sequence repeats (SSRs)—due to their codominance, polymorphism, and stability—have been widely applied in genetic identification and trait-association analysis. In this study, using comparative genomics strategy and the data of one high-quality whole genome and seven preliminarily assembled genome sequences, we constructed a database containing 25,779 polymorphic SSR loci to efficiently develop novel markers. Sixty-four SSR loci covering eight linkage groups were selected to design primer pairs. Sixty (93.75%) primer pairs yielded specific bands and 32 (50.00%) exhibited moderate-to-high levels of informativeness (PIC ranging from 0.264 to 0.728) in 94 Chinese cherry accessions. A total of 38 primer pairs exhibited high transferability across 13 Cerasus taxa. The marker SAUCps203 was species-specific in C. pseudocerasus by checking with 114 accessions from Cerasus and 16 relatives, suggesting its potential application in accurate identification of Chinese cherry or its interspecific hybrid. Moreover, 1081 out of 1122 individuals from three cross F1 populations of Chinese cherry were identified as true hybrid offspring by using only five SSR markers. Trait association analysis suggested that 20 SSR loci were significantly associated with soluble solids and fruit size, with explained phenotypic variance ranging from 9.02% to 26.35%. This study will provide a basis for SSR-based germplasm identification and further marker-assisted selection (MAS) of Chinese cherry. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
In Silico Genome-Wide Characterisation of the Lipid Transfer Protein Multigenic Family in Sunflower (H. annuus L.)
Plants 2022, 11(5), 664; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11050664 - 28 Feb 2022
Abstract
The sunflower (Helianthus annuus L.) is among the most widely cultivated crops in the world due to the oilseed production. Lipid transfer proteins (LTPs) are low molecular mass proteins encoded by a broad multigenic family in higher plants, showing a vast range [...] Read more.
The sunflower (Helianthus annuus L.) is among the most widely cultivated crops in the world due to the oilseed production. Lipid transfer proteins (LTPs) are low molecular mass proteins encoded by a broad multigenic family in higher plants, showing a vast range of functions; these proteins have not been characterised in sunflower at the genomic level. In this work, we exploited the reliable genome sequence of sunflower to identify and characterise the LTP multigenic family in H. annuus. Overall, 101 sunflower putative LTP genes were identified using a homology search and the HMM algorithm. The selected sequences were characterised through phylogenetic analysis, exon–intron organisation, and protein structural motifs. Sunflower LTPs were subdivided into four clades, reflecting their genomic and structural organisation. This gene family was further investigated by analysing the possible duplication origin of genes, which showed the prevalence of tandem and whole genome duplication events, a result that is in line with polyploidisation events that occurred during sunflower genome evolution. Furthermore, LTP gene expression was evaluated on cDNA libraries constructed on six sunflower tissues (leaf, root, ligule, seed, stamen, and pistil) and from roots treated with stimuli mimicking biotic and abiotic stress. Genes encoding LTPs belonging to three out of four clades responded specifically to external stimuli, especially to abscisic acid, auxin, and the saline environment. Interestingly, genes encoding proteins belonging to one clade were expressed exclusively in sunflower seeds. This work is a first attempt of genome-wide identification and characterisation of the LTP multigenic family in a plant species. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
EuPIP1;2, a Plasma Membrane Aquaporin Gene from Eucommia ulmoides, Enhances Drought and Salt Tolerance in Transgenic Tobacco
Agronomy 2022, 12(3), 615; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12030615 - 28 Feb 2022
Abstract
Aquaporins are a specific type of membrane channel proteins that efficiently transport water molecules and other small molecular substrates in plants. In this study, we isolated the plasma membrane aquaporin gene EuPIP1;2 from Eucommia ulmoides, an important medicinal plant in China. The [...] Read more.
