Multi-locus genome-wide association studies (ML-GWAS) reveal novel genomic regions associated with seedling and adult plant stage leaf rust resistance in bread wheat (Triticum aestivum L.)
Leaf rust is one of the important diseases limiting global wheat production and productivity. To identify quantitative trait nucleotides (QTNs) or genomic regions associated with seedling and adult plant leaf rust resistance, multilocus genome-wide association studies (ML-GWAS) were performed on a p...
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| Veröffentlicht in: | Heredity 2022-06, Vol.128 (6), p.434-449 |
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| creator | Vikas, V K Pradhan, Anjan Kumar Budhlakoti, Neeraj Mishra, Dwijesh Chandra Chandra, Tilak Bhardwaj, S C Kumar, Subodh Sivasamy, M Jayaprakash, P Nisha, R Shajitha, P Peter, John Geetha, M Mir, Reyazul Rouf Singh, Kuldeep Kumar, Sundeep |
| description | Leaf rust is one of the important diseases limiting global wheat production and productivity. To identify quantitative trait nucleotides (QTNs) or genomic regions associated with seedling and adult plant leaf rust resistance, multilocus genome-wide association studies (ML-GWAS) were performed on a panel of 400 diverse wheat genotypes using 35 K single-nucleotide polymorphism (SNP) genotyping assays and trait data of leaf rust resistance. Association analyses using six multi-locus GWAS models revealed a set of 201 significantly associated QTNs for seedling and 65 QTNs for adult plant resistance (APR), explaining 1.98-31.72% of the phenotypic variation for leaf rust. Among these QTNs, 51 reliable QTNs for seedling and 15 QTNs for APR were consistently detected in at least two GWAS models and were considered reliable QTNs. Three genomic regions were pleiotropic, each controlling two to three pathotype-specific seedling resistances to leaf rust. We also identified candidate genes, such as leucine-rich repeat receptor-like (LRR) protein kinases, P-loop containing nucleoside triphosphate hydrolase and serine-threonine/tyrosine-protein kinases (STPK), which have a role in pathogen recognition and disease resistance linked to the significantly associated genomic regions. The QTNs identified in this study can prove useful in wheat molecular breeding programs aimed at enhancing resistance to leaf rust and developing next-generation leaf rust-resistant varieties. |
| doi_str_mv | 10.1038/s41437-022-00525-1 |
| format | Article |
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To identify quantitative trait nucleotides (QTNs) or genomic regions associated with seedling and adult plant leaf rust resistance, multilocus genome-wide association studies (ML-GWAS) were performed on a panel of 400 diverse wheat genotypes using 35 K single-nucleotide polymorphism (SNP) genotyping assays and trait data of leaf rust resistance. Association analyses using six multi-locus GWAS models revealed a set of 201 significantly associated QTNs for seedling and 65 QTNs for adult plant resistance (APR), explaining 1.98-31.72% of the phenotypic variation for leaf rust. Among these QTNs, 51 reliable QTNs for seedling and 15 QTNs for APR were consistently detected in at least two GWAS models and were considered reliable QTNs. Three genomic regions were pleiotropic, each controlling two to three pathotype-specific seedling resistances to leaf rust. We also identified candidate genes, such as leucine-rich repeat receptor-like (LRR) protein kinases, P-loop containing nucleoside triphosphate hydrolase and serine-threonine/tyrosine-protein kinases (STPK), which have a role in pathogen recognition and disease resistance linked to the significantly associated genomic regions. The QTNs identified in this study can prove useful in wheat molecular breeding programs aimed at enhancing resistance to leaf rust and developing next-generation leaf rust-resistant varieties.