The haplotype-based analysis of Aegilops tauschii introgression into hard red winter wheat and its impact on productivity traits

Authors: NYINE, MOSES - Kansas State University; ADHIKARI, ELINA - Kansas State University; CLINESMITH, MARSHALL - Kansas State University; AIKEN, ROBERT - Kansas State University; BETZEN, BLISS - Kansas State University; HE, FEI - Kansas State University; AKHUNOVA, ALINA - Kansas State University; Jordan, Katherine; FRITZ, ALLAN - Kansas State University; AKHUNOV, EDUARD - Kansas State University; WANG, WEI - Kansas State University; DAVIDSON, DWIGHT - Kansas State University; YU, ZITONG - Kansas State University; GUO, YUANWEN - Kansas State University

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 5/30/2021
Publication Date: 5/30/2021
Citation: Nyine, M., Adhikari, E., Clinesmith, M., Aiken, R., Betzen, B., He, F., Akhunova, A., Jordan, K., Fritz, A., Akhunov, E., Wang, W., Davidson, D., Yu, Z., Guo, Y. 2021. The haplotype-based analysis of Aegilops tauschii introgression into hard red winter wheat and its impact on productivity traits. bioRxiv. https://doi.org/10.1101/2021.05.29.446303.
DOI: https://doi.org/10.1101/2021.05.29.446303

Interpretive Summary: Increasing wheat production is essential to keep pace with growing population size. Unfortunately, increasing grain yield is hampered by a lack of genetic diversity in current wheat varieties. One source of more diverse genetic material is found in wheat's wild relatives. To introduce more genetic diversity, we crossed six wheat cultivars with twenty-one donor lines of a wild wheat relative, Aegilops tauschii, to produce a population of introgression lines that each carry different pieces of the wild ancestor genome. These introgression lines were tested in the field under rainfed and drought conditions to test their effects on yield potential. We found that 23% of the introgression lines produce more grain yield than the parent wheat cultivars. In addition, we identified regions of the wild wheat genome that had positive effects on spikelet number per spike and kernel length. These new genetic resources should help breeders increase the quantity and stability of grain yield in future wheat cultivars.

Technical Abstract: Introgressions from wild relatives have a great potential to broaden beneficial allelic diversity available for crop improvement in breeding programs. Here, we assessed the impact of introgression from 21 diverse accessions of Aegilops tauschii, the diploid ancestor of the wheat D genome, into six hard red winter wheat cultivars on yield and yield component traits. We used 5.2 million imputed D genome SNPs identified by whole-genome sequencing of parental lines and the sequence-based genotyping of an introgression population including 351 BC1F3:5 lines. Phenotyping data collected from the irrigated and non-irrigated field trials revealed that up to 23% of the introgression lines produce more grain than the parents and check cultivars. Based on sixteen yield stability statistics, the yield of twelve introgression lines (3.4%) was stable across treatments, years and locations; five of these lines were also high yielding, producing 9.8% more grain than the average yield of check cultivars. The most significant SNP-trait and haplotype-trait associations were identified on chromosome arms 2DS and 6DL for spikelet number per spike (SNS), on chromosome arms 2DS, 3DS, 5DS and 7DS for grain length, and on chromosome arms 1DL, 2DS, 6DL and 7DS for grain width. Introgression of haplotypes from Ae. tauschii parents was associated with increase in SNS, which positively correlated with heading date, whereas haplotypes from hexaploid wheat parents were associated with increased grain width. While some introgressed haplotypes exhibited significant pleiotropic effects with the direction of effects on the yield component traits being largely consistent with the previously reported trade-offs, there were haplotype combinations associated with the positive trends in yield. The characterized repertoire of the introgressed haplotypes derived from Ae. tauschii accessions with the combined positive effects on yield and yield components traits in elite germplasm provides a valuable source of alleles for improving the productivity of winter wheat by optimizing the contribution of component traits to yield.