Mastrangelo Salvatore, Di Gerlando Rosalia, Tolone Marco, Tortorici Lina, Sardina Maria Teresa, Portolano Baldassare
Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Viale delle Scienze, 90128, Palermo, Italy.
BMC Genet. 2014 Oct 10;15:108. doi: 10.1186/s12863-014-0108-5.
The recent availability of sheep genome-wide SNP panels allows providing background information concerning genome structure in domestic animals. The aim of this work was to investigate the patterns of linkage disequilibrium (LD), the genetic diversity and population structure in Valle del Belice, Comisana, and Pinzirita dairy sheep breeds using the Illumina Ovine SNP50K Genotyping array.
Average r (2) between adjacent SNPs across all chromosomes was 0.155 ± 0.204 for Valle del Belice, 0.156 ± 0.208 for Comisana, and 0.128 ± 0.188 for Pinzirita breeds, and some variations in LD value across chromosomes were observed, in particular for Valle del Belice and Comisana breeds. Average values of r (2) estimated for all pairwise combinations of SNPs pooled over all autosomes were 0.058 ± 0.023 for Valle del Belice, 0.056 ± 0.021 for Comisana, and 0.037 ± 0.017 for Pinzirita breeds. The LD declined as a function of distance and average r (2) was lower than the values observed in other sheep breeds. Consistency of results among the several used approaches (Principal component analysis, Bayesian clustering, F ST, Neighbor networks) showed that while Valle del Belice and Pinzirita breeds formed a unique cluster, Comisana breed showed the presence of substructure. In Valle del Belice breed, the high level of genetic differentiation within breed, the heterogeneous cluster in Admixture analysis, but at the same time the highest inbreeding coefficient, suggested that the breed had a wide genetic base with inbred individuals belonging to the same flock. The Sicilian breeds were characterized by low genetic differentiation and high level of admixture. Pinzirita breed displayed the highest genetic diversity (He, Ne) whereas the lowest value was found in Valle del Belice breed.
This study has reported for the first time estimates of LD and genetic diversity from a genome-wide perspective in Sicilian dairy sheep breeds. Our results indicate that breeds formed non-overlapping clusters and are clearly separated populations and that Comisana sheep breed does not constitute a homogenous population. The information generated from this study has important implications for the design and applications of association studies as well as for development of conservation and/or selection breeding programs.
近期绵羊全基因组SNP芯片的出现，使得提供有关家畜基因组结构的背景信息成为可能。本研究的目的是利用Illumina绵羊SNP50K基因分型芯片，研究贝利切谷、科米萨纳和平齐里塔乳用绵羊品种的连锁不平衡（LD）模式、遗传多样性和群体结构。
贝利切谷品种所有染色体上相邻SNP之间的平均r²为0.155±0.204，科米萨纳品种为0.156±0.208，平齐里塔品种为0.128±0.188，并且观察到各染色体的LD值存在一些差异，特别是贝利切谷和科米萨纳品种。贝利切谷品种在所有常染色体上SNP的所有成对组合估计的平均r²值为0.058±0.023，科米萨纳品种为0.056±0.021，平齐里塔品种为0.037±0.017。LD随距离增加而下降，平均r²低于其他绵羊品种观察到的值。几种使用的方法（主成分分析、贝叶斯聚类、FST、邻接网络）结果的一致性表明，虽然贝利切谷和平齐里塔品种形成一个独特的聚类，但科米萨纳品种存在亚结构。在贝利切谷品种中，品种内高水平的遗传分化、混合分析中的异质聚类，但同时最高的近交系数，表明该品种具有广泛的遗传基础，近交个体属于同一群体。西西里品种的特点是遗传分化低和混合程度高。平齐里塔品种表现出最高的遗传多样性（He、Ne），而贝利切谷品种的值最低。
本研究首次从全基因组角度报道了西西里乳用绵羊品种的LD和遗传多样性估计。我们的结果表明，这些品种形成了不重叠的聚类，是明显分开的群体，并且科米萨纳绵羊品种不构成一个同质群体。本研究产生的信息对关联研究的设计和应用以及保护和/或选择育种计划的制定具有重要意义。
