Bedhiaf-Romdhani Sonia, Baazaoui Imen, Dodds Ken G, Brauning Rudiger, Anderson Rayna M, Van Stijn Tracey C, McCulloch Alan F, McEwan John Colin
Laboratoire des Productions Animales et Fourragères, INRA-Tunisie, Université de Carthage, Tunis, Tunisia.
Faculty of Sciences of Bizerte, University of Carthage, Bizerte, Tunisia.
Anim Genet. 2023 Jun;54(3):389-397. doi: 10.1111/age.13296. Epub 2023 Feb 1.
In developing countries, the use of simple and cost-efficient molecular technology is crucial for genetic characterization of local animal resources and better development of conservation strategies. The genotyping by sequencing (GBS) technique, also called restriction enzyme- reduced representational sequencing, is an efficient, cost-effective method for simultaneous discovery and genotyping of many markers. In the present study, we applied a two-enzyme GBS protocol (PstI/MspI) to discover and genotype SNP markers among 197 Tunisian sheep samples. A total of 100 333 bi-allelic SNPs were discovered and genotyped with an SNP call rate of 0.69 and mean sample depth 3.33. The genomic relatedness between 183 samples grouped the samples perfectly to their populations and pointed out a high genetic relatedness of inbred subpopulation reflecting the current adopted reproductive strategies. The genome-wide association study contrasting fat vs. thin-tailed breeds detected 41 significant variants including a peak positioned on OAR20. We identified FOXC1, GMDS, VEGFA, OXCT1, VRTN and BMP2 as the most promising for sheep tail-type trait. The GBS data have been useful to assess the population structure and improve our understanding of the genomic architecture of distinctive characteristics shaped by selection pressure in local sheep breeds. This study successfully investigates a cost-efficient method to discover genotypes, assign populations and understand insights into sheep adaptation to arid area. GBS could be of potential utility in livestock species in developing/emerging countries.
在发展中国家，使用简单且经济高效的分子技术对于当地动物资源的遗传特征分析以及更好地制定保护策略至关重要。测序基因分型（GBS）技术，也称为限制性酶切简化代表性测序，是一种用于同时发现和基因分型多个标记的高效、经济有效的方法。在本研究中，我们应用双酶GBS方案（PstI/MspI）在197个突尼斯绵羊样本中发现SNP标记并进行基因分型。共发现并基因分型了100333个双等位基因SNP，SNP检出率为0.69，平均样本深度为3.33。183个样本之间的基因组相关性将样本完美地按群体分组，并指出近交亚群体具有高度的遗传相关性，反映了当前采用的繁殖策略。全基因组关联研究对比肥尾与瘦尾品种，检测到41个显著变异，其中一个峰值位于OAR20上。我们确定FOXC1、GMDS、VEGFA、OXCT1、VRTN和BMP2是绵羊尾型性状最有前景的基因。GBS数据有助于评估群体结构，并增进我们对当地绵羊品种中受选择压力影响的独特特征的基因组结构的理解。本研究成功探索了一种经济有效的方法来发现基因型、划分群体，并深入了解绵羊对干旱地区的适应性。GBS在发展中/新兴国家的家畜物种中可能具有潜在用途。
