Data from: Genome-wide association and regional heritability mapping to identify loci underlying variation in nematode resistance and body weight in Scottish Blackface lambs

The genetic architecture underlying nematode resistance and body weight in Blackface lambs was evaluated comparing genome-wide association (GWA) and regional heritability mapping (RHM) approaches. The traits analysed were faecal egg count (FEC) and immunoglobulin A activity against third-stage larvae from Teladorsagia circumcincta, as indicators of nematode resistance, and body weight in a population of 752 Scottish Blackface lambs, genotyped with the 50k single-nucleotide polymorphism (SNP) chip. FEC for both Nematodirus and Strongyles nematodes (excluding Nematodirus), as well as body weight were collected at approximately 16, 20 and 24 weeks of age. In addition, a weighted average animal effect was estimated for both FEC and body weight traits. After quality control, 44 388 SNPs were available for the GWA analysis and 42 841 for the RHM, which utilises only mapped SNPs. The same fixed effects were used in both analyses: sex, year, management group, litter size and age of dam, with day of birth as covariate. Some genomic regions of interest for both nematode resistance and body weight traits were identified, using both GWA and RHM approaches. For both methods, strong evidence for association was found on chromosome 14 for Nematodirus average animal effect, chromosome 6 for Strongyles FEC at 16 weeks and chromosome 6 for body weight at 16 weeks. Across the entire data set, RHM identified more regions reaching the suggestive level than GWA, suggesting that RHM is capable of capturing some of the variation not detected by GWA analyses.

本研究通过对比全基因组关联分析（Genome-Wide Association, GWA）与区域遗传力定位（Regional Heritability Mapping, RHM）两种方法，评估了黑脸羔羊抗线虫性与体重的遗传结构。本研究的分析性状包括以粪便虫卵计数（Faecal Egg Count, FEC）和针对环状奥斯特塔根线虫（Teladorsagia circumcincta）第三期幼虫的免疫球蛋白A活性作为抗线虫性评价指标，以及体重；研究群体包含752只苏格兰黑脸羔羊，均通过50k单核苷酸多态性（Single-Nucleotide Polymorphism, SNP）芯片完成基因分型。研究分别在羔羊约16、20和24周龄时，采集尖尾线虫属（Nematodirus）与圆线亚目线虫（不含尖尾线虫属）的粪便虫卵计数数据，以及体重数据。此外，本研究还针对粪便虫卵计数和体重两项性状，估算了加权平均动物效应值。经过质量控制后，可用于全基因组关联分析的单核苷酸多态性位点共44388个；而区域遗传力定位仅使用已定位的单核苷酸多态性位点，可用位点为42841个。两项分析均采用相同的固定效应变量：性别、出生批次、管理组、产羔数以及母畜年龄，并以出生日龄作为协变量。通过全基因组关联分析与区域遗传力定位两种方法，本研究均鉴定出若干与抗线虫性和体重性状相关的潜在基因组区域。两种方法均检测到强关联信号：14号染色体上与尖尾线虫属平均动物效应相关的区域、16周龄时圆线亚目线虫粪便虫卵计数相关的6号染色体区域，以及16周龄时体重相关的6号染色体区域。在全数据集范围内，区域遗传力定位鉴定出的提示性关联区域数量多于全基因组关联分析，表明区域遗传力定位能够捕获部分全基因组关联分析未检测到的遗传变异。