title: Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars.
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.
authors: Commonwealth Scientific and Industrial Research Organization, Plant Industry and Food Futures National Research Flagship, Canberra, ACT 2601, Australia.
authors: Colin R
authors: CR
authors: Cavanagh
authors: Shiaoman
authors: S
authors: Chao
authors: Shichen
authors: S
authors: Wang
authors: Bevan Emma
authors: BE
authors: Huang
authors: Stuart
authors: S
authors: Stephen
authors: Seifollah
authors: S
authors: Kiani
authors: Kerrie
authors: K
authors: Forrest
authors: Cyrille
authors: C
authors: Saintenac
authors: Gina L
authors: GL
authors: Brown-Guedira
authors: Alina
authors: A
authors: Akhunova
authors: Deven
authors: D
authors: See
authors: Guihua
authors: G
authors: Bai
authors: Michael
authors: M
authors: Pumphrey
authors: Luxmi
authors: L
authors: Tomar
authors: Debbie
authors: D
authors: Wong
authors: Stephan
authors: S
authors: Kong
authors: Matthew
authors: M
authors: Reynolds
authors: Marta Lopez
authors: ML
authors: da Silva
authors: Harold
authors: H
authors: Bockelman
authors: Luther
authors: L
authors: Talbert
authors: James A
authors: JA
authors: Anderson
authors: Susanne
authors: S
authors: Dreisigacker
authors: Stephen
authors: S
authors: Baenziger
authors: Arron
authors: A
authors: Carter
authors: Viktor
authors: V
authors: Korzun
authors: Peter Laurent
authors: PL
authors: Morrell
authors: Jorge
authors: J
authors: Dubcovsky
authors: Matthew K
authors: MK
authors: Morell
authors: Mark E
authors: ME
authors: Sorrells
authors: Matthew J
authors: MJ
authors: Hayden
authors: Eduard
authors: E
authors: Akhunov
mesh_terms: D000483:Alleles; D018556:Crops, Agricultural / Q000235:genetics; D005787:Gene Frequency; D017343:Genes, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D005838:Genotype; D006239:Haplotypes; D020411:Oligonucleotide Array Sequence Analysis; D011003:Ploidies; D020641:Polymorphism, Single Nucleotide; D014908:Triticum / Q000235:genetics*
keywords: SNP genotyping; breeding history; polyploid wheat; selection scans; wheat improvement
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