Background Haemonchosis is a major economic problem in goat production in humid, tropical and subtropical regions. The disease is caused by an abomasal nematode, Haemonchus contortus, which is highly pathogenic in small ruminants. The aim of this study was to identifying single-nucleotide polymorphisms (SNP) that were associated with fecal egg counts (FEC) and could be used as markers to identify resistance to H. contortus in goats.

Results Ten novel variants in the CIITA, ATP2A3, HSPA8, STAT5B, ESYT1, and SERPING1 genes were associated with FEC in goats with a nominal significance level of P < 0.05. Two missense mutation in the exon region of the caprine CIITA gene resulted in replacement of arginine with cysteine at position 9473550 (R9473550C) and aspartic acid with glutamic acid at position 9473870 (D9473870E). Chinese goat breeds had significantly higher FEC than Bangladeshi goat breeds within their respective genotypes. Polymorphism information content (PIC), effective allele number (Ne), and heterozygosity (He) were greatest for the STAT5B_197_A > G SNP locus in all goat breeds. Pairwise coefficients of linkage disequilibrium (D´, r2) revealed complete LD (r2 = 1) between significant SNP polymorphisms in CIITA and SERPING1 and strong LD (r2 = 0.93 and 0.98) between polymorphisms in HSPA8 and ATP2A3, respectively. Correlation coefficient (r) between FEC and body weight (BW) was significantly positive (r = 0.56***, P < 0.001) but that between FEC and packed cell volume (PCV) was negatively significant (r = − 0.47**, P < 0.01) in the total population of goats. On the other hand, correlation coefficient (r) between BW and PCV was not significant in total population of goats. Association analysis revealed that haplotypes within ATP2A3, HSPA8, and SERPING1 were significantly associated with FEC. Quantitative real-time PCR revealed that the relative expression of mRNA was higher (P < 0.001) for resistant, compared to susceptible, groups of goats for all candidate genes except CIITA.

Conclusions This study identified SNP markers that can potentially be used in marker-assisted selection programs to develop goat breeds that are resistant to H. contortus.