Abstract
BackgroundSingle nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. Here, we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and population structure in a panel of 478 spring and winter wheat cultivars (Triticum aestivum) from 17 populations across the United States and Mexico.ResultsMost of the wheat oligo pool assay (OPA) SNPs that were polymorphic within the complete set of 478 cultivars were also polymorphic in all subpopulations. Higher levels of genetic differentiation were observed among wheat lines within populations than among populations. A total of nine genetically distinct clusters were identified, suggesting that some of the pre-defined populations shared significant proportion of genetic ancestry. Estimates of population structure (FST) at individual loci showed a high level of heterogeneity across the genome. In addition, seven genomic regions with elevated FST were detected between the spring and winter wheat populations. Some of these regions overlapped with previously mapped flowering time QTL. Across all populations, the highest extent of significant LD was observed in the wheat D-genome, followed by lower LD in the A- and B-genomes. The differences in the extent of LD among populations and genomes were mostly driven by differences in long-range LD ( > 10 cM).ConclusionsGenome- and population-specific patterns of genetic differentiation and LD were discovered in the populations of wheat cultivars from different geographic regions. Our study demonstrated that the estimates of population structure between spring and winter wheat lines can identify genomic regions harboring candidate genes involved in the regulation of growth habit. Variation in LD suggests that breeding and selection had a different impact on each wheat genome both within and among populations. The higher extent of LD in the wheat D-genome versus the A- and B-genomes likely reflects the episodes of recent introgression and population bottleneck accompanying the origin of hexaploid wheat. The assessment of LD and population structure in this assembled panel of diverse lines provides critical information for the development of genetic resources for genome-wide association mapping of agronomically important traits in wheat.
Highlights
Single nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments
Genetic diversity and population structure Our study provides an overview of genetic variation in US and CIMMYT spring and winter wheat cultivars using genome-wide distributed SNP markers
Such a widespread distribution of polymorphic loci among populations suggests that the SNP discovery performed in a set of genetically diverse wheat landraces and wild emmer wheat [19,36] was successful in recovering alleles represented in both growth habit groups
Summary
Single nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. The level of genetic diversity and linkage disequilibrium (LD) can be affected by various factors including demography and inbreeding [1,2,3,4,5,6], selection for favorable alleles [7,8], domestication [2,9,10], outcrossing of crop cultivars with genetically distinct lines of wild ancestors and landraces [1,11,12] and admixture [13,14]. The population bottleneck that accompanied tetraploid emmer wheat domestication about 10,000 years ago [17] reduced nucleotide diversity by 30 to 50% in the A- and B-genomes, depending on the study and diversity measure used [15,18]. The D-genome shows higher levels of LD than the A- and B-genomes [19,22]
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