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...

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Vydáno v:Proceedings of the National Academy of Sciences - PNAS Ročník 110; číslo 20; s. 8057
Hlavní autoři: Cavanagh, Colin R, Chao, Shiaoman, Wang, Shichen, Huang, Bevan Emma, Stephen, Stuart, Kiani, Seifollah, Forrest, Kerrie, Saintenac, Cyrille, Brown-Guedira, Gina L, Akhunova, Alina, See, Deven, Bai, Guihua, Pumphrey, Michael, Tomar, Luxmi, Wong, Debbie, Kong, Stephan, Reynolds, Matthew, da Silva, Marta Lopez, Bockelman, Harold, Talbert, Luther, Anderson, James A, Dreisigacker, Susanne, Baenziger, Stephen, Carter, Arron, Korzun, Viktor, Morrell, Peter Laurent, Dubcovsky, Jorge, Morell, Matthew K, Sorrells, Mark E, Hayden, Matthew J, Akhunov, Eduard
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States 14.05.2013
Témata:
Alleles
Crops, Agricultural - genetics
Gene Frequency
Genes, Plant
Genetic Variation
Genome, Plant
Genotype
Haplotypes
Oligonucleotide Array Sequence Analysis
Ploidies
Polymorphism, Single Nucleotide
Triticum - genetics
polyploid wheat
selection scans
wheat improvement
SNP genotyping
breeding history
ISSN:1091-6490, 1091-6490
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Shrnutí: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.
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ISSN:1091-6490
1091-6490
DOI:10.1073/pnas.1217133110