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. 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. 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.

中文翻译：

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ASIP 基因座的变异导致 Nellore 牛的毛色变暗

Nellore 牛 (Bos indicus) 以适应温暖潮湿的环境而闻名。头发长度和毛色可能会影响耐热性。Nellore 品种已被强烈选择用于白色外套，但公牛通常在头部、颈部、驼峰和膝盖上表现出较深的毛发，从浅灰色到黑色不等。鉴于毛色变化对牛群适应热带和亚热带环境的潜在贡献，我们的目标是绘制与 Nellore 公牛毛皮 (DHC) 深色相关的位置和功能候选遗传变异。我们使用来自 432 头 Nellore 公牛的数据对 DHC 进行了全基因组关联研究 (GWAS)，这些数据针对超过 777 k 的单核苷酸多态性 (SNP) 标记进行了基因分型。在 agouti 信号蛋白基因 (ASIP) 附近检测到单个主要关联信号。对 21 头公牛的全基因组序列 (WGS) 数据的分析揭示了与 DHC 相关的功能变异，包括涉及 ASIP (ASIP-SV1) 的结构重排。我们使用来自 13 头澳大利亚婆罗门小母牛的牛津纳米孔测序数据进一步表征了这种结构变异，这些母牛与 Nellore 牛有着共同的祖先；我们发现该变异源自 1155 bp 的缺失，随后插入了超过 150 bp 的转座因子，这可能会影响 ASIP 非编码外显子的募集。我们的结果表明变异的 ASIP 序列会导致身体特定部位的皮毛色素沉着变深，