Analysis of the genomic landscape of inbreeding in two divergent groups of Spanish Florida goats

The analysis of the genomic landscape of inbreeding using runs of homozygosity (ROH) patterns is becoming an interesting tool to partially understand phenotypic differences among individuals. In this study, we analysed genome‐wide ROH patterns in two groups of Florida goats. We first determined the inbreeding levels of each individual by calculating ROH‐based inbreeding coefficients (FROH). Then, the individuals were divided into two groups based on FROH: high inbreeding (HI, FROH >0.1) and low inbreeding (LI, FROH 8 Mb), with significant increases in CHI6, CHI11 and CHI28. Determination of genomic regions with significantly increased ROH (ROH islands—ROHi) showed 13 ROHi related to whole inbreeding and five ROHi associated with recent inbreeding analysis. Within these genomic regions, 123 and 101 genes were identified in HI and LI, respectively, including 10 and seven candidate genes previously related to production, fertility and heat resistance in goats and livestock species.