Genetic Diversity and Selection Signatures of Three Indonesian Indigenous Pig Populations From Eastern Indonesia Using Whole Genome Sequencing Data

ABSTRACT Indonesia is widely recognized as a megadiversity country, harboring a rich diversity of indigenous pig species that play significant roles in the cultural and religious practices of local communities. However, the limited availability of genomic and demographic data of these indigenous pigs has greatly impeded our understanding of their evolutionary history and population structure. To date, the genetic characteristics of indigenous pigs from Maluku, Southeast Sulawesi (Sultra), and East Nusa Tenggara (NTT) remain unknown. Here, we aimed to investigate the genetic diversity, population structure, and signatures of positive selection in indigenous pig populations from Maluku, Sultra, and NTT regions using whole‐genome sequencing. This study performed whole‐genome sequencing on 42 Indonesian indigenous pigs via Illumina HiSeq 4000, integrating datasets of Chinese domestic pigs, European domestic pigs, and wild boars for comparative genomic analysis. The results indicate that these pigs cluster phylogenetically with Southern Chinese breeds but are distinct from Northern Chinese and European pigs. Maluku pigs display genetic homogeneity, which indicates their purebred status. In contrast, Sultra and NTT pigs carry European alleles, suggesting historical introgression. The genetic diversity is higher in Sultra and NTT pigs than in Maluku pigs. Selective sweep analysis revealed predominantly population‐specific selection signals, highlighting the divergent evolution shaped by geographic isolation. Novel candidate genes for economic traits were identified, including FBXO36 in Maluku pigs, DIAPH3 in NTT pigs, and GTPBP4 in Sultra pigs. This study provides crucial insights for conservation strategies and breeding programs, emphasizing the need to preserve these unique genetic resources.