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Background  Gastrointestinal nematode infection (GNI) is the most important disease affecting the small ruminant industry in U.S. The environmental conditions in the southern United States are ideal for the survival of the most pathogenic gastrointestinal nematode,  Haemonchus contortus . Host genetic variation for resistance to  H. contortus  allows selective breeding for increased resistance of animals. This selection process increases the prevalence of particular alleles in sheep and goats and creates unique genetic patterns in the genome of these species. The aim of this study was to identify loci with divergent allelic frequencies in a candidate gene panel of 100 genes using two different approaches (frequentist and Bayesian) to estimate  F st outliers in three different breeds of sheep and goats exposed to  H. contortus .    Results  Our results for sheep populations showed SNPs under selection in  C3AR1 ,  CSF3 ,  SOCS2 ,  NOS2 ,  STAT5B ,  TGFB2  and  IL2RA  genes using frequentist and Bayesian approaches. For goats, SNPs in  CD1D ,  ITGA9 ,  IL12A ,  IL13RA1, CD86  and  TGFB2  genes were under selection. Common signatures of selection in both species were observed in  NOS2 ,  TGFB2  and  TLR4  genes. Directional selection was present in all SNPs evaluated in the present study.    Conclusions  A total of 13 SNPs within 7 genes of our candidate gene panel related to  H. contortus  exposure were identified under selection in sheep populations. For goats, 11 SNPs within 7 genes were identified under selection. Results from this study support the hypothesis that resistance to  H. contortus  is likely to be controlled by many loci. Shared signatures of selection related to mechanisms of immune protection against  H. contortus  infection in sheep and goats could be useful targets in breeding programs aimed to produce resistant animals with low FEC.

Signatures of selection for resistance to Haemonchus contortus in sheep and goats