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

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.

Genomic regions underlying susceptibility to bovine tuberculosis in Holstein-Friesian cattle

“…As discussed, reasons for such discrepancies include the complexity of the phenotype, the largely polygenic inheritance mode of the trait, genetic differences between populations and differences in methodologies used across studies. Additional reasons may be different allele frequencies of either the marker or causative mutation even when the same QTL is segregating in various populations, and possible mutation linkage phases that may not be the same between populations [20, 47]. Moreover, bTB is an infectious disease whose profile and transmission dynamics may differ across populations and geographic regions, thereby further complicating the genomic study of the underlying control mechanism.…”

Transcriptional profiling of the ovine abomasal lymph node reveals a role for timing of the immune response in gastrointestinal nematode resistance

“…Future work on validating the SNP of interest from this study would require a larger number of Scottish Blackface animals. As noted in reports on multiple studies, host resistance to GIN appears to be mediated by many genes, each with a relatively small effect (Kemper et al, 2011;Riggio et al, 2014). The candidate gene approach is therefore unlikely to capture all of the variation underlying known phenotypic differences; future work on identifying SNP to be used in selection programmes will likely focus on utilising a panel of SNP in addition to searching for individual causative mutations.…”

Association of MHC class II haplotypes with reduced faecal nematode egg count and IgA activity in British Texel sheep

“…12,13 Several groups have shown associations between genetic variants in the MHC and faecal egg counts. 5,[14][15][16][17] In particular, the DRB1*11:01 allele has been associated with lower faecal egg counts in Scottish Blackface 5 and Suffolk sheep. 15 However, this association was not confirmed in a population of Texel sheep.…”

“…The association between the MHC and nematode infection of sheep is one of the most convincing examples of an association with a major disease of livestock . Several groups have shown associations between genetic variants in the MHC and faecal egg counts . In particular, the DRB1*11:01 allele has been associated with lower faecal egg counts in Scottish Blackface and Suffolk sheep .…”