Investigation of selection signatures of dairy goats using whole-genome sequencing data.

Abstract

Dairy goats, a livestock species with a long history of milk production, are essential for the economic advancement of nations, particularly in regions experiencing growth. In this study, we gathered whole-genome resequencing data of 58 goats, including 34 dairy goats and 24 wild goats (Bezoar), to explore the selection signatures linked to milk production traits using ROH (Runs of homozygosity), CLR (composite likelihood ratio), Fst (Fixation index), XP-EHH (Ex-tended haplotype homozygosity across populations) and XP-CLR(Cross-population composite likelihood ratio test) methods. Analysis of five tests of selection signatures for dairy goats revealed a total of 210 genes, with 24 genes consistently identified in at least two approaches. These genes are associated with milk fat, milk protein, and fat yield. Gene enrichment analysis highlighted important GO and KEGG pathways related to milk production, such as the "acyl-CoA metabolic process", "glycerolipid biosynthetic process", "cellular response to fatty ac-id", "hormone metabolic process", "Galactose metabolism". Additionally, genes linked to repro-duction, immune response, and environmental adaptation were identified in dairy goats. The findings from our study offer profound understanding into the critical economic features of dairy goats and offer practical guidance for the improvement and development of crossbreeding initiatives across different dairy goat breeds.