16Wild relatives of hexaploid wheat (Triticum aestivum) are the reservoirs of novel allelic 17 diversity with great potential to improve many agronomic traits in wheat. Here, we 18 investigated the genome-wide patterns and efficiency of Aegilops tauschii allele introgression 19 into the winter wheat cultivars. The introgression population of 351 BC 1 F 3 : 5 lines was 20 selected based on phenology and development characteristics from crosses between six 21 hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. Complexity reduced genomic 22 library sequencing was used to develop SNP markers and infer the regions of identity-by-23 descent and the boundaries of the introgressed segments. Using a diverse panel of 116 Ae. 24 tauschii accessions, it was possible to infer that introgression lines had single or multiple IBD 25 segments from accessions of diverse geographic origin. Introgression frequency was high at 26 the ends of chromosomes and low in the large pericentromeric 2/3 of the chromosome arms 27 characterized by low crossover rate. While the effect of selection for free-threshing genotypes 28 was evident around the domestication gene Tg, reduction in the frequency of introgression 29 was limited to relatively small regions flanking the gene. These results suggest that the 30 effects of phenotypic selection on the introgressed wild relative's alleles at the early 31 generations of population development are strongly influenced by the distribution of 32 crossover frequency across genome, consistent with the Hill-Robertson effect. Our study 33 offers insights into the introgression population development to ensure retention of genetic 34 2 diversity across entire genome and presents a resource that will be valuable for deploying 35 wild relative diversity in breeding programs to create climate resilient and disease resistant 36 varieties with improved yield and quality traits. 37
38Introduction 39Wheat production is constrained by several biotic and abiotic factors, yet the demand 40 for wheat is expected to double by 2050. A yield increase of ~2.4 % per year has been 41 projected as required to close the gap between the current production level and an increasing 42 demand (Ray et al. 2013). While this goal can be achieved by improving agronomic 43 practices, expanding the production area and/or deployment of high-yielding wheat varieties, 44 the first two alternatives are unsustainable because land is a limited resource and most 45 effective agronomic practices are costly. Accelerated wheat improvement through extensive 46 deployment of available genomics tools and genetic resources, including close and distant 47 wild relatives of wheat, is viewed as the most effective and sustainable alternative to 48 increasing yield. 49Allohexaploid wheat, Triticum aestivum (2n = 6x = 42, AABBDD) resulted from 50 hybridization of Triticum turgidum (2n = 4x = 28, AABB) and Aegilops tauschii ssp. 51 strangulata (2n = 2x = 14, DD) (Kihara 1944; Luo et al. 2007;Wang et al. 2013). 52 Domestication of wheat followed by con...