Aquaporins are a specific type of membrane channel proteins that efficiently transport water molecules and other small molecular substrates in plants. In this study, we isolated the plasma membrane aquaporin gene EuPIP1;2 from Eucommia ulmoides, an important medicinal plant in China. The EuPIP1;2 protein was localized on the plasma membrane. Quantitative RT-PCR analysis revealed that EuPIP1;2 was constitutively expressed in all analyzed tissues, with the highest expression levels detected in the fruit and root. Overexpression of EuPIP1;2 in transgenic tobacco enhanced plant tolerance of drought and salinity. Under drought and salt stress, the transgenic lines exhibited higher percentage germination, longer roots, and enhanced percentage survival compared with wild-type plants. The contents of malonaldehyde and proline suggested that EuPIP1;2 improved drought and salt tolerance in transgenic lines by reducing damage to membranes and improving osmotic adjustment. We predict that EuPIP1;2 could be applied to improve drought and salt tolerance in transgenic plants. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Grain Quality Affected by Introducing Photorespiratory Bypasses into Rice
Agronomy 2022, 12(3), 566; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12030566 - 24 Feb 2022
Abstract
Grain quality is a critical component of high-yielding varieties to ensure acceptance by an ever-increasing population and living standards. During the past years, several photorespiration bypasses have been introduced into C3 plants, among which our GOC and GCGT bypasses exhibit increased photosynthesis and [...] Read more.
Grain quality is a critical component of high-yielding varieties to ensure acceptance by an ever-increasing population and living standards. During the past years, several photorespiration bypasses have been introduced into C3 plants, among which our GOC and GCGT bypasses exhibit increased photosynthesis and yield in rice. However, to the best of our knowledge, there are still no reports referring to effects of the bypasses on grain quality. Thus, the objective of this study is to determine the effect of GOC and GCGT bypasses on grain quality, and the mechanism of how photorespiratory bypasses affect grain quality was also investigated. Compared with the WT of Zhonghua 11, GOC4 and GCGT20 plants had higher nutritional quality and cooking quality as grain protein content was significantly increased by 11.27% and 14.97%, and alkali spreading value was significantly increased by 7.6% and 4.63%, respectively, whereas appearance quality appears to be negatively affected since the chalky rice rate was increased by 32.6% and 68%, respectively. Analyses also demonstrated that the changes in grain quality may result from the increased total nitrogen and constrained carbohydrate transport in the transgenic plants. Altogether, the results not only suggest that the increased photosynthesis and yield by introducing the photorespiratory bypasses can significantly affect grain quality parameters for rice, either positively or negatively, but also imply that the coordination of source–sink transport may play important roles in grain quality formation for high-yielding crops via increased photosynthetic efficiency. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Pomological Traits and Genome Size of Prunus armeniaca L. Considering to Geographical Origin
Horticulturae 2022, 8(3), 199; https://0-doi-org.brum.beds.ac.uk/10.3390/horticulturae8030199 - 24 Feb 2022
Abstract
Apricot (Prunus armeniaca L.) is an important fruit crop and member of the Prunus genus of the Rosaceae family that is planted in many temperate regions worldwide. The quality of fruit is assessed by many pomological parameters which can serve as a [...] Read more.
Apricot (Prunus armeniaca L.) is an important fruit crop and member of the Prunus genus of the Rosaceae family that is planted in many temperate regions worldwide. The quality of fruit is assessed by many pomological parameters which can serve as a decisive factor in apricot breeding, because the introduction of new cultivars is required. These parameters can differ with climate conditions, geographical location or geographic ecological origin. Similarly, another biological characteristic can be measured depending on these terms. The present study was conducted with the aim of estimating pomological traits together with the nuclear DNA content of 35 apricot cultivars with different geographical origins. Only CV values lower than 5% were considered in flow cytometry analysis. All analyzed cultivars were diploid and the genome size value ranged from 0.587 to 0.644 pg/2C, where Turkish apricots reached the highest value (on average 0.628 pg/2C) followed by the European group (on average 0.625 pg/2C). A Spearman-rank correlation was used and the different correlation was found for specific geographical groups of apricot cultivars. The genome size values of apricots and related botanical species P. mume, P. sibirica and P. ansu showed to be very similar values. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Evaluation of Germplasm and Development of Markers for Resistance to Plasmodiophora brassicae in Radish (Raphanussativus L.)
Agronomy 2022, 12(3), 554; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12030554 - 23 Feb 2022
Abstract
The rapid spread of clubroot disease caused by Plasmodiophora brassicae threatens radish (Raphanus sativus) production in China because some cultivation types lack clubroot-resistant (CR) genes. However, few molecular markers for clubroot resistance have been developed and used in hybrid breeding programs. [...] Read more.
