Signatures of selection in regional U.S. wheat populations

Authors: STHAPIT, SAJAL - Washington State University; Ruff, Travis; HOOKER, MARCUS - Washington State University; See, Deven

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/25/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary: This study investigates the regions of the genome that are fixed within any given region in the U.S. or breeding program. These fixed regions are potentially the sites of regional adaptation that are essential for advanced cultivar capabilities in micro climates throughout the breeding regions in the U.S.

Technical Abstract: Exploration of novel alleles from ex situ collection is still limited in modern plant breeding as these alleles exist in genetic backgrounds of landraces that are not adapted to modern production environments. The practice of backcross breeding results in preservation of the adapted background of elite parents but leaves little room for novel alleles from landraces to be incorporated. Selection of adaptation-associated linkage blocks instead of the entire adapted background may allow breeders to incorporate more of the landrace’s genetic background and to observe and evaluate novel alleles. Important adaptation-associated linkage blocks would have been selected over multiple cycles of breeding and hence are likely to exhibit strong signatures of positive selection or selective sweeps. We conducted genome wide scan for candidate selective sweeps using Fst, Rsb, and xpEHH in 4 regional spring, 4 regional winter, 5 market class, 4 state spring, and 9 state winter populations. We report multiple candidate selective sweeps in state, regional, and market class populations. Further validation of these candidate selective sweeps in specific breeding programs may lead to identification of set of loci that can be selected to restore population-specific adaptation without multiple backcrossing.