Background Nellore cattle (Bos indicus) are well-known for their adaptation to warm and humid environments. Hair length and coat color may impact heat tolerance. The Nellore breed has been strongly selected for white coat, but bulls generally exhibit darker hair ranging from light grey to black on the head, neck, hump, and knees. Given the potential contribution of coat color variation to the adaptation of cattle populations to tropical and sub-tropical environments, our aim was to map positional and functional candidate genetic variants associated with darkness of hair coat (DHC) in Nellore bulls. Results We performed a genome-wide association study (GWAS) for DHC using data from 432 Nellore bulls that were genotyped for more than 777 k single nucleotide polymorphism (SNP) markers. A single major association signal was detected in the vicinity of the agouti signaling protein gene (ASIP). The analysis of whole-genome sequence (WGS) data from 21 bulls revealed functional variants that are associated with DHC, including a structural rearrangement involving ASIP (ASIP-SV1). We further characterized this structural variant using Oxford Nanopore sequencing data from 13 Australian Brahman heifers, which share ancestry with Nellore cattle; we found that this variant originates from a 1155-bp deletion followed by an insertion of a transposable element of more than 150 bp that may impact the recruitment of ASIP non-coding exons. Conclusions Our results indicate that the variant ASIP sequence causes darker coat pigmentation on specific parts of the body, most likely through a decreased expression of ASIP and consequently an increased production of eumelanin.

Brazil is the largest exporter of beef in the world, and most of that beef derives from Nellore cattle. Although considered a zebu breed (Bos indicus), the history of Nellore cattle in Brazil is marked by the importation of bulls from India, the use of a Creole taurine (Bos taurus) maternal lineage to quickly expand the herds and backcrossing to Nellore bulls to recover zebu ancestry. As a consequence, the current Brazilian Nellore population carries an average taurine ancestry of approximately 1%. Although that percentage seems small, some taurine variants deviate substantially from that average, with the better-known cases being the PLAG1-Q haplotype involved with body size variation and the Guarani (P G ) polled variant producing hornless animals. Here, we report taurine haplotypes in 9074 Nellore animals genotyped for 539 657 imputed SNP markers. Apart from PLAG1-Q and P G , our analysis further revealed common taurine haplotypes (>3%) spanning genes related to immunity, growth, reproduction and hair and skin phenotypes. Using data from 22 economically important traits, we showed that many of the major QTL previously reported in the breed are at least partially driven by taurine haplotypes. As B. taurus and B. indicus haplotypes are highly divergent, presenting widely different sets of functional variants, our results provide promising targets for future scrutiny in Nellore cattle.