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

BACKGROUND: 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. 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. RESULTS: Most 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 (F(ST)) at individual loci showed a high level of heterogeneity across the genome. In addition, seven genomic regions with elevated F(ST) 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). CONCLUSIONS: Genome- 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.

Molecular and biochemical characterisation of polyphenol oxidases in developing kernels and senescing leaves of wheat (Triticum aestivum).

Polyphenol oxidases (PPOs) have been implicated in plant defence reactions. From an applied point of view, high PPO activity is associated with browning / darkening of fresh and processed food. Owing to its complex genome and economic importance, wheat (Triticum aestivum L.) represents an interesting system to advance our understanding of plant PPO function. We have previously shown that wheat PPOs are organised in a multigene family, consisting of two distinct phylogenetic clusters with three members each. In this study, we demonstrate that members of one cluster are not expressed in developing kernels or senescing flag leaves. Transcriptional regulation of one major gene in the other cluster largely controls PPO levels in these tissues, at least in the wheat varieties used for this study. Our data further indicate that the product of this gene is present as a latent enzyme during early kernel development, and that the latent enzyme is activated during later developmental phases. Enzyme activation can be achieved in vitro by limited tryptic digestion, but our data do not indicate activation by a proteolytic mechanism in vivo. Together, results presented in this study provide important insights into the regulation of wheat PPO function.