Beyond black and white: dissecting the genetic basis of skin depigmentation in Nellore cattle

Depigmentation defects in cattle are characterized by the absence of pigment in specific skin regions, increasing susceptibility to health issues and often leading to early culling. In Nellore cattle, depigmentation is primarily observed at the tail tip, mucous membranes, and as small patches across the body. This study aimed to estimate genetic parameters and perform a genome-wide association study (GWAS) for depigmentation in Nellore cattle. Data were sourced from the DeltaGen® breeding program, provided by Gensys®. Phenotypic records included 182,964 Nellore cattle, with a 6.8% incidence of depigmentation. Of these, 28,655 genotyped animals and 385,079 SNPs were available for the analysis. The ultra-fast generalized linear mixed model for binary traits (fastGWA-GLMM) was used for the GWAS, while variance components were estimated using a Bayesian threshold model and single-step methodology. The heritability of depigmentation was estimated at 0.12 on the observed scale and 0.54 on the liability scale. The GWAS identified 1,011 significant SNPs (p < 0.05 after Bonferroni correction) associated with depigmentation defects, located across chromosomes BTA6, BTA12, and BTA22. However, after performing a conditional GWAS to account for the top signal on BTA22, the original signal in the MITF region was no longer detected. In total, 234 genes were identified near the associated SNPs, including 129 protein-coding genes. Functional enrichment highlighted MITF, KIT and EDNRB as biologically relevant candidate genes. The gene ontology analysis highlighted biological processes related to melanogenesis, pigmentation, and hypopigmentation phenotypes, while the QTL enrichment analysis identified significant associations on BTA6 and BTA22. These findings improve our understanding of the genetic basis of depigmentation in Nellore cattle and may contribute to future selection strategies.