Understanding inbreeding and its impact on fitness and evolutionary potential is fundamental to species conservation and agriculture. Long stretches of homozygous genotypes, known as runs of homozygosity (ROH), result from inbreeding and their number and length can provide useful population-level information on the extent and age of inbreeding, as well as the location of signatures of selection. However, the utility of ROH for conservation is limited for natural populations where baseline data and genomic tools are lacking. Comparing ROH metrics in recently feral vs. domestic populations of well understood species like the horse could provide information on the genetic health of those populations as well as offer insight into how such metrics might compare between managed and unmanaged populations. Here we detected ROH, inbreeding coefficients, and ROH islands in a feral horse population from Sable Island, Canada, using ~41000 SNPs and contrasted results with those from 33 domestic breeds to assess the impacts of isolation on ROH abundance, length, distribution, and adaptive differentiation.
Results/Conclusions
ROH number, length, and ROH-based inbreeding coefficients (FROH) in Sable Island horses were typically greater than in domestic breeds. Short runs indicating relatively old inbreeding were more abundant than long runs in all populations, but some population bottlenecks likely occurred more recently in Sable Island horses. Nine ROH islands were detected in Sable Island horses, exhibiting very little overlap with those found in domestic breeds. GO analysis for Sable Island ROH islands revealed enrichment for genes associated with 3 different clusters of biological pathways largely associated with metabolism and immune function. This study indicates that Sable Island horses tend to be more inbred than their domestic counterparts and that most of this inbreeding is due to historical bottlenecks and founder effects rather than contemporary inbreeding. Unique ROH islands in the Sable Island population suggest adaptation to local selective pressures and highlight the value of this population as a reservoir of equine genetic variation. This research illustrates how ROH analyses can be applied to gain insights into the population history, genetic health, and adaptive differentiation of wild or feral populations of conservation concern.