The rapid spread of clubroot disease caused by Plasmodiophora brassicae threatens radish (Raphanus sativus) production in China because some cultivation types lack clubroot-resistant (CR) genes. However, few molecular markers for clubroot resistance have been developed and used in hybrid breeding programs. In this study, 27 immune and 6 highly resistant accessions were identified among 95 radish inbred lines. The genes Rsa10003637 and Rsa10025569/Rsa10025571 were respectively identified from an XYB36-2 reference genome as the homologs of Crr1 and CRa from Brassica rapa by means of homology and synteny analysis. The association between the degree of clubroot resistance and the genotype of these CR genes suggested that Rsa10025569-H3 can be used as a clubroot-resistant haplotype. The sequence identity of Rsa10025569 in clubroot-resistant lines (CR-60 and CR-88) and clubroot-susceptible lines (CR-10 and CR-35) was 92.47%, and there was a 699 bp insertion at the end of the fourth exon in the clubroot-susceptible line. Association analysis of a BC1F1 population derived from the cross CR-88 (resistance) × CR-10 (susceptible) revealed an apparent correlation between polymorphisms at the Rsa10025569 locus and degree of clubroot resistance. On the basis of the results, molecular marker-assisted selection was used to transfer disease resistance genes to susceptible varieties and a new CR germplasm of Xinlimei was obtained. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Comparisons of Anatomical Characteristics and Transcriptomic Differences between Heterografts and Homografts in Pyrus L.
Plants 2022, 11(5), 580; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11050580 - 22 Feb 2022
Abstract
Pear (Pyrus L.) is an important temperate fruit worldwide, and grafting is widely used in pear vegetative propagation. However, the mechanisms of graft healing or incompatibility remain poorly understood in Pyrus. To study the differences in graft healing in Pyrus, [...] Read more.
Pear (Pyrus L.) is an important temperate fruit worldwide, and grafting is widely used in pear vegetative propagation. However, the mechanisms of graft healing or incompatibility remain poorly understood in Pyrus. To study the differences in graft healing in Pyrus, the homograft “Qingzhen D1/Qingzhen D1” and the heterograft “QAUP-1/Qingzhen D1” as compatibility and incompatibility combinations were compared. Anatomical differences indicated the healing process was faster in homografts than in heterografts. During the healing process, four critical stages in graft union formation were identified in the two types of grafts. The expression of the genes associated with hormone signaling (auxin and cytokinins), and lignin biosynthesis was delayed in the healing process of heterografts. In addition, the PbBglu13 gene, encoded β-glucosidase, was more highly up-regulated in heterografts than in homografts to promote healing. Meanwhile, the most of DEGs related starch and sucrose metabolism were found to be up-regulated in heterografts; those results indicated that cellulose and sugar signals were also involved in graft healing. The results of this study improved the understanding of the differences in the mechanisms of graft healing between homografts and heterografts. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Molecular Characterization and Genetic Structure Evaluation of Breeding Populations of Fennel (Foeniculum vulgare Mill.)
Agronomy 2022, 12(3), 542; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12030542 - 22 Feb 2022
Abstract
Fennel, or Foeniculum vulgare Mill., is an important horticultural crop belonging to the Apiaceae family that is cultivated worldwide and used in the agri-food sector and for pharmaceutical preparations. Breeding strategies in this species usually involve three parental lines, including two maternal lines [...] Read more.
