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. 2014 Dec;131(6):426-36.
doi: 10.1111/jbg.12071. Epub 2014 Jan 8.

A joint analysis to identify loci underlying variation in nematode resistance in three European sheep populations

V Riggio  1 , R Pong-Wong, G Sallé, M G Usai, S Casu, C R Moreno, O Matika, S C Bishop
Affiliations
Free PMC article

A joint analysis to identify loci underlying variation in nematode resistance in three European sheep populations

V Riggio et al. J Anim Breed Genet. 2014 Dec.
Free PMC article

Abstract

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.

Keywords: Joint analysis; SNP; nematode resistance; regional heritability mapping; sheep.

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Figures

Figure 1
Figure 1
Plot of the likelihood ratio test (LRT) across the genome, considering the whole genomic relationship matrix for Strongyles average animal effect. Genome-wide p < 0.05 (solid line) and suggestive (dashed line) thresholds are also shown.
Figure 2
Figure 2
Plot of the likelihood ratio test (LRT) across the genome, considering the n-1 chromosome genomic relationship matrix for Strongyles average animal effect. Genome-wide p < 0.05 (solid line) and suggestive (dashed line) thresholds are also shown.
Figure 3
Figure 3
Plot of the likelihood ratio test (LRT) across chromosome 20, considering the n-1 chromosome genomic relationship matrix for Strongyles average animal effect. Genome-wide p < 0.05 (solid line) and suggestive (dashed line) thresholds are also shown.
Figure 4
Figure 4
Plot of the likelihood ratio test (LRT) across the genome, considering the n-1 chromosome genomic relationship matrix for data combining Nematodirus for Scottish Blackface population and Strongyles for Sarda × Lacaune and Martinik Black-Belly × Romane populations. Genome-wide p < 0.05 (solid line) and suggestive (dashed line) thresholds are also shown.
See this image and copyright information in PMC

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