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

Creator: Sehgal, D.
Creator: Mondal, S.
Creator: Crespo-Herrera, L.A.
Creator: Velu, G.
Creator: Juliana, P.
Creator: Huerta-Espino, J.
Creator: Shrestha, S.
Creator: Poland, J.A.
Creator: Singh, R.P.
Creator: Dreisigacker, S.
Year: 2020
URI: https://hdl.handle.net/10883/21095
Language: English
Publisher: Frontiers
Copyright: CIMMYT 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
Type: Article
Place of Publication: Switzerland
Volume: 11
DOI: 10.3389/fgene.2020.589490
Keywords: Haplotype Blocks
Keywords: Haplotype-Based GWAS
Keywords: Genotyping by Sequencing
Keywords: Elite Yield Trials
Keywords: Heat Map
Description: We 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.
Agrovoc: GENOMES
Agrovoc: GENOMICS
Agrovoc: PLANT BREEDING
Agrovoc: SPRING WHEAT
Related Datasets: https://hdl.handle.net/11529/10548504
ISSN: 1664-8021
Journal: Frontiers in Genetics
Article number: 589490


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  • Wheat
    Wheat - breeding, phytopathology, physiology, quality, biotech

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