Genome-wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments
KEY MESSAGE : Through genome-wide association study, loci for grain yield and yield components were identified in chromosomes 5A and 6A in spring wheat (Triticum aestivum). Genome-wide association study (GWAS) was conducted for grain yield (YLD) and yield components on a wheat association mapping in...
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| Veröffentlicht in: | Theoretical and applied genetics 2015-02, Vol.128 (2), p.353-363 |
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| creator | Sukumaran, Sivakumar Dreisigacker, Susanne Lopes, Marta Chavez, Perla Reynolds, Matthew P |
| description | KEY MESSAGE : Through genome-wide association study, loci for grain yield and yield components were identified in chromosomes 5A and 6A in spring wheat (Triticum aestivum). Genome-wide association study (GWAS) was conducted for grain yield (YLD) and yield components on a wheat association mapping initiative (WAMI) population of 287 elite, spring wheat lines grown under temperate irrigated high-yield potential condition in Ciudad Obregón, Mexico, during four crop cycles (from 2009–2010 to 2012–2013). The population was genotyped with high-density Illumina iSelect 90K single nucleotide polymorphisms (SNPs) assay. An analysis of traits across subpopulations indicated that lines with 1B/1R translocation had higher YLD, grain weight, and taller plants than lines without the translocation. GWAS using 18,704 SNPs identified 31 loci that explained 5–14 % of the variation in individual traits. We identified SNPs in chromosome 5A and 6A that were significantly associated with yield and yield components. Four loci were detected for YLD in chromosomes 3B, 5A, 5B, and 6A and the locus in 5A explained 5 % of the variation for grain number/m². The locus for YLD in chromosome 6A also explained 6 % of the variation in grain weight. Loci significantly associated with maturity were identified in chromosomes 2B, 3B, 4B, 4D, and 6A and for plant height in 1A and 6A. Loci were also detected for canopy temperature at grain filling (2D, 4D, 6A), chlorophyll index at grain filling (3B and 6A), biomass (3D and 6A) and harvest index (1D, 1B, and 3B) that explained 5–10 % variation. These markers will be further validated. |
| doi_str_mv | 10.1007/s00122-014-2435-3 |
| format | Article |
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Genome-wide association study (GWAS) was conducted for grain yield (YLD) and yield components on a wheat association mapping initiative (WAMI) population of 287 elite, spring wheat lines grown under temperate irrigated high-yield potential condition in Ciudad Obregón, Mexico, during four crop cycles (from 2009–2010 to 2012–2013). The population was genotyped with high-density Illumina iSelect 90K single nucleotide polymorphisms (SNPs) assay. An analysis of traits across subpopulations indicated that lines with 1B/1R translocation had higher YLD, grain weight, and taller plants than lines without the translocation. GWAS using 18,704 SNPs identified 31 loci that explained 5–14 % of the variation in individual traits. We identified SNPs in chromosome 5A and 6A that were significantly associated with yield and yield components. Four loci were detected for YLD in chromosomes 3B, 5A, 5B, and 6A and the locus in 5A explained 5 % of the variation for grain number/m². The locus for YLD in chromosome 6A also explained 6 % of the variation in grain weight. Loci significantly associated with maturity were identified in chromosomes 2B, 3B, 4B, 4D, and 6A and for plant height in 1A and 6A. Loci were also detected for canopy temperature at grain filling (2D, 4D, 6A), chlorophyll index at grain filling (3B and 6A), biomass (3D and 6A) and harvest index (1D, 1B, and 3B) that explained 5–10 % variation. These markers will be further validated.</description><identifier>ISSN: 0040-5752</identifier><identifier>EISSN: 1432-2242</identifier><identifier>DOI: 10.1007/s00122-014-2435-3</identifier><identifier>PMID: 25490985</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer-Verlag</publisher><subject>Agricultural production ; Agricultural research ; Agriculture ; Biochemistry ; biomass ; Biomedical and Life Sciences ; Biotechnology ; canopy ; Chlorophyll ; Chromosome Mapping ; Chromosomes ; Crop yields ; DNA, Plant - genetics ; Environmental aspects ; filling period ; Genes ; Genetic aspects ; Genetic Association Studies ; Genetic Markers ; Genetic research ; Genome-wide association studies ; Genomes ; Genotype ; grain yield ; Growth ; Growth (Plants) ; harvest index ; irrigation ; Life Sciences ; Linkage Disequilibrium ; loci ; Models, Genetic ; Original Paper ; Phenology ; Phenotype ; Plant Biochemistry ; Plant Breeding/Biotechnology ; Plant Genetics and Genomics ; Polymorphism, Single Nucleotide ; Quantitative trait loci ; Quantitative Trait, Heritable ; Seeds - growth & development ; single nucleotide polymorphism ; spring wheat ; temperature ; Triticum - genetics ; Triticum - growth & development ; Triticum aestivum ; Wheat</subject><ispartof>Theoretical and applied genetics, 2015-02, Vol.128 (2), p.353-363</ispartof><rights>Springer-Verlag Berlin Heidelberg 2014</rights><rights>COPYRIGHT 2015 Springer</rights><rights>Springer-Verlag Berlin Heidelberg 2015</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c714t-8ec0a1e5296e7699dbe5671c0ac4054ef589dcaabdd7002b76248216a34cfb213</citedby><cites>FETCH-LOGICAL-c714t-8ec0a1e5296e7699dbe5671c0ac4054ef589dcaabdd7002b76248216a34cfb213</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00122-014-2435-3$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00122-014-2435-3$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25490985$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Sukumaran, Sivakumar</creatorcontrib><creatorcontrib>Dreisigacker, Susanne</creatorcontrib><creatorcontrib>Lopes, Marta</creatorcontrib><creatorcontrib>Chavez, Perla</creatorcontrib><creatorcontrib>Reynolds, Matthew P</creatorcontrib><title>Genome-wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments</title><title>Theoretical and applied genetics</title><addtitle>Theor Appl Genet</addtitle><addtitle>Theor Appl Genet</addtitle><description>KEY MESSAGE : Through genome-wide association study, loci for grain yield and yield components were identified in chromosomes 5A and 6A in spring wheat (Triticum aestivum). Genome-wide association study (GWAS) was conducted for grain yield (YLD) and yield components on a wheat association mapping initiative (WAMI) population of 287 elite, spring wheat lines grown under temperate irrigated high-yield potential condition in Ciudad Obregón, Mexico, during four crop cycles (from 2009–2010 to 2012–2013). The population was genotyped with high-density Illumina iSelect 90K single nucleotide polymorphisms (SNPs) assay. An analysis of traits across subpopulations indicated that lines with 1B/1R translocation had higher YLD, grain weight, and taller plants than lines without the translocation. GWAS using 18,704 SNPs identified 31 loci that explained 5–14 % of the variation in individual traits. We identified SNPs in chromosome 5A and 6A that were significantly associated with yield and yield components. Four loci were detected for YLD in chromosomes 3B, 5A, 5B, and 6A and the locus in 5A explained 5 % of the variation for grain number/m². The locus for YLD in chromosome 6A also explained 6 % of the variation in grain weight. Loci significantly associated with maturity were identified in chromosomes 2B, 3B, 4B, 4D, and 6A and for plant height in 1A and 6A. Loci were also detected for canopy temperature at grain filling (2D, 4D, 6A), chlorophyll index at grain filling (3B and 6A), biomass (3D and 6A) and harvest index (1D, 1B, and 3B) that explained 5–10 % variation. These markers will be further validated.</description><subject>Agricultural production</subject><subject>Agricultural research</subject><subject>Agriculture</subject><subject>Biochemistry</subject><subject>biomass</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>canopy</subject><subject>Chlorophyll</subject><subject>Chromosome Mapping</subject><subject>Chromosomes</subject><subject>Crop yields</subject><subject>DNA, Plant - genetics</subject><subject>Environmental aspects</subject><subject>filling period</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic Association Studies</subject><subject>Genetic Markers</subject><subject>Genetic research</subject><subject>Genome-wide association studies</subject><subject>Genomes</subject><subject>Genotype</subject><subject>grain yield</subject><subject>Growth</subject><subject>Growth (Plants)</subject><subject>harvest index</subject><subject>irrigation</subject><subject>Life Sciences</subject><subject>Linkage Disequilibrium</subject><subject>loci</subject><subject>Models, Genetic</subject><subject>Original Paper</subject><subject>Phenology</subject><subject>Phenotype</subject><subject>Plant Biochemistry</subject><subject>Plant Breeding/Biotechnology</subject><subject>Plant Genetics and Genomics</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Quantitative trait loci</subject><subject>Quantitative Trait, Heritable</subject><subject>Seeds - growth & development</subject><subject>single nucleotide polymorphism</subject><subject>spring wheat</subject><subject>temperature</subject><subject>Triticum - genetics</subject><subject>Triticum - growth & development</subject><subject>Triticum aestivum</subject><subject>Wheat</subject><issn>0040-5752</issn><issn>1432-2242</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqNkl9r1TAYxoso7jj9AN5owBu96EzS_Gkvx9A5GAjOXYe0eVsz2uSYpDueL-FnNrVzeEREchF483seeN48RfGc4BOCsXwbMSaUlpiwkrKKl9WDYkNYRUtKGX1YbDBmuOSS06PiSYw3GGPKcfW4OKKcNbip-ab4fg7OT1DurAGkY_Sd1cl6h2KazR71PqAhaOvQ3sJokHYGBRh1AoNSnqeI8pt2CEabAMVtsG5Auy-gE9r67TyuZkPwO7eQCaYthCxHNgQ7_PQBd2uDdxO4FJ8Wj3o9Rnh2dx8X1-_ffT77UF5-PL84O70sO0lYKmvosCbAaSNAiqYxLXAhSR52DHMGPa8b02ndGiNz6FYKympKhK5Y17eUVMfF69V3G_zXGWJSk40djKN24OeoiBB5d3UlxX-gPC-fcFFl9NUf6I2fg8tBMsVknb8re95Tgx5BWdf7vMluMVWnDAsiKtrwTJ38hcrHwGQ776C3eX4geHMgyEyCb2nQc4zq4urTIUtWtgs-xgC9yh836bBXBKulWmqtlsrVUku11BLuxV24uZ3A3Ct-dSkDdAXWFkD4Lf0_XF-uol57pYdgo7q-opjwXNZGNlxWPwBD8OFI</recordid><startdate>20150201</startdate><enddate>20150201</enddate><creator>Sukumaran, Sivakumar</creator><creator>Dreisigacker, Susanne</creator><creator>Lopes, Marta</creator><creator>Chavez, Perla</creator><creator>Reynolds, Matthew P</creator><general>Springer-Verlag</general><general>Springer Berlin Heidelberg</general><general>Springer</general><general>Springer Nature B.V</general><scope>FBQ</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>ISR</scope><scope>3V.