Riggio V, Pong-Wong R, Sallé G, Usai M G, Casu S, Moreno C R, Matika O, Bishop S C
The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, UK.
J Anim Breed Genet. 2014 Dec;131(6):426-36. doi: 10.1111/jbg.12071. Epub 2014 Jan 8.
Gastrointestinal nematode infections are one of the main health/economic issues in sheep industries, worldwide. Indicator traits for resistance such as faecal egg count (FEC) are commonly used in genomic studies; however, published results are inconsistent among breeds. Meta (or joint)-analysis is a tool for aggregating information from multiple independent studies. The aim of this study was to identify loci underlying variation in FEC, as an indicator of nematode resistance, in a joint analysis using data from three populations (Scottish Blackface, Sarda × Lacaune and Martinik Black-Belly × Romane), genotyped with the ovine 50k SNP chip. The trait analysed was the average animal effect for Strongyles and Nematodirus FEC data. Analyses were performed with regional heritability mapping (RHM), fitting polygenic effects with either the whole genomic relationship matrix or matrices excluding the chromosome being interrogated. Across-population genomic covariances were set to zero. After quality control, 4123 animals and 38 991 SNPs were available for the analysis. RHM identified genome-wide significant regions on OAR4, 12, 14, 19 and 20, with the latter being the most significant. The OAR20 region is close to the major histocompatibility complex, which has often been proposed as a functional candidate for nematode resistance. This region was significant only in the Sarda × Lacaune population. Several other regions, on OAR1, 3, 4, 5, 7, 12, 19, 20 and 24, were significant at the suggestive level.
胃肠道线虫感染是全球绵羊产业中主要的健康/经济问题之一。在基因组研究中，通常使用诸如粪便虫卵计数（FEC）等抗性指标性状；然而，不同品种间已发表的结果并不一致。荟萃（或联合）分析是一种整合来自多个独立研究信息的工具。本研究的目的是通过对三个群体（苏格兰黑脸羊、撒丁岛羊×拉库内羊以及马提尼克黑腹羊×罗马尼羊）的数据进行联合分析，利用绵羊50k SNP芯片进行基因分型，来确定作为线虫抗性指标的FEC变异的潜在基因座。分析的性状是圆线虫和细颈线虫FEC数据的平均个体效应。使用区域遗传力定位（RHM）进行分析，通过全基因组关系矩阵或排除被检测染色体的矩阵来拟合多基因效应。设定跨群体基因组协方差为零。经过质量控制后，有4123只动物和38991个SNP可用于分析。RHM在绵羊4号、12号、14号、19号和20号染色体上鉴定出全基因组显著区域，其中20号染色体上的区域最为显著。绵羊20号染色体区域靠近主要组织相容性复合体，该复合体常被认为是线虫抗性的功能候选基因。该区域仅在撒丁岛羊×拉库内羊群体中显著。在绵羊1号、3号、4号、5号、7号、12号、19号、20号和24号染色体上的其他几个区域在提示水平上显著。
