Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars

dc.creatorCavanagh, C.R.
dc.creatorShiaoman Chao
dc.creatorShichen Wang
dc.creatorHuang, B.E.
dc.creatorStephen, S.
dc.creatorKiani, S.
dc.creatorForrest, K.L.
dc.creatorSaintenac, C.
dc.creatorBrown-Guedira, G.L.
dc.creatorAkhunova, A.
dc.creatorSee, D.
dc.creatorBai, G.
dc.creatorPumphrey, M.
dc.creatorTomar, L.
dc.creatorWong, D.
dc.creatorKong, S.
dc.creatorReynolds, M.P.
dc.creatorLopes, M.
dc.creatorBockelman, H.
dc.creatorTalbert, L.
dc.creatorAnderson, J.A.
dc.creatorDreisigacker, S.
dc.creatorBaenziger, P.S.
dc.creatorCarter, A.
dc.creatorKorzun, V.
dc.creatorMorrell, P.L.
dc.creatorDubcovsky, J.
dc.creatorMorell, M.K.
dc.creatorSorrells, M.E.
dc.creatorHayden, M.
dc.creatorAkhunov, E.
dc.date2013-11-25T02:37:42Z
dc.date2013-11-25T02:37:42Z
dc.date2013
dc.date.accessioned2023-07-17T19:57:21Z
dc.date.available2023-07-17T19:57:21Z
dc.identifier0027-8424
dc.identifierhttp://hdl.handle.net/10883/3303
dc.identifier10.1073/pnas.1217133110
dc.identifier.urihttps://repositorioslatinoamericanos.uchile.cl/handle/2250/7509117
dc.descriptionDomesticated crops experience strong human-mediated selection aimed at developing high-yielding varieties adapted to local conditions. To detect regions of the wheat genome subject to selection during improvement, we developed a high-throughput array to interrogate 9,000 gene-associated single-nucleotide polymorphisms (SNP) in a worldwide sample of 2,994 accessions of hexaploid wheat including landraces and modern cultivars. Using a SNP-based diversity map we characterized the impact of crop improvement on genomic and geographic patterns of genetic diversity. We found evidence of a small population bottleneck and extensive use of ancestral variation often traceable to founders of cultivars from diverse geographic regions. Analyzing genetic differentiation among populations and the extent of haplotype sharing, we identified allelic variants subjected to selection during improvement. Selective sweeps were found around genes involved in the regulation of flowering time and phenology. An introgression of a wild relative-derived gene conferring resistance to a fungal pathogen was detected by haplotype-based analysis. Comparing selective sweeps identified in different populations, we show that selection likely acts on distinct targets or multiple functionally equivalent alleles in different portions of the geographic range of wheat. The majority of the selected alleles were present at low frequency in local populations, suggesting either weak selection pressure or temporal variation in the targets of directional selection during breeding probably associated with changing agricultural practices or environmental conditions. The developed SNP chip and map of genetic variation provide a resource for advancing wheat breeding and supporting future population genomic and genome-wide association studies in wheat.
dc.description8057-8062
dc.formatPDF
dc.languageEnglish
dc.publisherNational Academy of Sciences
dc.publisherhttp://www.pnas.org/content/early/2013/04/26/1217133110
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.source20
dc.source110
dc.sourceProceedings of the National Academy of Sciences of the United States of America
dc.subjectAGRICULTURAL SCIENCES AND BIOTECHNOLOGY
dc.subjectSNP Genotyping
dc.subjectPolyploid Wheat
dc.subjectSelection Scans
dc.subjectBreeding History
dc.subjectSINGLE NUCLEOTIDE POLYMORPHISM
dc.subjectGENOTYPES
dc.subjectPOLYPLOIDY
dc.subjectWHEAT
dc.subjectSELECTION
dc.subjectCROP IMPROVEMENT
dc.subjectPLANT BREEDING
dc.subjectHISTORY
dc.titleGenome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars
dc.typeArticle


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