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）两种分析策略，评估了苏格兰黑脸羔羊抗线虫性状与体重的遗传架构。本研究分析的性状包括两类抗线虫指示性状：粪便虫卵计数（faecal egg count, FEC）以及针对环纹背带线虫（Teladorsagia circumcincta）三期幼虫的免疫球蛋白A活性，同时分析了752只苏格兰黑脸羔羊群体的体重性状；所有受试个体均通过50k单核苷酸多态性（single-nucleotide polymorphism, SNP）芯片完成基因分型。 研究分别在受试羔羊约16、20和24周龄时，采集其纽结线虫属（Nematodirus）、圆线虫属（Strongyles，不含纽结线虫属）的粪便虫卵计数数据与体重数据。此外，本研究还针对粪便虫卵计数与体重两类性状，分别估算了加权平均个体效应。 经过质量控制流程后，全基因组关联分析可使用的单核苷酸多态性位点共计44388个；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。两种分析采用完全一致的固定效应因子：性别、出生年份、饲养管理组、产羔数以及母畜年龄，并以出生日龄作为协变量。 本研究通过全基因组关联分析与区域遗传力定位两种方法，均鉴定出了与抗线虫性状及体重性状相关的候选基因组区域。针对两种分析方法，均在14号染色体上检测到与纽结线虫属加权平均个体效应显著关联的遗传位点，在6号染色体上检测到与16周龄圆线虫粪便虫卵计数、16周龄体重显著关联的遗传位点。 在全数据集范围内，区域遗传力定位鉴定出的达到提示性显著水平的基因组区域数量多于全基因组关联分析，这表明区域遗传力定位能够捕获部分全基因组关联分析未能检测到的遗传变异。