Putative Genomic Signatures of Local Adaptation in Five Local Indonesian Sheep Reveal Selection on Immunity, Reproduction, and Production Traits

ABSTRACT Indonesian sheep, shaped by survival, reproduction and productivity in humid tropical climates, may carry genomic regions associated with local adaptation and economically important traits that remain largely unexplored. This study performed genetic diversity analysis on 17,534 SNPs derived from the OvineSNP50 BeadChip genotyping array, involving 120 individuals among five local Indonesian sheep breeds: Batur, Garut, Sakub, Sumatra and Thin‐tail. Analysis of genetic structure, incorporating PCA, maximum‐likelihood phylogenetics analysis and Admixture analyses, demonstrated that each population displayed a uniquely homogeneous and distinctive ancestry profile, with the exception of Sakub and Thin‐tail. Additionally, a close genetic relationship among Sakub, Garut and Thin‐tail sheep was identified. We employed four complementary approaches of within and cross population selection signature analyses to identify putative selection signatures within 13 genomic regions. Several genes identified within the selection signature regions are potentially associated with the immune system (e.g., ATRNL1 , DDX58 and NELFCD ), wool traits and pigmentation (e.g., CERS4 and EDN3 ), reproductive traits (e.g., GNPDA2, NAMPT and NDRG1 ), milk traits (e.g., SLC39A8, ST3GAL1 and EVI5L ), meat traits (e.g., PIK3CG, CDHR3 and ANGPTL4 ), and adaptive traits (e.g., SLC26A4 and NDUFB6 ). Understanding the candidate genomic areas under selective pressure in sheep breeds may aid in identifying the associated genes and improve our comprehension of their involvement in local adaptation. Consequently, this research provides a preliminary genomic resource for the conservation and utilization of these sheep genetic resources in Indonesia.