Analysis of an Applied Core Collection of Adzuki Bean Germplasm by Using SSR Markers

Wang, Lixia; Cheng, Xuzhen; Wang, Suhua; Tian, Jichun

doi:10.1016/s2095-3119(12)60163-4

Cited by 10 publications

(4 citation statements)

References 31 publications

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“…Recently, a number of SSRs (simple sequence repeats) and SNPs (single-nucleotide polymorphisms) were exploited due to the developmental genomics in adzuki bean ( Chen et al, 2015 ; Kang et al, 2015 ). The genetic map resolution was also improved based on the SNP and SSR markers ( Wang et al, 2012 ; Suzuki et al, 2013 ; Lestari et al, 2014 ). Meanwhile, bZIP genes were demanded to be responsive to drought and salt stress in Vigna radiata and Vigna angularis with whole-genome sequences and quantitative real-time PCR analysis ( Wang et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Characterization of Drought-Responsive Transcriptome During Seed Germination in Adzuki Bean (Vigna angularis L.) by PacBio SMRT and Illumina Sequencing

et al. 2020

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The full-length single-molecular sequencing and short reads Illumina sequencing were combined to generate the transcripts of adzuki bean with high-quality. A total of 17,636 loci and 60,454 transcripts were detected in this study. To characterize the drought-responsive genes during seed germination in adzuki bean, two varieties, i.e., tolerant and sensitive to drought stress, were selected to conduct analysis of alternative splicing dynamics (AS) and differentially expressed genes (DEGs) by combining the newly assembled draft genome and public adzuki bean reference genome. AS analysis indicated that both the two varieties underwent a little more AS events under control conditions than under drought stress. Among the AS events, IR (intron retention) predominately accounted for 34.3%, whereas AD (alternative donor site) was the least frequent with 15.8%. Meanwhile, 562 long non-coding RNAs, 409 fusion genes and 1208 transcription factors were identified. Moreover, a total of 5,337 DEGs were identified in comparison of the two varieties with drought or control treatments. Notably, 82 DEGs were discovered in the two varieties under drought stress, which might be the candidate in regulation of seed germination to answer for different drought tolerance. The DEGs encoded proteins involved in primary or second metabolism, plant hormone signal transduction, transcript or translation processes, ubiquitin proteasome system, transcription factor, transporters, and so on. The results facilitate to increase the knowledge about the mechanism of drought tolerance during crop seed germination, and provide reference for the breeding of drought-tolerant adzuki bean.

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Section: Introductionmentioning

confidence: 99%

Characterization of Drought-Responsive Transcriptome During Seed Germination in Adzuki Bean (Vigna angularis L.) by PacBio SMRT and Illumina Sequencing

et al. 2020

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“…Forty-seven SSR markers developed for mung bean showed reliable banding and polymorphisms were used to analyze the genetic diversity of 230 rice bean accessions [ 1 ]. The number of SSR markers used in rice bean so far is fewer than those reported for other legumes, such as mung bean [ 6 ], adzuki bean [ 7 ], common bean [ 8 , 9 ], chickpea [ 10 ], pigeon pea [ 11 ] and soybean [ 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

Development of Gene-Based SSR Markers in Rice Bean (Vigna umbellata L.) Based on Transcriptome Data

Chen

Tian

et al. 2016

PLoS ONE

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Rice bean (Vigna umbellata (Thunb.) Ohwi & Ohashi) is a warm season annual legume mainly grown in East Asia. Only scarce genomic resources are currently available for this legume crop species and no simple sequence repeat (SSR) markers have been specifically developed for rice bean yet. In this study, approximately 26 million high quality cDNA sequence reads were obtained from rice bean using Illumina paired-end sequencing technology and assembled into 71,929 unigenes with an average length of 986 bp. Of these unigenes, 38,840 (33.2%) showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases. Furthermore, 30,170 (76.3%) could be classified into gene ontology categories, 25,451 (64.4%) into Swiss-Prot categories and 21,982 (55.6%) into KOG database categories (E-value < 1.0E-5). A total of 9,301 (23.5%) were mapped onto 118 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database. A total of 3,011 genic SSRs were identified as potential molecular markers. AG/CT (30.3%), AAG/CTT (8.1%) and AGAA/TTCT (20.0%) are the three main repeat motifs. A total of 300 SSR loci were randomly selected for validation by using PCR amplification. Of these loci, 23 primer pairs were polymorphic among 32 rice bean accessions. A UPGMA dendrogram revealed three major clusters among 32 rice bean accessions. The large number of SSR-containing sequences and genic SSRs in this study will be valuable for the construction of high-resolution genetic linkage maps, association or comparative mapping and genetic analyses of various Vigna species.

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“…Wild adzuki beans had higher allelic diversity than cultivated types. Structure analysis clearly separated the wild from the cultigen germplasm, with subdivisions in cultigens based on ecological regions of adaptation (Wang et al, 2012). High genetic differentiation was reported between wild adzuki beans and their wild relative Vigna minima.…”

Section: Morpho-agronomic Traits-based Diversitymentioning

confidence: 92%

Exploiting genetic and genomic resources to enhance productivity and abiotic stress adaptation of underutilized pulses

Dwivedi,

Chapman,

Abberton

et al. 2023

Front. Genet.

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Underutilized pulses and their wild relatives are typically stress tolerant and their seeds are packed with protein, fibers, minerals, vitamins, and phytochemicals. The consumption of such nutritionally dense legumes together with cereal-based food may promote global food and nutritional security. However, such species are deficient in a few or several desirable domestication traits thereby reducing their agronomic value, requiring further genetic enhancement for developing productive, nutritionally dense, and climate resilient cultivars. This review article considers 13 underutilized pulses and focuses on their germplasm holdings, diversity, crop-wild-crop gene flow, genome sequencing, syntenic relationships, the potential for breeding and transgenic manipulation, and the genetics of agronomic and stress tolerance traits. Recent progress has shown the potential for crop improvement and food security, for example, the genetic basis of stem determinacy and fragrance in moth bean and rice bean, multiple abiotic stress tolerant traits in horse gram and tepary bean, bruchid resistance in lima bean, low neurotoxin in grass pea, and photoperiod induced flowering and anthocyanin accumulation in adzuki bean have been investigated. Advances in introgression breeding to develop elite genetic stocks of grass pea with low β-ODAP (neurotoxin compound), resistance to Mungbean yellow mosaic India virus in black gram using rice bean, and abiotic stress adaptation in common bean, using genes from tepary bean have been carried out. This highlights their potential in wider breeding programs to introduce such traits in locally adapted cultivars. The potential of de-domestication or feralization in the evolution of new variants in these crops are also highlighted.

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Analysis of an Applied Core Collection of Adzuki Bean Germplasm by Using SSR Markers

Cited by 10 publications

References 31 publications

Characterization of Drought-Responsive Transcriptome During Seed Germination in Adzuki Bean (Vigna angularis L.) by PacBio SMRT and Illumina Sequencing

Characterization of Drought-Responsive Transcriptome During Seed Germination in Adzuki Bean (Vigna angularis L.) by PacBio SMRT and Illumina Sequencing

Development of Gene-Based SSR Markers in Rice Bean (Vigna umbellata L.) Based on Transcriptome Data

Exploiting genetic and genomic resources to enhance productivity and abiotic stress adaptation of underutilized pulses

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