Candidate selective sweeps in US wheat populations

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 signatures of positive selection or selective sweeps. We conducted genome‐wide scan for candidate selective sweeps (CSS) using Fst, Rsb, and xpEHH in state, regional, spring, winter, and market‐class population pairs and reported 446 CSS in 19 population pairs over time and 1033 CSS in 44 population pairs across geography and class. Further validation of these CSS in specific breeding programs may lead to identification of sets of loci that can be selected to restore population‐specific adaptation in pre‐breeding germplasms. Core Ideas Selective sweeps were reported in 63 US wheat populations over time and across regions, states, and market classes. Exploration of candidate selective sweeps may aid breeders in maintaining adaptation while incorporating novel alleles. Newer varieties were most differentiated from older varieties within the Pacific and soft white spring populations. The Pacific, hard red spring, and South Carolina populations were most differentiated from other regions and classes. Plain Language Summary Modern plant breeding in the United States has improved and adapted wheat varieties to diverse wheat‐growing regions, states, and use cases for over a century. Selection by wheat breeders is likely to have left signs of selection in many locations in the wheat genome. We used three complementary statistics to look for such signs of selection or candidate selective sweeps in 63 US wheat populations classified by geographic regions, states, whether they are spring‐ or fall‐planted, and market class. Some of these locations in the wheat genome may be crucial to adaptation of wheat to a specific region or use case. Continued improvement of wheat will partly rely on the use of novel genes from unrelated wheat populations. Exp