</description><identifier>ISSN: 0018-067X</identifier><identifier>EISSN: 1365-2540</identifier><identifier>DOI: 10.1038/s41437-022-00525-1</identifier><identifier>PMID: 35418669</identifier><language>eng</language><publisher>England: Springer Nature B.V</publisher><subject>Basidiomycota - genetics ; Bread ; Chromosome Mapping ; Crop production ; Disease resistance ; Disease Resistance - genetics ; Gene polymorphism ; Genome-wide association studies ; Genome-Wide Association Study ; Genomes ; Genomics ; Genotypes ; Genotyping ; Hydrolase ; Kinases ; Leaf rust ; Leaves ; Leucine ; Loci ; Nucleotides ; Phenotypic variations ; Plant breeding ; Plant Diseases - genetics ; Plant resistance ; Plants ; Polymorphism ; Protein kinase ; Protein Kinases ; Proteins ; Seedlings ; Seedlings - genetics ; Single-nucleotide polymorphism ; Threonine ; Triticum - genetics ; Tyrosine ; Wheat</subject><ispartof>Heredity, 2022-06, Vol.128 (6), p.434-449</ispartof><rights>2022. The Author(s), under exclusive licence to The Genetics Society.</rights><rights>The Author(s), under exclusive licence to The Genetics Society 2022.</rights><rights>The Author(s), under exclusive licence to The Genetics Society 2022</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c430t-4ef7a30eafea314bca44747cc81a7df06adebbe14e4f97c566e34780a443eabe3</citedby><cites>FETCH-LOGICAL-c430t-4ef7a30eafea314bca44747cc81a7df06adebbe14e4f97c566e34780a443eabe3</cites><orcidid>0000-0002-3196-211X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9177675/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9177675/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,315,728,781,785,886,27929,27930,53796,53798</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35418669$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Vikas, V K</creatorcontrib><creatorcontrib>Pradhan, Anjan Kumar</creatorcontrib><creatorcontrib>Budhlakoti, Neeraj</creatorcontrib><creatorcontrib>Mishra, Dwijesh Chandra</creatorcontrib><creatorcontrib>Chandra, Tilak</creatorcontrib><creatorcontrib>Bhardwaj, S C</creatorcontrib><creatorcontrib>Kumar, Subodh</creatorcontrib><creatorcontrib>Sivasamy, M</creatorcontrib><creatorcontrib>Jayaprakash, P</creatorcontrib><creatorcontrib>Nisha, R</creatorcontrib><creatorcontrib>Shajitha, P</creatorcontrib><creatorcontrib>Peter, John</creatorcontrib><creatorcontrib>Geetha, M</creatorcontrib><creatorcontrib>Mir, Reyazul Rouf</creatorcontrib><creatorcontrib>Singh, Kuldeep</creatorcontrib><creatorcontrib>Kumar, Sundeep</creatorcontrib><title>Multi-locus genome-wide association studies (ML-GWAS) reveal novel genomic regions associated with seedling and adult plant stage leaf rust resistance in bread wheat (Triticum aestivum L.)</title><title>Heredity</title><addtitle>Heredity (Edinb)</addtitle><description>Leaf rust is one of the important diseases limiting global wheat production and productivity. To identify quantitative trait nucleotides (QTNs) or genomic regions associated with seedling and adult plant leaf rust resistance, multilocus genome-wide association studies (ML-GWAS) were performed on a panel of 400 diverse wheat genotypes using 35 K single-nucleotide polymorphism (SNP) genotyping assays and trait data of leaf rust resistance. Association analyses using six multi-locus GWAS models revealed a set of 201 significantly associated QTNs for seedling and 65 QTNs for adult plant resistance (APR), explaining 1.98-31.72% of the phenotypic variation for leaf rust. Among these QTNs, 51 reliable QTNs for seedling and 15 QTNs for APR were consistently detected in at least two GWAS models and were considered reliable QTNs. Three genomic regions were pleiotropic, each controlling two to three pathotype-specific seedling resistances to leaf rust. 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The QTNs identified in this study can prove useful in wheat molecular breeding programs aimed at enhancing resistance to leaf rust and developing next-generation leaf rust-resistant varieties.