A genome scan for QTL affecting resistance to Haemonchus contortus in sheep1

Abstract

Gastrointestinal nematodes are one of the main health issues in sheep breeding. To identify loci affecting the resistance to Haemonchus contortus, a genome scan was carried out using 1,275 Romane × Martinik Black Belly backcross lambs. The entire population was challenged with Haemonchus contortus in 2 consecutive experimental infections, and fecal egg counts (FEC) and packed cell volumes were measured. A subgroup of 332 lambs with extreme FEC was necropsied to determine the total worm burden, length of female worms, sex ratio in the worm population, abomasal pH, and serum and mucosal G immunoglobulins (IgG) responses. Pepsinogen concentration was measured in another subset of 229 lambs. For QTL detection, 160 microsatellite markers were used as well as the Illumina OvineSNP50 BeadChip that provided 42,469 SNP markers after quality control. Linkage, association, and joint linkage and association analyses were performed with the QTLMAP software. Linkage disequilibrium (LD) was estimated within each pure breed, and association analyses were carried out either considering or not the breed origin of the haplotypes. Four QTL regions on sheep chromosomes (OAR)5, 12, 13, and 21 were identified as key players among many other QTL with small to moderate effects. A QTL on OAR21 affecting pepsinogen concentration exactly matched the pepsinogen (PGA5) locus. A 10-Mbp region affecting FEC after the 1st and 2nd infections was found on OAR12. The SNP markers outperformed microsatellites in the linkage analysis. Taking advantage of the LD helped to refine the locations of the QTL mapped on OAR5 and 13.

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

“…Moreover, these authors have identified regions on OAR 1 and 12, although these fell below the suggestive threshold. However, strong evidence for a region on OAR 12 affecting FEC was recently reported by Sallé et al (2012); in a study investigating experimentally infected Martinique Black Belly  Romane sheep, a cluster of highly significant SNPs on OAR 12 was associated with FEC. However, in the current study, no significant SNPs for either Nematodirus or Strongyles FEC on OAR 12 were detected with either approach.…”

“…More recently, GWA studies using higher density SNP panels have become more common. To our knowledge, however, few studies have been published so far using SNP chip data in sheep (for example, Kemper et al, 2011;Sallé et al, 2012). Comparisons across studies are not easy, given the complexity of the trait and the differences among populations and approaches used.…”

“…However, in the current study, no significant SNPs for either Nematodirus or Strongyles FEC on OAR 12 were detected with either approach. In addition, Sallé et al (2012) reported a QTL on OAR 3 associated with worm burden and FEC around 150 Mbp. We also identified a SNP in the same region for Nematodirus FEC at 24 weeks, which was below the significance threshold, but was highly significant (Po0.0001) when further tested as a single SNP in ASReml.…”

“…Several studies have reported quantitative trait loci (QTL) for nematode resistance in sheep (for example, Diez-Tascon et al, 2002;Crawford et al, 2006;Davies et al, 2006;Sallé et al, 2012). However, little overall consensus has emerged from these studies, an outcome compounded by the genetic complexity of the trait and the fact that these studies are very diverse, involving a variety of sheep breeds, nematode species and experimental approaches.…”

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

“…The phenotype available for the two remaining populations (SAR and MBR) was the 'average animal effect' for Strongyles FEC. A detail description of the animals in the MBR population was given in a study by Sallé et al (2012), and for the SAR population in a study by Sechi et al (2009).…”