Genome-wide association study on stem rust resistance in Kazakh spring barley lines.
Identifieur interne : 000390 ( Main/Exploration ); précédent : 000389; suivant : 000391Genome-wide association study on stem rust resistance in Kazakh spring barley lines.
Auteurs : Yerlan Turuspekov [Kazakhstan] ; Danara Ormanbekova [Kazakhstan] ; Aralbek Rsaliev [Kazakhstan] ; Saule Abugalieva [Kazakhstan]Source :
- BMC plant biology [ 1471-2229 ] ; 2016.
Descripteurs français
- KwdFr :
- Basidiomycota (physiologie), Génome végétal (MeSH), Hordeum (génétique), Hordeum (microbiologie), Locus de caractère quantitatif (MeSH), Maladies des plantes (génétique), Marqueurs génétiques (MeSH), Polymorphisme de nucléotide simple (MeSH), Tiges de plante (MeSH), Étude d'association pangénomique (MeSH).
- MESH :
- génétique : Hordeum, Maladies des plantes.
- microbiologie : Hordeum.
- physiologie : Basidiomycota.
- Génome végétal, Locus de caractère quantitatif, Marqueurs génétiques, Polymorphisme de nucléotide simple, Tiges de plante, Étude d'association pangénomique.
English descriptors
- KwdEn :
- MESH :
- chemical : Genetic Markers.
- genetics : Hordeum, Plant Diseases.
- microbiology : Hordeum.
- physiology : Basidiomycota.
- Genome, Plant, Genome-Wide Association Study, Plant Stems, Polymorphism, Single Nucleotide, Quantitative Trait Loci.
Abstract
BACKGROUND
Stem rust (SR) is one of the most economically devastating barley diseases in Kazakhstan, and in some years it causes up to 50 % of yield losses. Routine conventional breeding for resistance to stem rust is almost always in progress in all Kazakhstan breeding stations. However, molecular marker based approach towards new SR resistance genes identification and relevant marker-assisted selection had never been employed in Kazakhstan yet. In this study, as a preliminary step the GWAS (genome-wide association study) mapping was applied in attempt to identify reliable SNP markers and quantitative trait loci (QTL) associated with resistance to SR.
RESULTS
Barley collection of 92 commercial cultivars and promising lines was genotyped using a high-throughput single nucleotide polymorphism (9,000 SNP) Illumina iSelect array. 6,970 SNPs out of 9,000 total were polymorphic and scorable. 5,050 SNPs out of 6,970 passed filtering threshold and were used for association mapping (AM). All 92 accessions were phenotyped for resistance to SR by observing adult plants in artificially infected plots at the Research Institute for Biological Safety Problems in Dzhambul region of Kazakhstan. GLM analysis allowed the identification of 15 SNPs associated with the resistance at the heading time (HA) phase, and 2 SNPs at the seed's milky-waxy maturity (SM) phase. However, after application of 5 % Bonferroni multiple test correction, only 2 SNPs at the HA stage on the same position of chromosome 6H can be claimed as reliable markers for SR resistance. The MLM analysis after the Bonferroni correction did not reveal any associations in this study, although distribution lines in the quantile-quantile (QQ) plot indicates that overcorrection in the test due to both Q and K matrices usage.
CONCLUSIONS
Obtained data suggest that genome wide genotyping of 92 spring barley accessions from Kazakhstan with 9 K Illumina SNP array was highly efficient. Linkage disequilibrium based mapping approach allowed the identification of highly significant QTL for the SR resistance at the HA phase of growth on chromosome 6H. On the other hand, no significant QTL was detected at the SM phase, assuming that for a successful GWASmapping experiment a larger size population with more diverse genetic background should be tested. Obtained results provide additional information towards better understanding of SR resistance in barley.
