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

Abstract

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.

Accuracy of genomic prediction within and across populations for nematode resistance and body weight traits in sheep

“…The heritability estimates obtained either fitting only one chromosome or when simultaneously fitting one chromosome plus the whole G matrix showed that nematode resistance in sheep is a complex trait with contributions from many regions in the genome affecting these traits. However, with the exception of Nematodirus FEC at 16 weeks (Supplementary Figure S2; Riggio et al, 2013), the results favour a polygenic mode of inheritance, which is largely captured by additive relationships between animals. This is illustrated by the results when a chromosome at a time was fitted that overestimated the proportion of genetic variance explained as opposed to when one chromosome and the G matrix were simultaneously fitted.…”

“…The population comprised F2 and double backcross lambs from two originally different lines, bred from 10 sires (half-sib family size = 11-146). More details on the data structure and the phenotypes are given in a study by Riggio et al (2013). Faecal samples were collected from the rectum of each lamb at the time of weighing and used for FEC assays, using the modified McMaster technique as described by Gordon and Whitlock (1939) and Bairden (1991).…”

Genetic Traits of Relevance to Sustainability of Smallholder Sheep Farming Systems in South Africa

“…BMPR1B is located on chromosome 6 and have six different mutations for this gene, whereas B4GALNT2 is located on chromosome 11. Fecal egg count (FEC) is used to measure resistance to gastrointestinal parasites in sheep, and the causal variants for FEC using a genome wide association study were found on chromosome 14 (linked to Nematodrius average animal effect) and chromosome 6 (Strongyles FEC at 16 weeks) [90]. Various other genes have been linked to host resistance to different gastrointestinal parasites (Haemonchus contortus, Teladorsagia circumcinta, and Trichostrongylus colubriformis) [91].…”

“…This serves as a backbone for genome wide association studies (GWAS) that can be used to associate phenotypes with causal variants [23,89]. Causal variants have been identified for various traits important for sustainability including reproduction [23], gastrointestinal parasite resistance [90,91], growth and meat production [92][93][94], wool traits [95] and adaptation in extreme environments [96] (Table 2). Table 2.…”

Detection of a quantitative trait locus associated with resistance to infection with Trichuris suis in pigs

“…Several studies have detected QTLs associated with helminth infection in livestock and humans (e.g., WilliamsBlangero et al, 2008;Coppieters et al, 2009;Skallerup et al, 2012;Riggio et al, 2013); however, no such studies have been conducted for T. suis in pigs. This natural host-parasite system may also serve as a model for the closely related whipworm T. trichiura, which infects nearly 500 million people and has a significant socio-economic impact (Pullan et al, 2014).…”