Artificial selection in breeding extensively enriched a functional allelic variation in TaPHS1 for pre-harvest sprouting susceptibility in wheat

Authors: LIU, SHUBING - Shangdong Agricultural University; WANG, DAFENG - Shangdong Agricultural University; LIN, MENG - Kansas State University; SEHGAL, SUNISH - South Dakota State University; DONG, LEI - Shangdong Agricultural University; Bai, Guihua

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/3/2020
Publication Date: 10/17/2020
Citation: Liu, S., Wang, D., Lin, M., Sehgal, S., Dong, L., Bai, G. 2020. Artificial selection in breeding extensively enriched a functional allelic variation in TaPHS1 for pre-harvest sprouting susceptibility in wheat. Journal of Theoretical and Applied Genetics. 134:339–350. https://doi.org/10.1007/s00122-020-03700-2.
DOI: https://doi.org/10.1007/s00122-020-03700-2

Interpretive Summary: Pre-harvest sprouting (PHS) causes significant losses in wheat yield and quality. Previously, we cloned a PHS resistance gene, TaPHS1, and identified three causal mutations for increased PHS susceptibility. Here we identified a fourth allelic variation that results in increased PHS susceptibility. The susceptibility allele appears at a lower frequency in wild wheat progenitors than in modern wheat cultivars, probably due to artificial selection by modern breeding practices. The susceptibility allele was significantly associated with reduced PHS resistance in both common bread wheat and durum wheat. We identified DNA markers for the new variant that can be used in marker-assisted selection to transfer PHS resistance to new wheat cultivars.

Technical Abstract: Pre-harvest sprouting (PHS) causes significant losses in wheat yield and quality worldwide. Previously, we cloned a PHS resistance gene, TaPHS1, and identified three causal mutations for reduced seed dormancy (SD) and increased PHS susceptibility. Here we identified a fourth allelic variant consisting of a C to T transition in the 3’-UTR of TaPHS1, which was associated with reduced SD and PHS resistance. The T allele occurred in wild wheat progenitors and was likely the earliest functional mutation in TaPHS1 for PHS susceptibility. Allele frequency analysis revealed low frequency of the T allele in wild diploid and tetraploid wheat progenitors, but very high frequency in modern wheat cultivars and breeding lines, indicating that artificial selection quickly enriched the T allele during modern breeding. The T allele was significantly associated with short SD in both T. aestivum and T. durum, the two most cultivated species of wheat. This variation together with previously reported functional sequence variations co-regulated TaPHS1 expression levels and PHS resistance in different germplasms. Haplotype analysis of the four functional variations identified the best PHS resistance haplotype of TaPHS1. The resistance haplotype can be used in marker-assisted selection to transfer TaPHS1 to new wheat cultivars.