Genomic scans for selection signatures revealed candidate genes for adaptation and production traits in the Thai multibreed dairy cattle population

Abstract

The genetic improvement of dairy cattle for tropical environments demands a balance between high productivity and adaptability. Although previous studies have explored genomic signatures in various cattle breeds, limited insights exist for the genetically diverse Thai multibreed dairy cattle population developed through crossbreeding of multiple Bos taurus and Bos indicus breeds with Holstein. This study aimed to uncover selection signatures and candidate genes underpinning adaptation and production traits in this population. Using genotype data from 2661 animals (73,762 SNPs), population structure was revealed via Discriminant Analysis of Principal Components (DAPC), identifying four genetically distinct groups. Integrated haplotype score (iHS) analysis identified 376 to 500 genomic regions under selection across groups, harboring 962 to 1657 genes. Seven strong candidate genes – KLF12, MAP2K6, SPATA16, LAMA2, SLC25A28, WNT7A, and HHIPL2 – were linked to milk yield, fat synthesis, immune response, and adaptation. Annotation revealed 5036 to 7970 quantitative trait loci (QTLs) per group, with 26.53 % to 28–84 % overlapping with milk traits in groups 1 to 3, and 24.96 % with meat traits in group 4. The QTL enrichment highlighted significant traits such as milk fat yield, immunoglobulin G levels, tick resistance, and coat color, reflecting environmental selection pressures. These findings demonstrate how artificial selection shaped the genomic landscape of Thai dairy cattle, influencing traits critical for productivity, health, and climate resilience. This study provides a foundation for genomic selection strategies tailored to tropical dairy systems and underscores the potential of genetic marker information to enhance dairy cattle efficiency, productivity, and sustainability under region-specific challenges.