A genomic analysis of the University of Nebraska Replicated Recurrent Selection program

The inbred-hybrid system of maize breeding closely resembles a reciprocal full-sib (RFS) selection program. Studying changes in genetic variation as a result of RFS selection can help illuminate long-standing questions regarding the relative roles of selection and genetic drift and help understand the nature of adaptation occurring in selection programs. The University of Nebraska-Lincoln Replicated Recurrent Selection (UNL-RpRS) program underwent eight cycles of replicated RFS and S1-progeny selection, making it a powerful system to study genomic changes accompanying selection for inter-population performance. The objectives of this study were to identify regions of the genome under selection after eight cycles of selection and evaluate the effect eight cycles of selection for inter-population full-sib performance had in expanding genome-wide and localized population structure. We address these questions with a large set of individuals sampled from the UNL-RpRS program with dense genotyping-by-sequence data. We found evidence of parallel selection signatures in the UNL-RpRS program, with a region on chromosome 7 being implicated in three of the four selection systems studied. Regions that displayed selection signatures across independently run selection programs represent regions likely to be capitalizing on standing genetic variation and support a soft sweep model of adaptation. We did not find selection to be a strong force in diverging populations undergoing RFS. This could be due to the nature of adaptation occurring in these populations, underlying gene action, or a result of unstable genetic topographies.