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Identifying loci with breeding potential across temperate and tropical adaptation via EigenGWAS and EnvGWAS

Author: Jing Li
Author: Gou-Bo Chen
Author: Rasheed, A.
Author: Delin Li
Author: Sonder, K.
Author: Zavala Espinosa, C.
Author: Jiankang Wang
Author: Costich, D.E.
Author: Schnable, P.S.
Author: Hearne, S.
Author: Huihui Li
Year: 2019
ISSN: 0962-1083
Abstract: Understanding the genomic basis of adaptation in maize is important for gene discovery and the improvement of breeding germplasm, but much remains a mystery in spite of significant population genetics and archaeological research. Identifying the signals underpinning adaptation are challenging as adaptation often coincided with genetic drift, and the base genomic diversity of the species in massive. In this study, tGBS technology was used to genotype 1,143 diverse maize accessions including landraces collected from 20 countries and elite breeding lines of tropical lowland, highland, subtropical/midaltitude and temperate ecological zones. Based on 355,442 high-quality single nucleotide polymorphisms, 13 genomic regions were detected as being under selection using the bottom-up searching strategy, EigenGWAS. Of the 13 selection regions, 10 were first reported, two were associated with environmental parameters via EnvGWAS, and 146 genes were enriched. Combining large-scale genomic and ecological data in this diverse maize panel, our study supports a polygenic adaptation model of maize and offers a framework to enhance our understanding of both the mechanistic basis and the evolutionary consequences of maize domestication and adaptation. The regions identified here are promising candidates for further, targeted exploration to identify beneficial alleles and haplotypes for deployment in maize breeding.
Language: English
Publisher: Wiley
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 suitable license for that purpose.
Type: Article
Place: United Kingdom
Pages: 3544–3560
Issue: 15
Journal: Molecular Ecology
Volume: 28
DOI: 10.1111/mec.15169
Keywords: EigenGWAS
Keywords: EnvGWAS
Agrovoc: MAIZE
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This item appears in the following Collection(s)

  • Genetic Resources
    Genetic Resources including germplasm collections, wild relatives, genotyping, genomics, and IP
  • Socioeconomics
    Including topics such as farming systems, markets, impact & targeting, innovations, and GIS
  • Wheat
    Wheat - breeding, phytopathology, physiology, quality, biotech

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