Runs of homozygosity and selection signature in Santa Inês sheep: A genomic analysis

Abstract

Runs of homozygosity (ROH) and selection signatures are the results of selection processes in livestock species that have been shown to affect several traits in farm animals. The objective of this study was to investigate runs of homozygosity, identify selection signatures and the genes involved, in Santa Ines sheep. The genotype file contained 390 animals and 52,744 SNP markers. The ROH and selection signature analyses were conducted using the detectRUNS tool and PLINK software. The ROH analyses identified a selection signature for the five genetic groups on chromosome 16. When the level of similarity (90 %) within the genetic groups was increased, 8 selection signature regions were found on chromosomes 2, 3, 6, 7, 12, 16, and 18. The genes found in regions with selection signatures are related to several functions of great productive and adaptive interest, such as immunity (MYD88, NFKB1), growth (IGFBP2, IGFBP5, SKP2) and meat and milk quality (IL7R, RANBP3L). Chromosome 16 stands out because it concentrates genes associated with milk, meat and fat production, evidencing its importance for economic traits in the Santa Inês breed. On the other hand, the absence of genes annotated in specific regions, such as chromosome 12, suggests the need for additional studies to identify biological processes that have not yet been characterized. These results reinforce the relevance of exploring selection signatures and associated genes in genetic improvement programs, aiming to optimize the productivity and adaptability of Santa Inês sheep.