Exploration of fine-scale recombination rate variation in the domestic horse

Abstract

Total genetic map length and local recombination landscapes typically vary within and across populations. As a first step to understanding the recombination landscape in the domestic horse, we calculated population recombination rates and identified likely recombination hotspots using ~1.8 million SNP genotypes for 485 horses from 32 distinct breeds. The resulting breed-averaged recombination map spans 2.36 Gb and accounts for 2,939.07 cM. Recombination hotspots occur once per 23.8 Mb on average and account for approximately 9% of the physical map length. Regions with elevated recombination rates in the entire cohort were enriched for genes in pathways involving interaction with the environment: immune system processes (specifically, MHC class I and class II genes), responses to stimuli, and serotonin receptor pathways. We found significant correlations between differences in local recombination rates and population differentiation quantified by F_ST. Analysis of breed-specific maps revealed thousands of hotspot regions unique to particular breeds, as well as unique "coldspot" regions where a particular breed showed below-average recombination while all other breeds had evidence of a hotspot. Finally, we identified relative enrichment (p = 5.88 x 10^-27) for the in silico predicted recognition motif for equine PR/SET Domain 9 (PRDM9) in recombination hotspots. These results indicate that selective pressures and PRDM9 function contribute to variation in recombination rates across the domestic horse genome.