Journal article
Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars
Proceedings of the National Academy of Sciences - PNAS, Vol.110(20), pp.8057-8062
2013
Handle:
https://hdl.handle.net/2376/101103
PMCID: PMC3657823
PMID: 23630259
Abstract
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.
Metrics
12 Record Views
Details
- Title
- Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars
- Creators
- Colin R Cavanagh - Commonwealth Scientific and Industrial Research Organisation [Canberra]Deven See - United States Department of AgricultureShiaoman Chao - United States Department of AgricultureMichael Pumphrey - Department of Crop and Soil SciencesShichen Wang - Department of Plant PathologyMarta Lopez da Silva - International Maize and Wheat Improvement CenterBevan Emma Huang - Commonwealth Scientific and Industrial Research Organisation [Canberra]Arron Carter - Department of Crop and Soil SciencesStuart Stephen - Commonwealth Scientific and Industrial Research Organisation [Canberra]Seifollah Kiani - Department of Plant PathologyKerrie Forrest - Victorian AgriBiosciences CenterCyrille Saintenac - Department of Plant PathologyGina L Brown-Guedira - United States Department of AgricultureAlina Akhunova - Department of Plant PathologyGuihua Bai - USDA-ARS : Agricultural Research ServiceLuxmi Tomar - Chaudhary Charan Singh Haryana Agricultural UniversityDebbie Wong - Victorian AgriBiosciences CenterStephan Kong - Victorian AgriBiosciences CenterMatthew Reynolds - International Maize and Wheat Improvement CenterHarold Bockelman - USDA-ARS : Agricultural Research ServiceLuther Talbert - Montana State UniversityJames A Anderson - Department of Agronomy and Plant GeneticsSusanne Dreisigacker - International Maize and Wheat Improvement CenterStephen Baenziger - University of Nebraska [Lincoln]Viktor Korzun - KWS Lochow GmbHPeter Laurent Morrell - Department of Agronomy and Plant GeneticsJorge Dubcovsky - Department of Plant SciencesMatthew K Morell - Commonwealth Scientific and Industrial Research Organisation [Canberra]Mark E Sorrells - Cornell UniversityMatthew J Hayden - Victorian AgriBiosciences CenterEduard Akhunov - Department of Plant Pathology
- Publication Details
- Proceedings of the National Academy of Sciences - PNAS, Vol.110(20), pp.8057-8062
- Academic Unit
- Department of Plant Pathology ; Department of Veterinary Microbiology and Pathology; Department of Crop and Soil Sciences
- Publisher
- National Academy of Sciences
- Identifiers
- 99900546691601842
- Language
- English
- Resource Type
- Journal article