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 (F-ROH). Then, the individuals were divided into two groups based on F-ROH: high inbreeding (HI, F-ROH >0.1) and low inbreeding (LI, F-ROH <0.03). Finally, we performed an extensive in-depth analysis of ROH distribution in each group separately. We found a higher abundance of short ROH in LI, whereas long ROH was more frequent in HI. Furthermore, ROH abundance was not evenly distributed among chromosomes within groups, with some chromosomes showing larger numbers of ROH, like CHI6, CHI7 and CHI27. A different landscape was observed in recent inbreeding (ROH >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.

Automated summary

The genomic landscape of inbreeding was analyzed in Florida goats using runs of homozygosity (ROH) patterns as a tool to understand phenotypic differences. Inbreeding levels were determined for each individual using ROH-based inbreeding coefficients (F-ROH), and two groups were formed based on these levels. The distribution of ROH was analyzed in each group, showing differences in abundance and distribution among chromosomes. Genomic regions with increased ROH were identified, and candidate genes related to production, fertility, and heat resistance were found within these regions.