Table 7_Validation of selection signatures for coat color in the Podolica Italiana gray cattle breed.xlsx

Taurine and indicine gray cattle represent relevant livestock resources in many countries of the world. A gray coat color and pigmented skin, which are common in most of the gray cattle breeds, have been demonstrated to confer better adaptation to solar radiation and thermal stresses. In a previous study adopting the FST-outlier approach with BayeScan v2.0, we identified differentially selected genomic regions in a set of gray cattle breeds, including the Podolica Italiana, and contrasted these findings with four non-gray cattle breeds. More supported signals were detected on bovine chromosomes (BTAs) 2, 4, 14, and 26 that encompassed more than fifty genes known to be directly or indirectly related to one or more steps in pigment biology. In the present study, we aimed to validate the previously observed signals using the same methodological approach on three new Podolica Italiana sample sets (N = 30 animals each). These animals were selected from the ANABIC genetic station during performance tests as being representative of the Podolica Italiana population at three different timeframes separated by approximately 10 years each. We typed these samples to the loci of 23,027 quality-controlled single-nucleotide polymorphisms. We also analyzed the dataset using the haplotype-based approach available in hapFLK v1.4 software. Both the FST-outlier and hapFLK approaches validated the abovementioned signals on BTAs 2, 4, 14, and 26. Moreover, both methods detected additional supported regions on BTAs 7 and 18 that included a total of 42 genes, of which most were already known from literature to be implicated in pigmentation traits.

普通牛（Taurine）与瘤牛（Indicine）的灰被毛类群是全球多国重要的畜禽种质资源。多数灰牛品种普遍具备灰被毛与色素沉着皮肤的表型，该表型已被证实可提升个体对太阳辐射与热应激的适应能力。此前一项研究采用基于BayeScan v2.0的FST离群值（FST-outlier）分析方法，对包括意大利波德力克牛（Podolica Italiana）在内的多个灰牛品种开展基因组分析，鉴定出受选择分化显著的基因组区域，并将该结果与4个非灰牛品种进行对照。该研究在牛染色体（Bovine Chromosomes, BTAs）2、4、14和26上检测到更多支持性选择信号，这些区域共包含50余个已知直接或间接参与色素生物学相关通路的基因。本研究旨在采用相同的方法学策略，对3个全新的意大利波德力克牛样本集（每个样本集含30头个体）开展验证分析。这些样本均选自ANABIC遗传站的性能测定群体，代表了三个间隔约10年的不同时间节点的意大利波德力克牛种群。我们对这批样本的23027个经过质量控制的单核苷酸多态性（single-nucleotide polymorphisms）位点完成了基因分型。同时，我们还借助hapFLK v1.4软件的单倍型分析方法对该数据集进行了分析。FST离群值法与hapFLK法均验证了前述在BTAs 2、4、14和26上的选择信号。此外，两种分析方法均在BTAs 7和18上检测到额外的支持性选择区域，这些区域共包含42个基因，其中多数已被已有文献报道与色素沉着性状相关。