Abstract
BackgroundGastrointestinal 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 Fst outliers in three different breeds of sheep and goats exposed to H. contortus.ResultsOur 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.ConclusionsA 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.
Highlights
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 resistance based on Fecal egg count (FEC) is a heritable trait in both sheep and goats, with heritability estimates ranging between 0.01 to 0.65, and 0.1 to 0.33, respectively [7,8,9,10,11,12,13,14,15,16]
Genotyping, quality control and population structure in sheep and goats The sheep and goat DNA samples were sequenced with a median depth of 24x across 5000 probes The initial SNP data set consisted of 5346 SNPs for both sheep and goats
Summary
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. High disease incidence has been observed in the Southeast US regions [2] and infection with Haemonchus contortus is common throughout the year [3, 4] This blood sucking parasite inhabits the abomasum of the host and it is responsible for weight loss, anemia and reduced performance [2]. Host genetic variation for GNI promises great opportunities for selective breeding of sheep and goats with increased resistance to H. contortus. In accordance, breeding studies of small ruminants have revealed a FEC reduction after concurrent selective breeding of naturally resistant sheep to GIN infection [17,18,19]
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