Fennel, or Foeniculum vulgare Mill., is an important horticultural crop belonging to the Apiaceae family that is cultivated worldwide and used in the agri-food sector and for pharmaceutical preparations. Breeding strategies in this species usually involve three parental lines, including two maternal lines (one cytoplasmic male-sterile line and an ideotype representative maintainer line) that are crossed to obtain an ideotype representative of the cytoplasmic male-sterile line and one paternal line, used as a pollinator in crosses with the progeny of the derived maternal lines. From this cross, F1 hybrid progenies are obtained, which are characterized by high levels of heterozygosity and hybrid vigor. In this study, over 450 plants, representing 8 breeding populations and their respective 3 parental and 1 progeny line, were genotyped by means of codominant molecular markers. The 12 highly polymorphic microsatellites enabled the analyses of the genetic variability, distinctiveness and stability of each breeding line. Moreover, the genetic structure of the core collection was investigated, which, together with the homozygosity, gene flow and genetic similarity results, allowed the identification of unsuitable lines to be used in breeding plans due to their low homozygosity (10.4% in the pollinator line of population 7). Moreover, the Bayesian reconstruction of the core collection’s genetic structure, based on the codominant markers used, allowed us to confirm the distinctiveness results obtained from the genetic similarity investigation and the computed gene flow estimates. Among these, a trend in hybrid heterozygosity was also observed, that increased when the genetic similarity between the respective parental lines decreased. Thus, this research proposes a suitable method for genotyping fennel populations in pre- and post-breeding approaches, such as marker-assisted breeding or breeding line distinctiveness and stability verifications. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Electrophysiological, Morphologic, and Transcriptomic Profiling of the Ogura-CMS, DGMS and Maintainer Broccoli Lines
Plants 2022, 11(4), 561; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11040561 - 21 Feb 2022
Cited by 1
Abstract
To better serve breeding of broccoli, the electrophysiological, morphological and transcriptomic profiling of the isogenic Ogura-CMS, DGMS and their maintainer fertile lines, were carried out by scanning electron microscopy, investigation of agronomic traits and RNA-sequencing analysis. The agronomic traits of plant height, length [...] Read more.
To better serve breeding of broccoli, the electrophysiological, morphological and transcriptomic profiling of the isogenic Ogura-CMS, DGMS and their maintainer fertile lines, were carried out by scanning electron microscopy, investigation of agronomic traits and RNA-sequencing analysis. The agronomic traits of plant height, length of the largest leaf, plant spread angle, single head weight, head width and stem diameter showed stronger performance in Ogura-CMS broccoli than in DGMS line or maintainer fertile line. However, the Ogura-CMS broccoli was poorer in the seed yield and seed germination than in the DGMS line and maintainer fertile line. Additionally, the DGMS broccoli had longer maturation and flowering periods than the Ogura-CMS and maintainer fertile lines. There were obvious differences in the honey gland, happening in the male sterility and fertile lines of broccoli. Additionally, the mechanism regulating Ogura-CMS and DGMS in broccoli was investigated using florets transcriptome analyses of the Ogura-CMS, DGMS and maintainer fertile lines. As a result, a total of 2670 differentially expressed genes (DEGs) were detected, including 1054 up- and 1616 downregulated genes in the Ogura-CMS and DGMS lines compared to the maintainer fertile line. A number of functionally known genes involved in plant hormones (auxin, salicylic acid and brassinosteroid), five Mitochondrial Oxidative Phosphorylation (OXPHOS) genes of atp8, LOC106319879, LOC106324734, LOC106314622 and LOC106298585, and three upregulated genes (Lhcb1, Lhcb3 and Lhcb5) associated with the photosynthesis-antenna protein pathway, were obviously detected to be highly associated with reproductive development including flowering time, maturity and reproductive period in the Ogura-CMS and DGMS broccoli comparing to their maintainer fertile line. Our research would provide a comprehensive foundation for understanding the differences of electrophysiological, morphological and transcriptomic profiles in the Ogura-CMS, DGMS and maintainer broccoli, and as well as being beneficial to exploring the mechanism of male sterility in Brassica crops. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Combination of Marker-Assisted Backcross Selection of Yr59 and Phenotypic Selection to Improve Stripe Rust Resistance and Agronomic Performance in Four Elite Wheat Cultivars
Agronomy 2022, 12(2), 497; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12020497 - 17 Feb 2022
Abstract
In this study, we successfully introgressed and validated Yr59 into four elite wheat cultivars, Jimai 22, Chuanmai 42, Zhengmai 9023 and Xinmai 26 through marker-assisted backcross selection. Used as female parents, these four cultivars were crossed with wheat line PI 660061 (Yr59 [...] Read more.
