The Valdostana is a local dual purpose cattle breed developed in Italy. Three populations are recognized within this breed, based on coat colour, production level, morphology and temperament: Valdostana Red Pied (VPR), Valdostana Black Pied (VPN) and Valdostana Chestnut (VCA). Here, we investigated putative genomic regions under selection among these three populations using the Bovine 50K SNP array by combining three different statistical methods based either on allele frequencies (FST ) or extended haplotype homozygosity (iHS and Rsb). In total, 8, 5 and 8 chromosomes harbouring 13, 13 and 16 genomic regions potentially under selection were identified by at least two approaches in VPR, VPN and VCA, respectively. Most of these candidate regions were population-specific but we found one common genomic region spanning 2.38 Mb on BTA06 which either overlaps or is located close to runs of homozygosity islands detected in the three populations. This region included inter alia two well-known genes: KDR, a well-established coat colour gene, and CLOCK, which plays a central role in positive regulation of inflammatory response and in the regulation of the mammalian circadian rhythm. The other candidate regions identified harboured genes associated mainly with milk and meat traits as well as genes involved in immune response/inflammation or associated with behavioural traits. This last category of genes was mainly identified in VCA, which is selected for fighting ability. Overall, our results provide, for the first time, a glimpse into regions of the genome targeted by selection in Valdostana cattle. Finally, this study illustrates the relevance of using multiple complementary approaches to identify genomic regions putatively under selection in livestock.

中文翻译：

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三个瓦尔多斯塔纳牛群中选择特征的全基因组检测

Valdostana 是一种在意大利发展起来的当地两用牛品种。根据毛色、生产水平、形态和气质，在该品种中识别出三个种群：瓦尔多斯塔纳红斑马 (VPR)、瓦尔多斯塔纳黑斑马 (VPN) 和瓦尔多斯塔纳板栗 (VCA)。在这里，我们使用 Bovine 50K SNP 阵列通过结合基于等位基因频率 (FST) 或扩展单倍型纯合性（iHS 和 Rsb）的三种不同统计方法，研究了在这三个群体中选择的推定基因组区域。总共，分别通过 VPR、VPN 和 VCA 中的至少两种方法确定了 8、5 和 8 条染色体，其中包含 13、13 和 16 个可能被选择的基因组区域。这些候选区域中的大多数是特定于人群的，但我们发现了一个跨越 2 个的常见基因组区域。BTA06 上的 38 Mb 与在三个种群中检测到的纯合岛运行重叠或靠近。该区域尤其包括两个众所周知的基因：KDR，一种成熟的毛色基因，和 CLOCK，它在炎症反应的正调节和哺乳动物昼夜节律的调节中起核心作用。其他候选区域确定了主要与牛奶和肉类特征相关的基因以及参与免疫反应/炎症或与行为特征相关的基因。这最后一类基因主要在 VCA 中鉴定，它是根据战斗能力选择的。总体而言，我们的结果首次提供了对 Valdostana 牛选择目标基因组区域的一瞥。最后，