DOI: 10.1186/s12870-015-0686-z
PubMed: 26821649
PubMed Central: PMC4895317
Affiliations:
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type="wicri:Area/Main/Exploration">000408</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Genome-wide association study on stem rust resistance in Kazakh spring barley lines.</title><author><name sortKey="Turuspekov, Yerlan" sort="Turuspekov, Yerlan" uniqKey="Turuspekov Y" first="Yerlan" last="Turuspekov">Yerlan Turuspekov</name><affiliation wicri:level="3"><nlm:affiliation>Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan. yerlant@yahoo.com.</nlm:affiliation><country xml:lang="fr">Kazakhstan</country><wicri:regionArea>Institute of Plant Biology and Biotechnology, Almaty</wicri:regionArea><placeName><settlement type="city">Almaty</settlement><region nuts="2">Oblys d'Almaty</region></placeName></affiliation></author><author><name sortKey="Ormanbekova, Danara" sort="Ormanbekova, Danara" uniqKey="Ormanbekova D" first="Danara" last="Ormanbekova">Danara Ormanbekova</name><affiliation wicri:level="3"><nlm:affiliation>Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan. or.danara@gmail.com.</nlm:affiliation><country xml:lang="fr">Kazakhstan</country><wicri:regionArea>Institute of Plant Biology and Biotechnology, Almaty</wicri:regionArea><placeName><settlement type="city">Almaty</settlement><region nuts="2">Oblys d'Almaty</region></placeName></affiliation></author><author><name sortKey="Rsaliev, Aralbek" sort="Rsaliev, Aralbek" uniqKey="Rsaliev A" first="Aralbek" last="Rsaliev">Aralbek Rsaliev</name><affiliation wicri:level="1"><nlm:affiliation>Research Institute for Biological Safety Problems, Gvardeiskiy vil, Dzhambul region, Kazakhstan. aralbek@mail.ru.</nlm:affiliation><country xml:lang="fr">Kazakhstan</country><wicri:regionArea>Research Institute for Biological Safety Problems, Gvardeiskiy vil, Dzhambul region</wicri:regionArea><wicri:noRegion>Dzhambul region</wicri:noRegion></affiliation></author><author><name sortKey="Abugalieva, Saule" sort="Abugalieva, Saule" uniqKey="Abugalieva S" first="Saule" last="Abugalieva">Saule Abugalieva</name><affiliation wicri:level="3"><nlm:affiliation>Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan. absaule@yahoo.com.</nlm:affiliation><country xml:lang="fr">Kazakhstan</country><wicri:regionArea>Institute of Plant Biology and Biotechnology, Almaty</wicri:regionArea><placeName><settlement type="city">Almaty</settlement><region nuts="2">Oblys d'Almaty</region></placeName></affiliation></author></analytic><series><title level="j">BMC plant biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Basidiomycota (physiology)</term><term>Genetic Markers (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Genome-Wide Association Study (MeSH)</term><term>Hordeum (genetics)</term><term>Hordeum (microbiology)</term><term>Plant Diseases (genetics)</term><term>Plant Stems (MeSH)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Quantitative Trait Loci (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Basidiomycota (physiologie)</term><term>Génome végétal (MeSH)</term><term>Hordeum (génétique)</term><term>Hordeum (microbiologie)</term><term>Locus de caractère quantitatif (MeSH)</term><term>Maladies des plantes (génétique)</term><term>Marqueurs génétiques (MeSH)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Tiges de plante (MeSH)</term><term>Étude d'association pangénomique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Genetic Markers</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Hordeum</term><term>Plant Diseases</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Hordeum</term><term>Maladies des plantes</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Hordeum</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Hordeum</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Basidiomycota</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Basidiomycota</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genome, Plant</term><term>Genome-Wide Association Study</term><term>Plant Stems</term><term>Polymorphism, Single Nucleotide</term><term>Quantitative Trait Loci</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Génome végétal</term><term>Locus de caractère quantitatif</term><term>Marqueurs génétiques</term><term>Polymorphisme de nucléotide simple</term><term>Tiges de plante</term><term>Étude d'association pangénomique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Stem rust (SR) is one of the most economically devastating barley diseases in Kazakhstan, and in some years it causes up to 50 % of yield losses. Routine conventional breeding for resistance to stem rust is almost always in progress in all Kazakhstan breeding stations. However, molecular marker based approach towards new SR resistance genes identification and relevant marker-assisted selection had never been employed in Kazakhstan yet. In this study, as a preliminary step the GWAS (genome-wide association study) mapping was applied in attempt to identify reliable SNP markers and quantitative trait loci (QTL) associated with resistance to SR.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>Barley collection of 92 commercial cultivars and promising lines was genotyped using a high-throughput single nucleotide polymorphism (9,000 SNP) Illumina iSelect array. 6,970 SNPs out of 9,000 total were polymorphic and scorable. 5,050 SNPs out of 6,970 passed filtering threshold and were used for association mapping (AM). All 92 accessions were phenotyped for resistance to SR by observing adult plants in artificially infected plots at the Research Institute for Biological Safety Problems in Dzhambul region of Kazakhstan. GLM analysis allowed the identification of 15 SNPs associated with the resistance at the heading time (HA) phase, and 2 SNPs at the seed's milky-waxy maturity (SM) phase. However, after application of 5 % Bonferroni multiple test correction, only 2 SNPs at the HA stage on the same position of chromosome 6H can be claimed as reliable markers for SR resistance. The MLM analysis after the Bonferroni correction did not reveal any associations in this study, although distribution lines in the quantile-quantile (QQ) plot indicates that overcorrection in the test due to both Q and K matrices usage.