Application of Haplotype-Based Genetics in Wheat

The complex pattern of haplotype blocks in crop genomes is defined by the interplay of conscious and unconscious selection, demographic events and recombination rate variation. The haplotype map of the wheat genome was developed using the high-density genotyping data generated using the 90K wheat iSelect genotyping chip, whole exome capture assay and genotyping-by-sequencing (GBS). This map was applied to detect the targets of selection, inferring the ancestry of chromosomal segments in wheat cultivars and performing imputation of missing genotypes in whole-genome genotyping experiments. In order to fully utilize high-density genotyping data, we applied a “chromosome painting” approach that uses information about linkage disequilibrium to identify shared haplotypes and build a co-ancestry matrix for inferring fine-scale population structure. Chromosome painting was used to trace the ancestry of haplotypes in modern cultivars by comparing recipient haplotypes with the contributing donor populations of landraces. By applying statistical tests detecting regions of genome showing reduced diversity and excessive haplotype sharing we have identified the targets of selection associated with development of modern cultivars. By combining the high-quality 90K iSelect genotyping with GBS we tested the efficiency of different genotype imputation approaches. The power of association scans was increased after genotype imputation demonstrating that with the availability of the reference genome sequence and high-density haplotypic data GBS can be effectively utilized for genome-wide association study in polyploid wheat. This study demonstrates that the developed high-density SNP variation map provides a powerful tool for the detailed population genetic analyses and studying the impact of genotypic variation on the manifestation of agronomic phenotypes in wheat.