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

Domesticated 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-nucle...

ver descrição completa

Detalhes bibliográficos
Autores: Cavanagh, C.R., Shiaoman Chao, Shichen Wang, Huang, B.E., Stephen, S., Kiani, S., Forrest, K.L., Saintenac, C., Brown-Guedira, G., Akhunova, A., See, D., Guihua Bai, Pumphrey, M., Tomar, L., Wong, D., Kong, S., Reynolds, M.P., Lopes, M., Bockelman, H., Talbert, L.E., Anderson, J., Dreisigacker, S., Baenziger, P.S., Carter, A., Korzun, V., Morrell, P.L., Dubcovsky, J., Morell, M.K., Sorrells, M.E., Hayden, M., Akhunov, E.
Tipo de documento: artigo
Estado:Versão publicada
Data de publicação:2013
País:México
Recursos:Centro Internacional de Mejoramiento de Maíz y Trigo
Repositório:Repositorio Institucional de Publicaciones Multimedia del CIMMYT
OAI Identifier:oai:repository.cimmyt.org:10883/3303
Acesso em linha:http://hdl.handle.net/10883/3303
Access Level:Acceso aberto
Palavra-chave:AGRICULTURAL SCIENCES AND BIOTECHNOLOGY
SNP Genotyping
Polyploid Wheat
Selection Scans
Breeding History
SINGLE NUCLEOTIDE POLYMORPHISM
GENOTYPES
POLYPLOIDY
WHEAT
SELECTION
CROP IMPROVEMENT
PLANT BREEDING
HISTORY
id MX_7e65951f1bbb30676b58cbafd2e65e2f
oai_identifier_str oai:repository.cimmyt.org:10883/3303
network_acronym_str MX
network_name_str México
repository_id_str
spelling Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivarsCavanagh, C.R.Shiaoman ChaoShichen WangHuang, B.E.Stephen, S.Kiani, S.Forrest, K.L.Saintenac, C.Brown-Guedira, G.Akhunova, A.See, D.Guihua BaiPumphrey, M.Tomar, L.Wong, D.Kong, S.Reynolds, M.P.Lopes, M.Bockelman, H.Talbert, L.E.Anderson, J.Dreisigacker, S.Baenziger, P.S.Carter, A.Korzun, V.Morrell, P.L.Dubcovsky, J.Morell, M.K.Sorrells, M.E.Hayden, M.Akhunov, E.AGRICULTURAL SCIENCES AND BIOTECHNOLOGYSNP GenotypingPolyploid WheatSelection ScansBreeding HistorySINGLE NUCLEOTIDE POLYMORPHISMGENOTYPESPOLYPLOIDYWHEATSELECTIONCROP IMPROVEMENTPLANT BREEDINGHISTORYDomesticated 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.8057-8062National Academy of Scienceshttp://www.pnas.org/content/early/2013/04/26/12171331102013-11-25T02:37:42Z2013-11-25T02:37:42Z2013info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlePDFapplication/pdf0027-8424http://hdl.handle.net/10883/330310.1073/pnas.121713311020110Proceedings of the National Academy of Sciences of the United States of Americareponame:Repositorio Institucional de Publicaciones Multimedia del CIMMYTinstname:Centro Internacional de Mejoramiento de Maíz y Trigoinstacron:CIMMYTEnglishCIMMYT 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.Open Accessinfo:eu-repo/semantics/openAccessoai:repository.cimmyt.org:10883/33032024-10-11T19:57:52Z
dc.title.none.fl_str_mv Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars
title Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars
spellingShingle Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars
Cavanagh, C.R.
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY
SNP Genotyping
Polyploid Wheat
Selection Scans
Breeding History
SINGLE NUCLEOTIDE POLYMORPHISM
GENOTYPES
POLYPLOIDY
WHEAT
SELECTION
CROP IMPROVEMENT
PLANT BREEDING
HISTORY
title_short Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars
title_full Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars
title_fullStr Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars
