Haplotype-based, genome-wide association study reveals stable genomic regions for grain yield in CIMMYT spring bread wheat

dc.creatorSehgal, D.
dc.creatorMondal, S.
dc.creatorCrespo Herrera, L.A.
dc.creatorVelu, G.
dc.creatorJuliana, P.
dc.creatorHuerta-Espino, J.
dc.creatorShrestha, S.
dc.creatorPoland, J.A.
dc.creatorSingh, R.P.
dc.creatorDreisigacker, S.
dc.date2021-01-12T01:20:15Z
dc.date2021-01-12T01:20:15Z
dc.date2020
dc.date.accessioned2023-07-17T20:06:36Z
dc.date.available2023-07-17T20:06:36Z
dc.identifierhttps://hdl.handle.net/10883/21095
dc.identifier10.3389/fgene.2020.589490
dc.identifier.urihttps://repositorioslatinoamericanos.uchile.cl/handle/2250/7512881
dc.descriptionWe untangled key regions of the genetic architecture of grain yield (GY) in CIMMYT spring bread wheat by conducting a haplotype-based, genome-wide association study (GWAS), together with an investigation of epistatic interactions using seven large sets of elite yield trials (EYTs) consisting of a total of 6,461 advanced breeding lines. These lines were phenotyped under irrigated and stress environments in seven growing seasons (2011–2018) and genotyped with genotyping-by-sequencing markers. Genome-wide 519 haplotype blocks were constructed, using a linkage disequilibrium-based approach covering 14,036 Mb in the wheat genome. Haplotype-based GWAS identified 7, 4, 10, and 15 stable (significant in three or more EYTs) associations in irrigated (I), mild drought (MD), severe drought (SD), and heat stress (HS) testing environments, respectively. Considering all EYTs and the four testing environments together, 30 stable associations were deciphered with seven hotspots identified on chromosomes 1A, 1B, 2B, 4A, 5B, 6B, and 7B, where multiple haplotype blocks were associated with GY. Epistatic interactions contributed significantly to the genetic architecture of GY, explaining variation of 3.5–21.1%, 3.7–14.7%, 3.5–20.6%, and 4.4– 23.1% in I, MD, SD, and HS environments, respectively. Our results revealed the intricate genetic architecture of GY, controlled by both main and epistatic effects. The importance of these results for practical applications in the CIMMYT breeding program is discussed.
dc.languageEnglish
dc.publisherFrontiers
dc.relationhttps://hdl.handle.net/11529/10548504
dc.rightsCIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose
dc.rightsOpen Access
dc.source11
dc.source1664-8021
dc.sourceFrontiers in Genetics
dc.source589490
dc.subjectAGRICULTURAL SCIENCES AND BIOTECHNOLOGY
dc.subjectHaplotype Blocks
dc.subjectHaplotype-Based GWAS
dc.subjectGenotyping by Sequencing
dc.subjectElite Yield Trials
dc.subjectHeat Map
dc.subjectGENOMES
dc.subjectGENOMICS
dc.subjectPLANT BREEDING
dc.subjectSPRING WHEAT
dc.titleHaplotype-based, genome-wide association study reveals stable genomic regions for grain yield in CIMMYT spring bread wheat
dc.typeArticle
dc.typePublished Version
dc.coverageSwitzerland


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