A SNP-Based Genome-Wide Association Study to Mine Genetic Loci Associated to Salinity Tolerance in Mungbean (Vigna radiata L.).
Identifieur interne : 000096 ( Main/Exploration ); précédent : 000095; suivant : 000097A SNP-Based Genome-Wide Association Study to Mine Genetic Loci Associated to Salinity Tolerance in Mungbean (Vigna radiata L.).
Auteurs : Caleb Manamik Breria [Taïwan] ; Ching-Hsiang Hsieh [Taïwan] ; Tsair-Bor Yen [Taïwan] ; Jo-Yi Yen [Taïwan] ; Thomas J. Noble [Australie] ; Roland Schafleitner [Taïwan]Source :
- Genes [ 2073-4425 ] ; 2020.
Abstract
Mungbean (Vigna radiata (L.) R. Wilzeck var. radiata) is a protein-rich short-duration legume that fits well as a rotation crop into major cereal production systems of East and South-East Asia. Salinity stress in arid areas affects mungbean, being more of a glycophyte than cereals. A significant portion of the global arable land is either salt or sodium affected. Thus, studies to understand and improve salt-stress tolerance are imminent. Here, we conducted a genome-wide association study (GWAS) to mine genomic loci underlying salt-stress tolerance during seed germination of mungbean. The World Vegetable Center (WorldVeg) mungbean minicore collection representing the diversity of mungbean germplasm was utilized as the study panel and variation for salt stress tolerance was found in this germplasm collection. The germplasm panel was classed into two agro-climatic groups and showed significant differences in their germination abilities under salt stress. A total of 5288 SNP markers obtained through genotyping-by-sequencing (GBS) were used to mine alleles associated with salt stress tolerance. Associated SNPs were identified on chromosomes 7 and 9. The associated region at chromosome 7 (position 2,696,072 to 2,809,200 bp) contains the gene Vradi07g01630, which was annotated as the ammonium transport protein (AMT). The associated region in chromosome 9 (position 19,390,227 bp to 20,321,817 bp) contained the genes Vradi09g09510 and Vradi09g09600, annotated as OsGrx_S16-glutaredoxin subgroup II and dnaJ domain proteins respectively. These proteins were reported to have functions related to salt-stress tolerance.
DOI: 10.3390/genes11070759
PubMed: 32646058
PubMed Central: PMC7397256
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A SNP-Based Genome-Wide Association Study to Mine Genetic Loci Associated to Salinity Tolerance in Mungbean (<i>Vigna radiata</i> L.).</title><author><name sortKey="Breria, Caleb Manamik" sort="Breria, Caleb Manamik" uniqKey="Breria C" first="Caleb Manamik" last="Breria">Caleb Manamik Breria</name><affiliation wicri:level="1"><nlm:affiliation>World Vegetable Center, Biotechnology and Molecular Breeding, Shanhua, Tainan 74199, Taiwan.</nlm:affiliation><country xml:lang="fr">Taïwan</country><wicri:regionArea>World Vegetable Center, Biotechnology and Molecular Breeding, Shanhua, Tainan 74199</wicri:regionArea><wicri:noRegion>Tainan 74199</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Industry, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan.</nlm:affiliation><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Plant Industry, National Pingtung University of Science and Technology, Neipu, Pingtung 912</wicri:regionArea><wicri:noRegion>Pingtung 912</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan.</nlm:affiliation><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Neipu, Pingtung 912</wicri:regionArea><wicri:noRegion>Pingtung 912</wicri:noRegion></affiliation></author><author><name sortKey="Hsieh, Ching Hsiang" sort="Hsieh, Ching Hsiang" uniqKey="Hsieh C" first="Ching-Hsiang" last="Hsieh">Ching-Hsiang Hsieh</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Industry, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan.</nlm:affiliation><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Plant Industry, National Pingtung University of Science and Technology, Neipu, Pingtung 912</wicri:regionArea><wicri:noRegion>Pingtung 912</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan.