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Breeding-assisted genomics: applying meta- GWAS for milling and baking quality in CIMMYT wheat breeding program

Author: Battenfield, S.D.
Author: Sheridan, J.L.
Author: Silva, L.D.C.E.
Author: Miclaus, K.J.
Author: Dreisigacker, S.
Author: Wolfinger, R.D.
Author: Peña Bautista, R.J.
Author: Singh, R.P.
Author: Jackson, E.W.
Author: Fritz, A.K.
Author: Guzman, C.
Author: Poland, J.A.
Year: 2018
ISSN: 1932-6203
ISSN: ESSN: 1932-6203
Descriptors: Breeding
Descriptors: Genomics
Descriptors: Wheats
Abstract: One of the biggest challenges for genetic studies on natural or unstructured populations is the unbalanced datasets where individuals are measured at different times and environments. This problem is also common in crop and animal breeding where many individuals are only evaluated for a single year and large but unbalanced datasets can be generated over multiple years. Many wheat breeding programs have focused on increasing bread wheat (Triticum aestivum L.) yield, but processing and end-use quality are critical components when considering its use in feeding the rising population of the next century. The challenges with end-use quality trait improvements are high cost and seed amounts for testing, the latter making selection in early breeding populations impossible. Here we describe a novel approach to identify marker-trait associations within a breeding program using a meta-genome wide association study (GWAS), which combines GWAS analysis from multiyear unbalanced breeding nurseries, in a manner reflecting meta-GWAS in humans. This method facilitated mapping of processing and end-use quality phenotypes from advanced breeding lines (n = 4,095) of the CIMMYT bread wheat breeding program from 2009 to 2014. Using the meta-GWAS we identified marker-trait associations, allele effects, candidate genes, and can select using markers generated in this process. Finally, the scope of this approach can be broadly applied in ‘breeding-assisted genomics’ across many crops to greatly increase our functional understanding of plant genomes.
Language: English
Publisher: Public Library of Science
Publisher: Public Library of Science
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 indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the sutable license for that purpose.
Type: Article
Place: San Francisco, Calif., U.S.
Pages: art. e0204757
Journal issue: 11
Journal: PLoS One
Journal volume: 13
DOI: 10.1371/journal.pone.0204757
Keywords: Haplotypes
Keywords: Genome-Wide Association Studies
Keywords: Nutrient And Storage Proteins
dc.relation.CRP: Wheat
Agrovoc: WHEAT
Agrovoc: WHEAT
Agrovoc: BREAD
Agrovoc: FLOUR
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  • Wheat
    Wheat - breeding, phytopathology, physiology, quality, biotech

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