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

Authors: NYINE, MOSES - Kansas State University; ADHIKARI, ELINA - Kansas State University; CLINESMITH, MARSHALL - Kansas State University; Jordan, Katherine; ALAN, FRITZ - Kansas State University; AKHUNOV, EDUARD - Kansas State University

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/29/2020
Publication Date: 10/1/2020
Citation: Nyine, M., Adhikari, E., Clinesmith, M., Jordan, K., Alan, F., Akhunov, E. 2020. Genomic patterns of introgression in interspecific populations created by crossing wheat with its wild relative. G3, Genes/Genomes/Genetics. 10:3651-3661. https://doi.org/10.1534/g3.120.401479.
DOI: https://doi.org/10.1534/g3.120.401479

Interpretive Summary: Wheat production is constantly trying to keep pace with growing demand but is hindered by a lack of genetic diversity for increased yield and adequate resistance against evolving disease pressures and environmental stresses. A valuable source of diverse genetic material can be found in wheat's wild relatives. We crossed six wheat cultivars with twenty-one donor lines of a wild wheat relative, Aegilops tauschii. After a series of breeding cycles and selection for agronomic performance in the field, we traced the frequency and distribution of remaining DNA segments from the wild relative into the cultivated wheat genome. We found that the DNA from the wild relative occurred primarily near the tips of the chromosomes, which is where recombination rates are highest. This introgression pattern must be considered by breeders when trying to incorporate wild genetic material into new wheat cultivars in modern breeding programs. To achieve maximum introgression of new genetic diversity, selection for agronomic type should be delayed until later generations to allow genetic recombination to break up linkages of desirable traits with undesirable agronomic traits.

Technical Abstract: Introgression from wild relatives is a valuable source of novel allelic diversity for breeding. We investigated the genomic patterns of introgression from Aegilops tauschii, the diploid ancestor of the wheat D genome, into winter wheat (Triticum aestivum) cultivars. The population of 351 BC1F3:5 lines was selected based on phenology from crosses between six hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. SNP markers developed for this population and a diverse panel of 116 Ae. tauschii accessions by complexity-reduced genome sequencing were used to detect introgression based on the identity-by-descent analysis. Overall, introgression frequency positively correlated with recombination rate, with a high incidence of introgression at the ends of chromosomes and low in the pericentromeric regions, and was negatively related to sequence divergence between the parental genomes. Reduced introgression in the pericentromeric low-recombining regions spans nearly 2/3 of each chromosome arm, suggestive of the polygenic nature of introgression barriers that could be associated with multilocus negative epistasis between the alleles of wild and cultivated wheat. On the contrary, negative selection against the wild allele of Tg, controlling free threshing trait and located in the high-recombining chromosomal region, led to reduced introgression only within ~10 Mbp region around Tg. These results are consistent with the effect of selection on linked variation described by the Hill-Robertson effect, and offer insights into the introgression population development for crop improvement to ensure retention of introgressed diversity across entire genome.