Understanding the introgression process from Aegilops tauschii into hexaploid wheat through identity by descent analysis and its effect on genetic diversity

Wild relatives of hexaploid wheat (Triticum aestivum) are the reservoirs of novel allelic diversity with great potential to improve many agronomic traits in wheat. Here, we investigated the genome-wide patterns and efficiency of Aegilops tauschii allele introgression into the winter wheat cultivars. The introgression population of 351 BC1F3:5 lines was selected based on phenology and development characteristics from crosses between six hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. Complexity reduced genomic library sequencing was used to develop SNP markers and infer the regions of identity-by-descent and the boundaries of the introgressed segments. Using a diverse panel of 116 Ae. tauschii accessions, it was possible to infer that introgression lines had single or multiple IBD segments from accessions of diverse geographic origin. Introgression frequency was high at the ends of chromosomes and low in the large pericentromeric 2/3 of the chromosome arms characterized by low crossover rate. While the effect of selection for free-threshing genotypes was evident around the domestication gene Tg, reduction in the frequency of introgression was limited to relatively small regions flanking the gene. These results suggest that the effects of phenotypic selection on the introgressed wild relative9s alleles at the early generations of population development are strongly influenced by the distribution of crossover frequency across genome, consistent with the Hill-Robertson effect. Our study offers insights into the introgression population development to ensure retention of genetic diversity across entire genome and presents a resource that will be valuable for deploying wild relative diversity in breeding programs to create climate resilient and disease resistant varieties with improved yield and quality traits.