An integrated framework reinstating the environmental dimension for GWAS and genomic selection in crops

dc.creatorXianran Li
dc.creatorTingting Guo
dc.creatorJinyu Wang
dc.creatorBekele, W.A.
dc.creatorSukumaran, S.
dc.creatorVanous, A.E.
dc.creatorMcNellie, J.P.
dc.creatorCortes, L.T.
dc.creatorLopes, M.S.
dc.creatorLamkey, K.R.
dc.creatorWestgate, M.E.
dc.creatorMcKay, J.K.
dc.creatorArchontoulis, S.V.
dc.creatorReynolds, M.P.
dc.creatorTinker, N. A.
dc.creatorSchnable, P.S.
dc.creatorJianming Yu
dc.date2021-05-07T00:20:14Z
dc.date2021-05-07T00:20:14Z
dc.date2021
dc.date.accessioned2023-07-17T20:07:42Z
dc.date.available2023-07-17T20:07:42Z
dc.identifierhttps://hdl.handle.net/10883/21499
dc.identifier10.1016/j.molp.2021.03.010
dc.identifier.urihttps://repositorioslatinoamericanos.uchile.cl/handle/2250/7513280
dc.descriptionIdentifying mechanisms and pathways involved in gene–environment interplay and phenotypic plasticity is a long-standing challenge. It is highly desirable to establish an integrated framework with an environmental dimension for complex trait dissection and prediction. A critical step is to identify an environmental index that is both biologically relevant and estimable for new environments. With extensive field-observed complex traits, environmental profiles, and genome-wide single nucleotide polymorphisms for three major crops (maize, wheat, and oat), we demonstrated that identifying such an environmental index (i.e., a combination of environmental parameter and growth window) enables genome-wide association studies and genomic selection of complex traits to be conducted with an explicit environmental dimension. Interestingly, genes identified for two reaction-norm parameters (i.e., intercept and slope) derived from flowering time values along the environmental index were less colocalized for a diverse maize panel than for wheat and oat breeding panels, agreeing with the different diversity levels and genetic constitutions of the panels. In addition, we showcased the usefulness of this framework for systematically forecasting the performance of diverse germplasm panels in new environments. This general framework and the companion CERIS-JGRA analytical package should facilitate biologically informed dissection of complex traits, enhanced performance prediction in breeding for future climates, and coordinated efforts to enrich our understanding of mechanisms underlying phenotypic variation.
dc.description874-887
dc.languageEnglish
dc.publisherCell Press
dc.relationhttps://www.cell.com/molecular-plant/fulltext/S1674-2052(21)00085-X?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS167420522100085X%3Fshowall%3Dtrue#supplementaryMaterial
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.source6
dc.source14
dc.source1752-9866
dc.sourceMolecular Plant
dc.subjectAGRICULTURAL SCIENCES AND BIOTECHNOLOGY
dc.subjectPhenotypic Plasticity
dc.subjectGenome-Wide Association Study
dc.subjectGenomic Selection
dc.subjectFlowering Time
dc.subjectReaction Norm
dc.subjectPHENOTYPIC PLASTICITY
dc.subjectGENOTYPE ENVIRONMENT INTERACTION
dc.subjectMARKER-ASSISTED SELECTION
dc.subjectFLOWERING
dc.titleAn integrated framework reinstating the environmental dimension for GWAS and genomic selection in crops
dc.typeArticle
dc.typePublished Version
dc.coverageUSA


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