Artificial selection is one of the major forces modifying the genetic composition of livestock populations. Identifying genes under selection could be useful to elucidate their impact on phenotypic variation. We aimed to identify genomic regions targeted by selection for dairy and pigmentation traits in Murciano-Granadina goats. Performance of a selection scan based on the integrated haplotype score test in a population of 1183 Murciano-Granadina goats resulted in the identification of 77 candidate genomic regions/SNPs. The most significant selective sweeps mapped to chromosomes 1 (69.86 Mb), 4 (41.80–49.95 Mb), 11 (65.74 Mb), 12 (31.24 and 52.51 Mb), 17 (34.76–37.67 Mb), 22 (31.75 Mb), and 26 (26.69–31.05 Mb). By using previously generated RNA-Seq data, we built a catalogue of 6414 genes that are differentially expressed across goat lactation (i.e. 78 days post-partum, early lactation; 216 days post-partum, late lactation; 285 days post-partum, dry period). Interestingly, 183 of these genes mapped to selective sweeps and several of them display functions related with lipid, protein, and carbohydrate metabolism, insulin signaling, cell proliferation, as well as mammary development and involution. Of particular interest are the CSN3 and CSN1S2 genes, which encode two major milk proteins. Additionally, we found three pigmentation genes (GLI3, MC1R, and MITF) co-localizing with selective sweeps. Performance of a genome-wide association study and Sanger sequencing and TaqMan genotyping experiments revealed that the c.801C>G (p.Cys267Trp) polymorphism in the melanocortin 1 receptor (MC1R) gene is the main determinant of the black (GG or GC genotypes) and brown (CC genotypes) colorations of Murciano-Granadina goats.

中文翻译：

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检测 Murciano-Granadina 山羊基因组上的选择足迹

人工选择是改变家畜种群遗传组成的主要力量之一。识别选择的基因可能有助于阐明它们对表型变异的影响。我们旨在通过选择 Murciano-Granadina 山羊的乳制品和色素沉着性状来确定目标基因组区域。在 1183 只 Murciano-Granadina 山羊群体中基于综合单倍型评分测试进行选择扫描，结果鉴定了 77 个候选基因组区域/SNP。映射到染色体 1 (69.86 Mb)、4 (41.80–49.95 Mb)、11 (65.74 Mb)、12 (31.24 和 52.51 Mb)、17 (34.76–37.67 Mb)、252 (3)1 的最重要的选择性扫描和 26 (26.69–31.05 Mb)。通过使用先前生成的 RNA-Seq 数据，我们构建了一个包含 6414 个基因的目录，这些基因在山羊泌乳期间差异表达（即。e. 产后 78 天，泌乳早期；产后 216 天，泌乳晚期；产后 285 天，干燥期）。有趣的是，这些基因中有 183 个映射到选择性扫描，其中一些显示出与脂质、蛋白质和碳水化合物代谢、胰岛素信号传导、细胞增殖以及乳腺发育和退化相关的功能。特别感兴趣的是CSN3和CSN1S2基因，编码两种主要的牛奶蛋白。此外，我们发现三个色素沉着基因（GLI3、MC1R和MITF）与选择性扫描共定位。全基因组关联研究和 Sanger 测序和 TaqMan 基因分型实验的表现表明，黑皮质素 1 受体 ( MC1R ) 基因中的 c.801C>G (p.Cys267Trp) 多态性是黑色素（GG 或 GC 基因型）的主要决定因素Murciano-Granadina 山羊的）和棕色（CC 基因型）着色。