Wide genome involvement in response to long-term selection for antibody response in an experimental population of White Leghorn chickens

Abstract

Long-term selection experiments provide a powerful approach to gain empirical insights into adaptation. They allow researchers to uncover the targets of selection and how these contribute to the mode and tempo of adaptation. Here we report results from a pooled genome re-sequencing study to investigate the consequences of 39 generations of bidirectional selection in White Leghorn chickens on a humoral immune trait: antibody response to sheep red blood cells. We observed wide genome involvement in response to this selection regime, with over 200 candidate sweep regions characterised by spans of high genetic differentiation (FST). These sweep signatures, encompassing almost 20% of the chicken genome (208.8 Mb), are primarily the result from bidirectional selection on haplotypes present in the base population. These extensive genomic changes highlight both the extent of standing genetic variation at immune loci available at the onset of selection, as well as how the long-term selection response results from selection on a highly polygenic genetic architecture. Furthermore, we present three examples of strong candidate genes that may have contributed to the profound phenotypic response to selection.\n\nData AvailabilityPooled genome data generated for this study will become available via SRA upon acceptance of manuscript