Shihabi Mario, Lukic Boris, Cubric-Curik Vlatka, Brajkovic Vladimir, Oršanić Milan, Ugarković Damir, Vostry Luboš, Curik Ino
Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia.
Department for Animal Production and Biotechnology, Faculty of Agrobiotechnical Sciences Osijek, J.J. Strossmayer University of Osijek, Osijek, Croatia.
Front Genet. 2022 Apr 11;13:887582. doi: 10.3389/fgene.2022.887582. eCollection 2022.
Sheep are one of the most important livestock species in Croatia, found mainly in the Mediterranean coastal and mountainous regions along the East Adriatic coast, well adapted to the environment and mostly kept extensively. Our main objective was therefore to map the positive selection of the X-chromosome (18,983 SNPs that passed quality control), since nothing is known about the adaptation genes on this chromosome for any of the breeds from the Balkan cluster. Analyses were performed on a sample of eight native Croatian breeds (101 females and 100 males) representing the East Adriatic metapopulation and on 10 mouflons (five females and males), all sampled in Croatia. Three classical within-population approaches (extreme Runs of Homozygosity islands, integrated Haplotype Score, and number of Segregating Sites by Length) were applied along with our new approach called Haplotype Richness Drop (HRiD), which uses only the information contained in male haplotypes. We have also shown that phylogenetic analyses, such as the Median-joining network, can provide additional information when performed with the selection signals identified by HRiD. Our new approach identifies positive selection signals by searching for genomic regions that exhibit a sudden decline in haplotype richness. In total, we identified 14 positive selection signals, 11 using the classical approach and three using the HRiD approach, all together containing 34 annotated genes. The most reliable selection signal was mapped by all four approaches in the same region, overlapping between 13.17 and 13.60 Mb, and assigned to the CA5B, ZRSR2, AP1S2, and GRPR genes. High repeatability (86%) of results was observed, as 12 identified selection signals were also confirmed in other studies with sheep. HRiD offers an interesting possibility to be used complementary to other approaches or when only males are genotyped, which is often the case in genomic breeding value estimations. These results highlight the importance of the X-chromosome in the adaptive architecture of domestic ruminants, while our novel HRiD approach opens new possibilities for research.
绵羊是克罗地亚最重要的家畜品种之一，主要分布在亚得里亚海沿岸东部的地中海沿海和山区，对环境适应性良好，大多以粗放方式饲养。因此，我们的主要目标是绘制X染色体（18,983个通过质量控制的单核苷酸多态性）的正选择图谱，因为对于巴尔干集群中的任何品种，关于该染色体上的适应基因我们一无所知。对代表亚得里亚海东部复合种群的八个克罗地亚本土品种（101只雌性和100只雄性）的样本以及10只摩弗伦羊（五只雌性和五只雄性）进行了分析，所有样本均采自克罗地亚。应用了三种经典的群体内方法（纯合性极端片段、整合单倍型得分和按长度划分的分离位点数）以及我们称为单倍型丰富度下降（HRiD）的新方法，该方法仅使用雄性单倍型中包含的信息。我们还表明，系统发育分析，如中介连接网络，在与HRiD识别的选择信号一起进行时，可以提供额外信息。我们的新方法通过搜索单倍型丰富度突然下降的基因组区域来识别正选择信号。总共，我们识别出14个正选择信号，其中11个使用经典方法，3个使用HRiD方法，总共包含34个注释基因。所有四种方法在同一区域绘制出最可靠的选择信号，重叠区间为13.17至13.60兆碱基，并对应于CA5B、ZRSR2、AP1S2和GRPR基因。观察到结果具有高重复性（86%），因为在其他绵羊研究中也证实了12个识别出的选择信号。HRiD提供了一种有趣的可能性，可作为其他方法的补充使用，或者在仅对雄性进行基因分型时使用，而这在基因组育种值估计中经常出现。这些结果突出了X染色体在家养反刍动物适应性结构中的重要性，而我们新颖的HRiD方法为研究开辟了新的可能性。