</nlm:affiliation><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Neipu, Pingtung 912</wicri:regionArea><wicri:noRegion>Pingtung 912</wicri:noRegion></affiliation></author><author><name sortKey="Yen, Tsair Bor" sort="Yen, Tsair Bor" uniqKey="Yen T" first="Tsair-Bor" last="Yen">Tsair-Bor Yen</name><affiliation wicri:level="1"><nlm:affiliation>Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan.</nlm:affiliation><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Neipu, Pingtung 912</wicri:regionArea><wicri:noRegion>Pingtung 912</wicri:noRegion></affiliation></author><author><name sortKey="Yen, Jo Yi" sort="Yen, Jo Yi" uniqKey="Yen J" first="Jo-Yi" last="Yen">Jo-Yi Yen</name><affiliation wicri:level="1"><nlm:affiliation>World Vegetable Center, Biotechnology and Molecular Breeding, Shanhua, Tainan 74199, Taiwan.</nlm:affiliation><country xml:lang="fr">Taïwan</country><wicri:regionArea>World Vegetable Center, Biotechnology and Molecular Breeding, Shanhua, Tainan 74199</wicri:regionArea><wicri:noRegion>Tainan 74199</wicri:noRegion></affiliation></author><author><name sortKey="Noble, Thomas J" sort="Noble, Thomas J" uniqKey="Noble T" first="Thomas J" last="Noble">Thomas J. 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74199</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32646058</idno><idno type="pmid">32646058</idno><idno type="doi">10.3390/genes11070759</idno><idno type="pmc">PMC7397256</idno><idno type="wicri:Area/Main/Corpus">000039</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000039</idno><idno type="wicri:Area/Main/Curation">000039</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000039</idno><idno type="wicri:Area/Main/Exploration">000039</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">A SNP-Based Genome-Wide Association Study to Mine Genetic Loci Associated to Salinity Tolerance in Mungbean (<i>Vigna radiata</i> L.).</title><author><name sortKey="Breria, Caleb Manamik" sort="Breria, Caleb Manamik" uniqKey="Breria C" first="Caleb Manamik" last="Breria">Caleb Manamik Breria</name><affiliation wicri:level="1"><nlm:affiliation>World Vegetable Center, Biotechnology and Molecular Breeding, Shanhua, Tainan 74199, Taiwan.</nlm:affiliation><country xml:lang="fr">Taïwan</country><wicri:regionArea>World Vegetable Center, Biotechnology and Molecular Breeding, Shanhua, Tainan 74199</wicri:regionArea><wicri:noRegion>Tainan 74199</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Industry, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan.</nlm:affiliation><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Plant Industry, National Pingtung University of Science and Technology, Neipu, Pingtung 912</wicri:regionArea><wicri:noRegion>Pingtung 912</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan.</nlm:affiliation><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Neipu, Pingtung 912</wicri:regionArea><wicri:noRegion>Pingtung 912</wicri:noRegion></affiliation></author><author><name sortKey="Hsieh, Ching Hsiang" sort="Hsieh, Ching Hsiang" uniqKey="Hsieh C" first="Ching-Hsiang" last="Hsieh">Ching-Hsiang Hsieh</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Industry, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan.</nlm:affiliation><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Plant Industry, National Pingtung University of Science and Technology, Neipu, Pingtung 912</wicri:regionArea><wicri:noRegion>Pingtung 912</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan.</nlm:affiliation><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Neipu, Pingtung 912</wicri:regionArea><wicri:noRegion>Pingtung 912</wicri:noRegion></affiliation></author><author><name sortKey="Yen, Tsair Bor" sort="Yen, Tsair Bor" uniqKey="Yen T" first="Tsair-Bor" last="Yen">Tsair-Bor Yen</name><affiliation wicri:level="1"><nlm:affiliation>Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan.</nlm:affiliation><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Neipu, Pingtung 912</wicri:regionArea><wicri:noRegion>Pingtung 912</wicri:noRegion></affiliation></author><author><name sortKey="Yen, Jo Yi" sort="Yen, Jo Yi" uniqKey="Yen J" first="Jo-Yi" last="Yen">Jo-Yi Yen</name><affiliation wicri:level="1"><nlm:affiliation>World Vegetable Center, Biotechnology and Molecular Breeding, Shanhua, Tainan 74199, Taiwan.