</scope><scope>7SS</scope><scope>7TK</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20150201</creationdate><title>Genome-wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments</title><author>Sukumaran, Sivakumar ; Dreisigacker, Susanne ; Lopes, Marta ; Chavez, Perla ; Reynolds, Matthew P</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c714t-8ec0a1e5296e7699dbe5671c0ac4054ef589dcaabdd7002b76248216a34cfb213</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Agricultural production</topic><topic>Agricultural research</topic><topic>Agriculture</topic><topic>Biochemistry</topic><topic>biomass</topic><topic>Biomedical and Life Sciences</topic><topic>Biotechnology</topic><topic>canopy</topic><topic>Chlorophyll</topic><topic>Chromosome Mapping</topic><topic>Chromosomes</topic><topic>Crop yields</topic><topic>DNA, Plant - 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Academic</collection><jtitle>Theoretical and applied genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sukumaran, Sivakumar</au><au>Dreisigacker, Susanne</au><au>Lopes, Marta</au><au>Chavez, Perla</au><au>Reynolds, Matthew P</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments</atitle><jtitle>Theoretical and applied genetics</jtitle><stitle>Theor Appl Genet</stitle><addtitle>Theor Appl Genet</addtitle><date>2015-02-01</date><risdate>2015</risdate><volume>128</volume><issue>2</issue><spage>353</spage><epage>363</epage><pages>353-363</pages><issn>0040-5752</issn><eissn>1432-2242</eissn><abstract>KEY MESSAGE : Through genome-wide association study, loci for grain yield and yield components were identified in chromosomes 5A and 6A in spring wheat (Triticum aestivum). Genome-wide association study (GWAS) was conducted for grain yield (YLD) and yield components on a wheat association mapping initiative (WAMI) population of 287 elite, spring wheat lines grown under temperate irrigated high-yield potential condition in Ciudad Obregón, Mexico, during four crop cycles (from 2009–2010 to 2012–2013). The population was genotyped with high-density Illumina iSelect 90K single nucleotide polymorphisms (SNPs) assay. An analysis of traits across subpopulations indicated that lines with 1B/1R translocation had higher YLD, grain weight, and taller plants than lines without the translocation. GWAS using 18,704 SNPs identified 31 loci that explained 5–14 % of the variation in individual traits. We identified SNPs in chromosome 5A and 6A that were significantly associated with yield and yield components. Four loci were detected for YLD in chromosomes 3B, 5A, 5B, and 6A and the locus in 5A explained 5 % of the variation for grain number/m². The locus for YLD in chromosome 6A also explained 6 % of the variation in grain weight. Loci significantly associated with maturity were identified in chromosomes 2B, 3B, 4B, 4D, and 6A and for plant height in 1A and 6A. Loci were also detected for canopy temperature at grain filling (2D, 4D, 6A), chlorophyll index at grain filling (3B and 6A), biomass (3D and 6A) and harvest index (1D, 1B, and 3B) that explained 5–10 % variation. These markers will be further validated.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer-Verlag</pub><pmid>25490985</pmid><doi>10.1007/s00122-014-2435-3</doi><tpages>11</tpages></addata></record> |
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| subjects | Agricultural production Agricultural research Agriculture Biochemistry biomass Biomedical and Life Sciences Biotechnology canopy Chlorophyll Chromosome Mapping Chromosomes Crop yields DNA, Plant - genetics Environmental aspects filling period Genes Genetic aspects Genetic Association Studies Genetic Markers Genetic research Genome-wide association studies Genomes Genotype grain yield Growth Growth (Plants) harvest index irrigation Life Sciences Linkage Disequilibrium loci Models, Genetic Original Paper Phenology Phenotype Plant Biochemistry Plant Breeding/Biotechnology Plant Genetics and Genomics Polymorphism, Single Nucleotide Quantitative trait loci Quantitative Trait, Heritable Seeds - growth & development single nucleotide polymorphism spring wheat temperature Triticum - genetics Triticum - growth & development Triticum aestivum Wheat |
| title | Genome-wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments |
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