Genomic patterns of introgression in interspecific populations created by crossing wheat with its wild relative

Abstract

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...

Wheat speciation and adaptation: perspectives from reticulate evolution

“…2B, label k) was introduced into the D subgenome of bread wheat. To date, there is no evidence showing that T. urartu contributed gene flow to bread wheat (Nyine et al 2020;Zhou et al 2020). This is possibly due to the low survival rate of unreduced gametes and hybrid offspring, as well as the narrow geographical distribution of ancestral diploid populations (Matsuoka 2011;Scott et al 2019).…”

“…In many crops, such as rice (Meyer et al 2016) and soybean (Wang et al 2019), introgression from wild populations into cultivated species could increase the diversity of cultivated populations substantially. Many researches have demonstrated that the frequent introgression contributed to the restoration of genetic diversity in bread wheat (Cheng et al 2019;He et al 2019;Nyine et al 2020;Zhou et al 2020). Tetraploid introgression to hexaploid was more frequent and relatively recent, probably due to the higher survival rate of the offspring after homologous hybridization.…”

“…The introgressed alleles associated with local adaptation could be the key to evolutionary success to local conditions and expansion around the world (Nyine et al 2020). In potato, introgression is more likely to be highly expressed and stress-induced.…”

“…Recent studies showed that the tremendous diversity loss of bread wheat, during the bottleneck events of polyploidization and domestication, was mainly compensated by extensive introgression from wild populations (Cheng et al 2019;He et al 2019;Nyine et al 2020;Zhou et al 2020) (Fig. 3A).…”

Uncovering candidate genes involved in photosynthetic capacity using unexplored genetic variation in Spring Wheat

“…tauschii donors in the synthetic subpopulation can vary substantially, from as little as 0.5% to as high as 43% of the D subgenome, a larger range than identified in studies using synthetic octoploids as primary Ae. tauschii donors (0.075 % to 13.5 %) 36 . Through comparison of sister lines within the panel we also show that the content of the donor genome is not necessarily linked to the number of subsequent crosses post introduction of primary synthetic material (SF6, ST4).…”