Ben-Jemaa Slim, Senczuk Gabriele, Ciani Elena, Ciampolini Roberta, Catillo Gennaro, Boussaha Mekki, Pilla Fabio, Portolano Baldassare, Mastrangelo Salvatore
Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, University of Carthage, Ariana, Tunisia.
Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, Italy.
Front Genet. 2021 Apr 28;12:675569. doi: 10.3389/fgene.2021.675569. eCollection 2021.
The Maremmana cattle is an ancient Podolian-derived Italian breed raised in semi-wild conditions with distinctive morphological and adaptive traits. The aim of this study was to detect potential selection signatures in Maremmana using medium-density single nucleotide polymorphism array. Putative selection signatures were investigated combining three statistical approaches designed to quantify the excess of haplotype homozygosity either within (integrated haplotype score, ) or among pairs of populations ( and ), and contrasting the Maremmana with a single reference population composed of a pool of seven Podolian-derived Italian breeds. Overall, the three haplotype-based analyses revealed selection signatures distributed over 19 genomic regions. Of these, six relevant candidate regions were identified by at least two approaches. We found genomic signatures of selective sweeps spanning genes related to mitochondrial function, muscle development, growth, and meat traits (, , , , and ), which reflects the different breeding schemes between Maremmana (semi-wild conditions) and the other Podolian-derived Italian breeds (semi-extensive). We also identified several genes linked to Maremmana adaptation to the environment of the western-central part of Italy, known to be hyperendemic for malaria and other tick-borne diseases. These include several chemokine (C-C motif) ligand genes crucially involved in both innate and adaptive immune responses to intracellular parasite infections and other genes playing key roles in pulmonary disease (, , and ) or strongly associated with malaria resistance/susceptibility (). Our results provide a glimpse into diverse selection signatures in Maremmana cattle and can be used to enhance our understanding of the genomic basis of environmental adaptation in cattle.
马雷马纳牛是一种源自古老波多利牛的意大利品种，在半野生条件下饲养，具有独特的形态和适应特征。本研究的目的是使用中密度单核苷酸多态性阵列检测马雷马纳牛潜在的选择印记。通过结合三种统计方法来研究推定的选择印记，这些方法旨在量化群体内部（综合单倍型评分，iHS）或成对群体之间（FST和XP-EHH）单倍型纯合性的过量情况，并将马雷马纳牛与由七个源自波多利牛的意大利品种组成的单一参考群体进行对比。总体而言，基于单倍型的三种分析揭示了分布在19个基因组区域的选择印记。其中，至少两种方法鉴定出了六个相关候选区域。我们发现了选择性清除的基因组印记，其跨越了与线粒体功能、肌肉发育、生长和肉质性状相关的基因（ATP5G1、ACSL1、CAST、MYF6和PRKAG3），这反映了马雷马纳牛（半野生条件）与其他源自波多利牛的意大利品种（半粗放型）之间不同的育种方案。我们还鉴定出了几个与马雷马纳牛适应意大利中西部环境相关的基因，该地区以疟疾和其他蜱传疾病高度流行而闻名。这些基因包括几个趋化因子（C-C基序）配体基因，它们在对细胞内寄生虫感染的先天性和适应性免疫反应中都起着关键作用，以及其他在肺部疾病中起关键作用（IL6、IL1B和SPP1）或与疟疾抗性/易感性密切相关（APOL1）的基因。我们的结果让我们得以一窥马雷马纳牛多样的选择印记，并可用于增进我们对牛环境适应基因组基础的理解。
