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.

Figure 1

Manhattan plot displaying the GWA results (−log₁₀(P) of the corresponding Pc1df, P-values corrected for the genomic inflation factor λ) and Q–Q plot (below) of observed P-values against the expected P-values for Nematodirus average animal effect. Genome-wide P<0.05 (solid line) and suggestive (dashed line) thresholds are also shown.

Figure 2

Manhattan plot displaying the GWA results (−log₁₀(P) of the corresponding Pc1df, P-values corrected for the genomic inflation factor λ) and Q–Q plot (below) of observed P-values against the expected P-values for Strongyles FEC at 16 weeks. Genome-wide P<0.05 (solid line) and suggestive (dashed line) thresholds are also shown.

Figure 3

Manhattan plot displaying the GWA results (−log₁₀(P) of the corresponding Pc1df, P-values corrected for the genomic inflation factor λ) and Q–Q plot (below) of observed P-values against the expected P-values for body weight average animal effect. Genome-wide P<0.05 (solid line) and suggestive (dashed line) thresholds are also shown.

Figure 4

Plot of the LRT across the genome (a) and for chromosome 14 (b) for Nematodirus average animal effect. The windows indicated by the purple rectangle in plot (b) were analysed using smaller windows (that is, 50 SNPs). These windows are reported in plot (c) and highlighted by a purple rectangle. Genome-wide P<0.05 (in green) and suggestive (in red) thresholds are also shown in (b) and (c). In plots (b) and (c), the first SNP identified by the purple rectangles is OAR14_40458094.1 (position 38703731 bp) and the last one is s26895.1 (position 51406211 bp).