In this study, we successfully introgressed and validated Yr59 into four elite wheat cultivars, Jimai 22, Chuanmai 42, Zhengmai 9023 and Xinmai 26 through marker-assisted backcross selection. Used as female parents, these four cultivars were crossed with wheat line PI 660061 (Yr59). After two backcrosses and marker-assisted selection, the progenies were selfed and advanced to the BC2F4 generation. A total of 123 BC2F4 lines were selected based on agronomic traits and stripe rust resistance, and their BC2F5 and BC2F6 progenies were further evaluated for stripe rust resistance and agronomic traits. Seven markers linked with relevant genes, including Xbarc32, Xwgp5175, Xwmc557 and Xcfa2040 linked with Yr59; Xwmc658 with YrJ22; WE173 and Xbarc181 with Yr26, were used to genotype the breeding lines. A total of 109 introgression lines with positive markers for Yr59 were identified for further stripe rust and agronomic trait evaluation. Finally, 16 lines had higher levels resistance to stripe rust, and similar or superior agronomic traits compared to their parents were obtained. These lines can be released as new cultivars for various regions after regional tests and also can be used as resistance stocks for regional breeding programs to develop new cultivars with adequate and durable resistance to stripe rust. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Discovery of Major Quantitative Trait Loci and Candidate Genes for Fresh Seed Dormancy in Groundnut
Agronomy 2022, 12(2), 404; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12020404 - 06 Feb 2022
Abstract
Spanish bunch groundnut varieties occupy most of the cultivated area in Asia and Africa, and these varieties lack required 2-3 weeks of fresh seed dormancy (FSD) hampering kernel quality. Genomic breeding can help to improve commercial groundnut cultivars for FSD in a shorter [...] Read more.
Spanish bunch groundnut varieties occupy most of the cultivated area in Asia and Africa, and these varieties lack required 2-3 weeks of fresh seed dormancy (FSD) hampering kernel quality. Genomic breeding can help to improve commercial groundnut cultivars for FSD in a shorter time with greater precision. In this regard, a recombinant inbred line (RIL) population from the cross ICGV 02266 (non-dormant) × ICGV 97045 (dormant) was developed and genotyped with a 5 K mid-density genotyping assay. A linkage map was constructed with 325 SNP loci spanning a total map length of 2335.3 cM and five major QTLs were identified on chromosomes Ah01, Ah11, Ah06, Ah16 and Ah17. Based on differential gene expression using transcriptomic information from dormant (Tifrunner) and non-dormant (ICGV 91114) genotypes, histone deacetylases, histone-lysine N-methyltransferase, cytochrome P450, protein kinases, and ethylene-responsive transcription factor were identified as key regulators involved in the hormonal regulation of dormancy. Six Kompetitive Allele Specific PCR (KASP) markers were successfully validated in the diverse panel including selected RILs of the same population and germplasm lines. These validated KASP markers could facilitate faster breeding of new varieties with desired dormancy using marker-assisted early generation selection. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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Article
Detection of Chromosomal Segments Introgressed from Wild Species of Carrot into Cultivars: Quantitative Trait Loci Mapping for Morphological Features in Backcross Inbred Lines
Plants 2022, 11(3), 391; https://0-doi-org.brum.beds.ac.uk/10.3390/plants11030391 - 30 Jan 2022
Abstract
Cultivated carrot is thought to have been domesticated from a wild species, and various phenotypes developed through human domestication and selection over the past several centuries. Little is known about the genomic contribution of wild species to the phenotypes of present-day cultivars, although [...] Read more.
Cultivated carrot is thought to have been domesticated from a wild species, and various phenotypes developed through human domestication and selection over the past several centuries. Little is known about the genomic contribution of wild species to the phenotypes of present-day cultivars, although several studies have focused on identifying genetic loci that contribute to the morphology of storage roots. A backcross inbred line (BIL) population derived from a cross between the wild species Daucus carota ssp. carota “Songzi” and the orange cultivar “Amsterdam forcing” was developed. The morphological features in the BIL population became more diverse after several generations of selfing BC2F1 plants. Only few lines retained features of wild parent. Genomic resequencing of the two parental lines and the BILs resulted in 3,223,651 single nucleotide polymorphisms (SNPs), and 13,445 bin markers were generated using a sliding window approach. We constructed a genetic map with 2027 bins containing 154,776 SNPs; the total genetic distance was 1436.43 cM and the average interval between the bins was 0.71 cm. Five stable QTLs related to root length, root shoulder width, dry material content of root, and ratio of root shoulder width to root middle width were consistently detected on chromosome 2 in both years and explained 23.4–66.9% of the phenotypic variance. The effects of introgressed genomic segments from the wild species on the storage root are reported and will enable the identification of functional genes that control root morphological traits in carrot. Full article
(This article belongs to the Topic Plant Breeding, Genetics and Genomics)
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