</nlm:affiliation><country xml:lang="fr">Taïwan</country><wicri:regionArea>World Vegetable Center, Biotechnology and Molecular Breeding, Shanhua, Tainan 74199</wicri:regionArea><wicri:noRegion>Tainan 74199</wicri:noRegion></affiliation></author><author><name sortKey="Noble, Thomas J" sort="Noble, Thomas J" uniqKey="Noble T" first="Thomas J" last="Noble">Thomas J. Noble</name><affiliation wicri:level="1"><nlm:affiliation>Centre of Tropical Agriculture and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4000, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Centre of Tropical Agriculture and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4000</wicri:regionArea><wicri:noRegion>Queensland 4000</wicri:noRegion></affiliation></author><author><name sortKey="Schafleitner, Roland" sort="Schafleitner, Roland" uniqKey="Schafleitner R" first="Roland" last="Schafleitner">Roland Schafleitner</name><affiliation wicri:level="1"><nlm:affiliation>World Vegetable Center, Biotechnology and Molecular Breeding, Shanhua, Tainan 74199, Taiwan.</nlm:affiliation><country xml:lang="fr">Taïwan</country><wicri:regionArea>World Vegetable Center, Biotechnology and Molecular Breeding, Shanhua, Tainan 74199</wicri:regionArea><wicri:noRegion>Tainan 74199</wicri:noRegion></affiliation></author></analytic><series><title level="j">Genes</title><idno type="eISSN">2073-4425</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Mungbean (<i>Vigna radiata</i> (L.) R. Wilzeck var. <i>radiata</i>) is a protein-rich short-duration legume that fits well as a rotation crop into major cereal production systems of East and South-East Asia. Salinity stress in arid areas affects mungbean, being more of a glycophyte than cereals. A significant portion of the global arable land is either salt or sodium affected. Thus, studies to understand and improve salt-stress tolerance are imminent. Here, we conducted a genome-wide association study (GWAS) to mine genomic loci underlying salt-stress tolerance during seed germination of mungbean. The World Vegetable Center (WorldVeg) mungbean minicore collection representing the diversity of mungbean germplasm was utilized as the study panel and variation for salt stress tolerance was found in this germplasm collection. The germplasm panel was classed into two agro-climatic groups and showed significant differences in their germination abilities under salt stress. A total of 5288 SNP markers obtained through genotyping-by-sequencing (GBS) were used to mine alleles associated with salt stress tolerance. Associated SNPs were identified on chromosomes 7 and 9. The associated region at chromosome 7 (position 2,696,072 to 2,809,200 bp) contains the gene <i>Vradi07g01630</i>, which was annotated as the ammonium transport protein (AMT). The associated region in chromosome 9 (position 19,390,227 bp to 20,321,817 bp) contained the genes <i>Vradi09g09510</i> and <i>Vradi09g09600</i>, annotated as OsGrx_S16-glutaredoxin subgroup II and dnaJ domain proteins respectively. These proteins were reported to have functions related to salt-stress tolerance.</div></front></TEI><pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">32646058</PMID><DateRevised><Year>2020</Year><Month>08</Month><Day>18</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2073-4425</ISSN><JournalIssue CitedMedium="Internet"><Volume>11</Volume><Issue>7</Issue><PubDate><Year>2020</Year><Month>Jul</Month><Day>07</Day></PubDate></JournalIssue><Title>Genes</Title><ISOAbbreviation>Genes (Basel)</ISOAbbreviation></Journal><ArticleTitle>A SNP-Based Genome-Wide Association Study to Mine Genetic Loci Associated to Salinity Tolerance in Mungbean (<i>Vigna radiata</i> L.).</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">E759</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.3390/genes11070759</ELocationID><Abstract><AbstractText>Mungbean (<i>Vigna radiata</i> (L.) R. Wilzeck var. <i>radiata</i>) is a protein-rich short-duration legume that fits well as a rotation crop into major cereal production systems of East and South-East Asia. Salinity stress in arid areas affects mungbean, being more of a glycophyte than cereals. A significant portion of the global arable land is either salt or sodium affected. Thus, studies to understand and improve salt-stress tolerance are imminent. Here, we conducted a genome-wide