</description><subject>Basidiomycota - genetics</subject><subject>Bread</subject><subject>Chromosome Mapping</subject><subject>Crop production</subject><subject>Disease resistance</subject><subject>Disease Resistance - genetics</subject><subject>Gene polymorphism</subject><subject>Genome-wide association studies</subject><subject>Genome-Wide Association Study</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotypes</subject><subject>Genotyping</subject><subject>Hydrolase</subject><subject>Kinases</subject><subject>Leaf rust</subject><subject>Leaves</subject><subject>Leucine</subject><subject>Loci</subject><subject>Nucleotides</subject><subject>Phenotypic variations</subject><subject>Plant breeding</subject><subject>Plant Diseases - genetics</subject><subject>Plant 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genome-wide association studies (ML-GWAS) reveal novel genomic regions associated with seedling and adult plant stage leaf rust resistance in bread wheat (Triticum aestivum L.)</title><author>Vikas, V K ; Pradhan, Anjan Kumar ; Budhlakoti, Neeraj ; Mishra, Dwijesh Chandra ; Chandra, Tilak ; Bhardwaj, S C ; Kumar, Subodh ; Sivasamy, M ; Jayaprakash, P ; Nisha, R ; Shajitha, P ; Peter, John ; Geetha, M ; Mir, Reyazul Rouf ; Singh, Kuldeep ; Kumar, Sundeep</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c430t-4ef7a30eafea314bca44747cc81a7df06adebbe14e4f97c566e34780a443eabe3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Basidiomycota - genetics</topic><topic>Bread</topic><topic>Chromosome Mapping</topic><topic>Crop production</topic><topic>Disease resistance</topic><topic>Disease Resistance - genetics</topic><topic>Gene polymorphism</topic><topic>Genome-wide association 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diseases limiting global wheat production and productivity. To identify quantitative trait nucleotides (QTNs) or genomic regions associated with seedling and adult plant leaf rust resistance, multilocus genome-wide association studies (ML-GWAS) were performed on a panel of 400 diverse wheat genotypes using 35 K single-nucleotide polymorphism (SNP) genotyping assays and trait data of leaf rust resistance. Association analyses using six multi-locus GWAS models revealed a set of 201 significantly associated QTNs for seedling and 65 QTNs for adult plant resistance (APR), explaining 1.98-31.72% of the phenotypic variation for leaf rust. Among these QTNs, 51 reliable QTNs for seedling and 15 QTNs for APR were consistently detected in at least two GWAS models and were considered reliable QTNs. Three genomic regions were pleiotropic, each controlling two to three pathotype-specific seedling resistances to leaf rust. We also identified candidate genes, such as leucine-rich repeat receptor-like (LRR) protein kinases, P-loop containing nucleoside triphosphate hydrolase and serine-threonine/tyrosine-protein kinases (STPK), which have a role in pathogen recognition and disease resistance linked to the significantly associated genomic regions. The QTNs identified in this study can prove useful in wheat molecular breeding programs aimed at enhancing resistance to leaf rust and developing next-generation leaf rust-resistant varieties.</abstract><cop>England</cop><pub>Springer Nature B.V</pub><pmid>35418669</pmid><doi>10.1038/s41437-022-00525-1</doi><tpages>16</tpages><orcidid>https://orcid.org/0000-0002-3196-211X</orcidid><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; Nature; EZB-FREE-00999 freely available EZB journals; PubMed Central; Alma/SFX Local Collection |
| subjects | Basidiomycota - genetics Bread Chromosome Mapping Crop production Disease resistance Disease Resistance - genetics Gene polymorphism Genome-wide association studies Genome-Wide Association Study Genomes Genomics Genotypes Genotyping Hydrolase Kinases Leaf rust Leaves Leucine Loci Nucleotides Phenotypic variations Plant breeding Plant Diseases - genetics Plant resistance Plants Polymorphism Protein kinase Protein Kinases Proteins Seedlings Seedlings - genetics Single-nucleotide polymorphism Threonine Triticum - genetics Tyrosine Wheat |
| title | Multi-locus genome-wide association studies (ML-GWAS) reveal novel genomic regions associated with seedling and adult plant stage leaf rust resistance in bread wheat (Triticum aestivum L.) |
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