Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.)

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.

Association mapping for photosynthesis and yield traits under two moisture conditions and their drought indices in winter bread wheat (Triticum aestivum L.) using SSR markers

“…The D-genome exhibited the highest extent of LD decay distance as compared to A and B genomes. Similar results were also reported in a previous study on wheat genotypes (Chao et al, 2010). More extended LD decay distance in the D-genome than in the A and B genomes could be due to the introduction of new haplotype, which can increase the extent of LD from Aegilops tauschii (D-genome donor) into the Dgenome of hexaploid wheat.…”

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

“…Low genetic differentiation between landraces and modern cultivars suggests that selection during wheat breeding, when we consider the total population, has not dramatically altered allele frequency genome-wide, but may have been accomplished by selection on a relatively limited number of loci. At the same time strong geographic differentiation among wheat populations found in the current and previously published studies (25)(26)(27)(28) and the relatedness of landraces and cultivars suggest that the use of distinct founders as well as allele-frequency divergence from the ancestral population of landraces could have contributed to the development of regional breeding populations. Relatively few alleles were exclusive to to wheat cultivars.…”

“…Although multiple studies have reported the genetic basis of individual phenotypes associated with wheat improvement and adaptation (9,12,(20)(21)(22)(23)(24) or sought to characterize the structure of genetic variation in regional populations (25)(26)(27)(28), the genome-scale impact of selection for improvement on the patterns of genetic variation in wheat remains largely unknown. Here we performed single-nucleotide polymorphism (SNP) discovery in the wheat transcriptome and developed a high-throughput SNP genotyping array.…”

Analysis of Genetic Diversity in Synthetic Wheat Assemblage (T. turgidum^|^times;Aegilops tauschii; 2n=6x=42; AABBDD) for Winter Wheat Breeding

“…However, several variations in the LD pattern of the germplasm reflected a complexity of the evolutionary and breeding history of wheat (Dubcovsky and Dvorak 2007). The lower values of LD observed in WSHs are in concordance of what has been previously reported by Chao et al (2010) using the SNP marker system. They reported that CIMMYT wheat populations with the lowest LD among completely linked loci and the slowest rate of LD decay was possibly a consequence of an intensive use of synthetic wheat lines.…”

“…A number of LD-based mapping and diversity studies in wheat have been conducted at the genome or chromosome levels (Breseghello and Sorrells 2006, Chao et al 2007, Somers et al 2004, Horvath et al 2009, Chao et al 2010, Hao et al 2011, Maccaferri et al 2011. Nevertheless it is important to characterize germplasm for examining the extent of LD to study the genetic diversity.…”