association study (GWAS) to mine genomic loci underlying salt-stress tolerance during seed germination of mungbean. The World Vegetable Center (WorldVeg) mungbean minicore collection representing the diversity of mungbean germplasm was utilized as the study panel and variation for salt stress tolerance was found in this germplasm collection. The germplasm panel was classed into two agro-climatic groups and showed significant differences in their germination abilities under salt stress. A total of 5288 SNP markers obtained through genotyping-by-sequencing (GBS) were used to mine alleles associated with salt stress tolerance. Associated SNPs were identified on chromosomes 7 and 9. The associated region at chromosome 7 (position 2,696,072 to 2,809,200 bp) contains the gene <i>Vradi07g01630</i>, which was annotated as the ammonium transport protein (AMT). The associated region in chromosome 9 (position 19,390,227 bp to 20,321,817 bp) contained the genes <i>Vradi09g09510</i> and <i>Vradi09g09600</i>, annotated as OsGrx_S16-glutaredoxin subgroup II and dnaJ domain proteins respectively. These proteins were reported to have functions related to salt-stress tolerance.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Breria</LastName><ForeName>Caleb Manamik</ForeName><Initials>CM</Initials><AffiliationInfo><Affiliation>World Vegetable Center, Biotechnology and Molecular Breeding, Shanhua, Tainan 74199, Taiwan.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Plant Industry, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hsieh</LastName><ForeName>Ching-Hsiang</ForeName><Initials>CH</Initials><AffiliationInfo><Affiliation>Department of Plant Industry, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yen</LastName><ForeName>Tsair-Bor</ForeName><Initials>TB</Initials><AffiliationInfo><Affiliation>Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yen</LastName><ForeName>Jo-Yi</ForeName><Initials>JY</Initials><AffiliationInfo><Affiliation>World Vegetable Center, Biotechnology and Molecular Breeding, Shanhua, Tainan 74199, Taiwan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Noble</LastName><ForeName>Thomas J</ForeName><Initials>TJ</Initials><AffiliationInfo><Affiliation>Centre of Tropical Agriculture and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4000, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schafleitner</LastName><ForeName>Roland</ForeName><Initials>R</Initials><Identifier Source="ORCID">0000-0003-3637-7603</Identifier><AffiliationInfo><Affiliation>World Vegetable Center, Biotechnology and Molecular Breeding, Shanhua, Tainan 74199, Taiwan.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>81180341</GrantID><Agency>Federal Ministry for Economic Cooperation and Development, Germany,</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>07</Month><Day>07</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Genes (Basel)</MedlineTA><NlmUniqueID>101551097</NlmUniqueID><ISSNLinking>2073-4425</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">genome-wide association mapping</Keyword><Keyword MajorTopicYN="N">legume</Keyword><Keyword MajorTopicYN="N">molecular markers</Keyword><Keyword MajorTopicYN="N">mungbean</Keyword><Keyword MajorTopicYN="N">salt-stress</Keyword><Keyword MajorTopicYN="N">single nucleotide polymorphism</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>06</Month><Day>03</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>06</Month><Day>28</Day></PubMedPubDate><PubMedPubDate 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Ching Hsiang" sort="Hsieh, Ching Hsiang" uniqKey="Hsieh C" first="Ching-Hsiang" last="Hsieh">Ching-Hsiang Hsieh</name><name sortKey="Schafleitner, Roland" sort="Schafleitner, Roland" uniqKey="Schafleitner R" first="Roland" last="Schafleitner">Roland Schafleitner</name><name sortKey="Yen, Jo Yi" sort="Yen, Jo Yi" uniqKey="Yen J" first="Jo-Yi" last="Yen">Jo-Yi Yen</name><name sortKey="Yen, Tsair Bor" sort="Yen, Tsair Bor" uniqKey="Yen T" first="Tsair-Bor" last="Yen">Tsair-Bor Yen</name></country><country name="Australie"><noRegion><name sortKey="Noble, Thomas J" sort="Noble, Thomas J" uniqKey="Noble T" first="Thomas J" last="Noble">Thomas J. 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