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>Obtained data suggest that genome wide genotyping of 92 spring barley accessions from Kazakhstan with 9 K Illumina SNP array was highly efficient. Linkage disequilibrium based mapping approach allowed the identification of highly significant QTL for the SR resistance at the HA phase of growth on chromosome 6H. On the other hand, no significant QTL was detected at the SM phase, assuming that for a successful GWASmapping experiment a larger size population with more diverse genetic background should be tested. Obtained results provide additional information towards better understanding of SR resistance in barley.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26821649</PMID><DateCompleted><Year>2016</Year><Month>09</Month><Day>22</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2229</ISSN><JournalIssue CitedMedium="Internet"><Volume>16 Suppl 1</Volume><PubDate><Year>2016</Year><Month>Jan</Month><Day>27</Day></PubDate></JournalIssue><Title>BMC plant biology</Title><ISOAbbreviation>BMC Plant Biol</ISOAbbreviation></Journal><ArticleTitle>Genome-wide association study on stem rust resistance in Kazakh spring barley lines.</ArticleTitle><Pagination><MedlinePgn>6</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12870-015-0686-z</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Stem rust (SR) is one of the most economically devastating barley diseases in Kazakhstan, and in some years it causes up to 50 % of yield losses. Routine conventional breeding for resistance to stem rust is almost always in progress in all Kazakhstan breeding stations. However, molecular marker based approach towards new SR resistance genes identification and relevant marker-assisted selection had never been employed in Kazakhstan yet. In this study, as a preliminary step the GWAS (genome-wide association study) mapping was applied in attempt to identify reliable SNP markers and quantitative trait loci (QTL) associated with resistance to SR.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Barley collection of 92 commercial cultivars and promising lines was genotyped using a high-throughput single nucleotide polymorphism (9,000 SNP) Illumina iSelect array. 6,970 SNPs out of 9,000 total were polymorphic and scorable. 5,050 SNPs out of 6,970 passed filtering threshold and were used for association mapping (AM). All 92 accessions were phenotyped for resistance to SR by observing adult plants in artificially infected plots at the Research Institute for Biological Safety Problems in Dzhambul region of Kazakhstan. GLM analysis allowed the identification of 15 SNPs associated with the resistance at the heading time (HA) phase, and 2 SNPs at the seed's milky-waxy maturity (SM) phase. However, after application of 5 % Bonferroni multiple test correction, only 2 SNPs at the HA stage on the same position of chromosome 6H can be claimed as reliable markers for SR resistance. The MLM analysis after the Bonferroni correction did not reveal any associations in this study, although distribution lines in the quantile-quantile (QQ) plot indicates that overcorrection in the test due to both Q and K matrices usage.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Obtained data suggest that genome wide genotyping of 92 spring barley accessions from Kazakhstan with 9 K Illumina SNP array was highly efficient. Linkage disequilibrium based mapping approach allowed the identification of highly significant QTL for the SR resistance at the HA phase of growth on chromosome 6H. On the other hand, no significant QTL was detected at the SM phase, assuming that for a successful GWASmapping experiment a larger size population with more diverse genetic background should be tested. Obtained results provide additional information towards better understanding of SR resistance in barley.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Turuspekov</LastName><ForeName>Yerlan</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan. yerlant@yahoo.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ormanbekova</LastName><ForeName>Danara</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan. or.danara@gmail.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rsaliev</LastName><ForeName>Aralbek</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Research Institute for Biological Safety Problems, Gvardeiskiy vil, Dzhambul region, Kazakhstan. aralbek@mail.ru.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Abugalieva</LastName><ForeName>Saule</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan. absaule@yahoo.com.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>01</Month><Day>27</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Plant Biol</MedlineTA><NlmUniqueID>100967807</NlmUniqueID><ISSNLinking>1471-2229</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005819">Genetic Markers</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001487" MajorTopicYN="N">Basidiomycota</DescriptorName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005819" MajorTopicYN="N">Genetic Markers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055106" MajorTopicYN="Y">Genome-Wide Association Study</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001467" MajorTopicYN="N">Hordeum</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018547" MajorTopicYN="N">Plant Stems</DescriptorName></MeshHeading><MeshHeading><DescriptorName 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d'Almaty"><name sortKey="Turuspekov, Yerlan" sort="Turuspekov, Yerlan" uniqKey="Turuspekov Y" first="Yerlan" last="Turuspekov">Yerlan Turuspekov</name></region><name sortKey="Abugalieva, Saule" sort="Abugalieva, Saule" uniqKey="Abugalieva S" first="Saule" last="Abugalieva">Saule Abugalieva</name><name sortKey="Ormanbekova, Danara" sort="Ormanbekova, Danara" uniqKey="Ormanbekova D" first="Danara" last="Ormanbekova">Danara Ormanbekova</name><name sortKey="Rsaliev, Aralbek" sort="Rsaliev, Aralbek" uniqKey="Rsaliev A" first="Aralbek" last="Rsaliev">Aralbek Rsaliev</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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