Genetic parameters and haplotype-based genome-wide association study of indicator traits for gastrointestinal parasite resistance in Santa Ines sheep

Genetic parameters are of great importance in animal breeding since they determine the strategies necessary to increase the genetic progress in economic traits, for example indicator traits for resistance to endoparasites in sheep. Furthermore, genetic markers have been used to identify genomic regions associated with economically important traits, which can help increase the genetic response through genomic selection. Therefore, this study aimed to estimate genetic parameters and perform a haplotype-based genome wide association study (GWAS) to identify genomic regions associated with indicator traits for endoparasite resistance in Santa Ines sheep. Haplotype GWAS was performed using linkage disequilibrium blocks (haploblocks) defined by the Haploview software. Records from 1725 animals for Famacha© (FAM, N = 5560), packed cell volume (PCV, N = 5135), total plasma protein (TPP, N = 4356), and fecal egg count (FEC, N = 4248) were used for analysis. The pedigree file contained information from 4821 animals; of these, 638 animals were genotyped using the Ovine SNP50 Genotyping BeadChip. Heritability estimates were moderate for FAM (0.26), PCV (0.26), TPP (0.16), and log-transformed FEC (0.19). Genomic regions that explained more than 0.3 % of the total additive genetic variance of the traits were defined as significant. These regions overlapped with quantitative traits loci associated with eosinophil number, fecal egg count, hematocrit, and immunoglobulin levels. In the top regions for the traits evaluated we found genes individually involved in inflammatory response, immunity, macrophage function in host-pathogen interactions, and other biological functions. All indicator traits for resistance to gastrointestinal parasites evaluated in this study exhibited sufficient genetic variability to respond to selection and can be used to improve the health and consequently the production of Santa Ines sheep.