Mastrangelo Salvatore, Ben Jemaa Slim, Ciani Elena, Sottile Gianluca, Moscarelli Angelo, Boussaha Mekki, Montedoro Marina, Pilla Fabio, Cassandro Martino
Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy.
Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, Université de Carthage, Ariana, Tunisia.
J Anim Breed Genet. 2020 Nov;137(6):609-621. doi: 10.1111/jbg.12476. Epub 2020 Mar 26.
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 (F ) 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.
瓦尔多斯塔纳牛是在意大利培育的一种当地两用牛品种。根据毛色、生产水平、形态和性情，该品种内可分为三个群体：瓦尔多斯塔纳红白花牛（VPR）、瓦尔多斯塔纳黑白花牛（VPN）和瓦尔多斯塔纳栗色牛（VCA）。在此，我们通过结合基于等位基因频率（F）或扩展单倍型纯合性（iHS和Rsb）的三种不同统计方法，利用牛50K SNP芯片研究了这三个群体中可能受到选择的基因组区域。在VPR、VPN和VCA中，分别通过至少两种方法鉴定出8条、5条和8条染色体上存在潜在选择的13个、13个和16个基因组区域。这些候选区域大多是群体特异性的，但我们发现一个跨越BTA06上2.38 Mb的共同基因组区域，该区域与在这三个群体中检测到的纯合性岛重叠或紧邻。该区域尤其包括两个知名基因：KDR，一个已确定的毛色基因；以及CLOCK，它在炎症反应的正向调节和哺乳动物昼夜节律的调节中起核心作用。鉴定出的其他候选区域包含主要与牛奶和肉类性状相关的基因，以及参与免疫反应/炎症或与行为性状相关的基因。最后一类基因主要在VCA中被鉴定出来，VCA因其战斗能力而被选育。总体而言，我们的结果首次揭示了瓦尔多斯塔纳牛中受到选择的基因组区域。最后，本研究说明了使用多种互补方法来鉴定家畜中可能受到选择的基因组区域的相关性。
