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

Author
item CAVANAGH, COLIN - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item Chao, Shiaoman
item WANG, SHICHEN - Kansas State University
item HUANG, BEVAN - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item STEPHAN, STUART - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item KIANI, SEIFOLLAH - Kansas State University
item FORREST, KERRIE - Queensland Department Of Primary Industries & Fisheries
item SAINTENAC, CYRILLE - Kansas State University
item Brown-Guedira, Gina
item AKHUNOVA, ALINA - Kansas State University
item See, Deven
item Bai, Guihua
item Pumphrey, Michael
item TOMAR, LUXMI - Haryana Agricultural University
item WONG, DEBBIE - Department Of Primary Industries
item KONG, STEPHAN - Department Of Primary Industries
item REYNOLDS, MATTHEW - International Maize & Wheat Improvement Center (CIMMYT)
item LOPEZ DA SILVA, MARTA - International Maize & Wheat Improvement Center (CIMMYT)
item Bockelman, Harold
item TALBERT, LUTHER - Montana State University
item ANDERSON, JAMES - University Of Minnesota
item DREISIGACKER, SUSANNE - International Maize & Wheat Improvement Center (CIMMYT)
item BAENZIGER, STEPHEN - University Of Nebraska
item CARTER, ARRON - Washington State University
item KORZUN, VIKTOR - Kws Saat Ag
item MORRELL, PETER - University Of Minnesota
item DUBCOVSKY, JORGE - University Of California
item MORELL, MATTHEW - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item SORRELLS, MARK - Cornell University - New York
item HAYDEN, MATTHEW - Department Of Primary Industries
item AKHUNOV, EDUARD - Kansas State University

Submitted to: Proceedings of the National Academy of Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/25/2013
Publication Date: 5/14/2013
Publication URL: http://handle.nal.usda.gov/10113/57900
Citation: Cavanagh, C., Chao, S., Wang, S., Huang, B.E., Stephan, S., Kiani, S., Forrest, K., Saintenac, C., Brown Guedira, G.L., Akhunova, A., See, D.R., Bai, G., Pumphrey, M.O., Tomar, L., Wong, D., Kong, S., Reynolds, M., Lopez Da Silva, M., Bockelman, H.E., Talbert, L., Anderson, J.A., Dreisigacker, S., Baenziger, S., Carter, A., Korzun, V., Morrell, P.L., Dubcovsky, J., Morell, M., Sorrells, M., Hayden, M., Akhunov, E. 2013. Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landrace and cultivars. Proceedings of the National Academy of Sciences. 110:8057-8062.

Interpretive Summary: Domesticated crops have experienced strong human-driven selection aimed at the development of improved 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 DNA markers based on single nucleotide differences, known as single nucleotide polymorphisms (SNPs), in a worldwide sample of 2,994 accessions of hexaploid wheat including landraces and modern cultivars. The genetic locations of 7500 of those SNPs on 21 wheat chromosomes were determined and were the basis for this study. The results from genetic diversity analyses showed that wheat improvement has mainly relied on preexisting variation in landraces, and the transition from landraces to cultivars has had little effect on diversity. The analyses further revealed that genetic variation present in cultivars was mainly explained by the geographic origin of breeding pools, and that chromosomal regions targeted by selection for wheat improvement have changed over time, potentially reflecting breeding efforts aimed at developing higher yielding varieties adapted to new or changing local conditions. The limited usage of exotic germplasm for wheat improvement as found in this study provides an important take home message in that breeders can broaden the genetic diversity by integrating landraces and wild relatives in their efforts on wheat improvement.

Technical Abstract: Domesticated crops have experienced strong human-driven selection aimed at the development of improved 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 DNA markers based on single nucleotide differences, known as single nucleotide polymorphisms (SNPs), in a worldwide sample of 2,994 accessions of hexaploid wheat including landraces and modern cultivars. The genetic locations of 7500 of those SNPs on 21 wheat chromosomes were determined and were the basis for this study. The results from genetic diversity analyses showed that wheat improvement has mainly relied on preexisting variation in landraces, and the transition from landraces to cultivars has had little effect on diversity. The analyses further revealed that genetic variation present in cultivars was mainly explained by the geographic origin of breeding pools, and that chromosomal regions targeted by selection for wheat improvement have changed over time, potentially reflecting breeding efforts aimed at developing higher yielding varieties adapted to new or changing local conditions. The limited usage of exotic germplasm for wheat improvement as found in this study provides an important take home message in that breeders can broaden the genetic diversity by integrating landraces and wild relatives in their efforts on wheat improvement.