The effect of selection on allele frequencies and diversity in wheat (Triticum aestivum)

Advancing wheat lines through stages of testing resulted in large genome changes. Consistent changes across cohorts and selection stages were noted though most changes appeared specific. Diversity was lost within a cohort, primarily at the last stage of advancement, though diversity across cohorts was not greatly impacted. The results can be used to develop informed crossing strategies. Effective selection increases the frequency of favorable alleles but can reduce genetic variation. The extent of allele frequency changes (AFC) that occur as wheat lines are advanced through stages of testing is not well documented. Our objectives were to determine the magnitude of AFC in a wheat breeding program, determine the consistency of AFC, and the effect of selection on population structure and diversity. We calculated the AFC for 1,173 markers on 4,678 wheat lines from ten cohorts that went through four stages of selection, primarily for yield. We determined the AFC for 48,093 marker/cohort/selection stage combinations and determined that 23.5% of these AFC's were greater than expected by drift and were attributed to selection. Most large AFC occurred in the final stage of selection. Eighty-nine markers had AFCs that showed signs of consistent unidirectional selection over cohorts and stages of selection, while 68.3% of the AFCs attributed to selection were cohort/selection-stage and directional specific. Within a cohort an average of 24.1% of makers had become fixed in stage-4 of testing, though few markers become fixed in more than one cohort. Each cohort experienced somewhat unique genome changes, likely due to selection in a unique array of environments. The genetic distance between cohorts of lines in stage-4 testing was similar to that among stage-1 lines. Crossing among the best lines from multiple cohorts would mitigate the loss of diversity within a single cohort and likely recombine favorable alleles selected across a wide array of environments.