The genomics behind beauty: disentangling the complex coat color genetic architecture of gir breed

Abstract

Coat color in cattle is a phenotypic trait of high biological, zootechnical, and economic relevance, having historically been used as a visual criterion in selection programs and as a marker associated with adaptive and productive processes. In zebu breeds such as Gir (Bos indicus), this trait exhibits wide phenotypic variability, constituting an important component of breed identity and attracting scientific interest in tropical dairy production systems. Pigmentation results from the activity of melanocytes, which are responsible for melanin synthesis within melanosomes and is regulated by molecular networks that control the production of eumelanin and pheomelanin through specific signaling pathways. Within the context of population genomics, parameters such as linkage disequilibrium (LD) and effective population size (Ne) allow the characterization of population genetic structure, whereas genome-wide association studies (GWAS) enable the investigation of the genetic architecture underlying coat color. In this study, phenotypic records from 50,341 animals classified into 25 coat color categories were used, along with genomic data from 55,154 Gir cattle. After quality control, 389,172 SNPs were retained for the analyses. Heritability estimates ranged from 0.16 to 0.75, indicating moderate to high genetic control. The average LD (r²) was 0.064 at 50 kb, while effective population size declined from 53.9 individuals in generation 50 to 13.8 individuals in generation 5. Genomic windows of 0.5 Mb explained up to 24% of the additive genetic variance, enabling the identification of 52 candidate genes associated with coat color variation. The identified genes are related to processes such as melanocyte migration and development, cellular differentiation, cytoskeleton organization, signal transduction, and melanogenesis pathways. Taken together, the results indicate that coat color variation in the Gir breed is controlled by a complex and polygenic genetic architecture, involving multiple genes with pleiotropic effects, with implications for genetic improvement programs, conservation strategies, and the valorization of the breed in tropical production systems. Keywords: pigmentation; genetic variability; coat color.