title_full_unstemmed Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars
title_sort Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars
dc.creator.none.fl_str_mv Cavanagh, C.R.
Shiaoman Chao
Shichen Wang
Huang, B.E.
Stephen, S.
Kiani, S.
Forrest, K.L.
Saintenac, C.
Brown-Guedira, G.
Akhunova, A.
See, D.
Guihua Bai
Pumphrey, M.
Tomar, L.
Wong, D.
Kong, S.
Reynolds, M.P.
Lopes, M.
Bockelman, H.
Talbert, L.E.
Anderson, J.
Dreisigacker, S.
Baenziger, P.S.
Carter, A.
Korzun, V.
Morrell, P.L.
Dubcovsky, J.
Morell, M.K.
Sorrells, M.E.
Hayden, M.
Akhunov, E.
author Cavanagh, C.R.
author_facet Cavanagh, C.R.
Shiaoman Chao
Shichen Wang
Huang, B.E.
Stephen, S.
Kiani, S.
Forrest, K.L.
Saintenac, C.
Brown-Guedira, G.
Akhunova, A.
See, D.
Guihua Bai
Pumphrey, M.
Tomar, L.
Wong, D.
Kong, S.
Reynolds, M.P.
Lopes, M.
Bockelman, H.
Talbert, L.E.
Anderson, J.
Dreisigacker, S.
Baenziger, P.S.
Carter, A.
Korzun, V.
Morrell, P.L.
Dubcovsky, J.
Morell, M.K.
Sorrells, M.E.
Hayden, M.
Akhunov, E.
author_role author
author2 Shiaoman Chao
Shichen Wang
Huang, B.E.
Stephen, S.
Kiani, S.
Forrest, K.L.
Saintenac, C.
Brown-Guedira, G.
Akhunova, A.
See, D.
Guihua Bai
Pumphrey, M.
Tomar, L.
Wong, D.
Kong, S.
Reynolds, M.P.
Lopes, M.
Bockelman, H.
Talbert, L.E.
Anderson, J.
Dreisigacker, S.
Baenziger, P.S.
Carter, A.
Korzun, V.
Morrell, P.L.
Dubcovsky, J.
Morell, M.K.
Sorrells, M.E.
Hayden, M.
Akhunov, E.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv AGRICULTURAL SCIENCES AND BIOTECHNOLOGY
SNP Genotyping
Polyploid Wheat
Selection Scans
Breeding History
SINGLE NUCLEOTIDE POLYMORPHISM
GENOTYPES
POLYPLOIDY
WHEAT
SELECTION
CROP IMPROVEMENT
PLANT BREEDING
HISTORY
topic AGRICULTURAL SCIENCES AND BIOTECHNOLOGY
SNP Genotyping
Polyploid Wheat
Selection Scans
Breeding History
SINGLE NUCLEOTIDE POLYMORPHISM
GENOTYPES
POLYPLOIDY
WHEAT
SELECTION
CROP IMPROVEMENT
PLANT BREEDING
HISTORY
description Domesticated 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.
publishDate 2013
dc.date.none.fl_str_mv 2013-11-25T02:37:42Z
2013-11-25T02:37:42Z
2013
dc.type.none.fl_str_mv info:eu-repo/semantics/publishedVersion
info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv 0027-8424
http://hdl.handle.net/10883/3303
10.1073/pnas.1217133110
identifier_str_mv 0027-8424
10.1073/pnas.1217133110
url http://hdl.handle.net/10883/3303
dc.language.none.fl_str_mv English
language_invalid_str_mv English
dc.rights.none.fl_str_mv Open Access
info:eu-repo/semantics/openAccess
rights_invalid_str_mv Open Access
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv PDF
application/pdf
dc.publisher.none.fl_str_mv National Academy of Sciences
http://www.pnas.org/content/early/2013/04/26/1217133110
publisher.none.fl_str_mv National Academy of Sciences
http://www.pnas.org/content/early/2013/04/26/1217133110
dc.source.none.fl_str_mv 20
110
Proceedings of the National Academy of Sciences of the United States of America
reponame:Repositorio Institucional de Publicaciones Multimedia del CIMMYT
instname:Centro Internacional de Mejoramiento de Maíz y Trigo
instacron:CIMMYT
instname_str Centro Internacional de Mejoramiento de Maíz y Trigo
instacron_str CIMMYT
institution CIMMYT
reponame_str Repositorio Institucional de Publicaciones Multimedia del CIMMYT
collection Repositorio Institucional de Publicaciones Multimedia del CIMMYT
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1858175865928548352
score 15.811543

Registros relacionados