Single nucleotide polymorphisms in candidate genes are significantly associated with resistance to Haemonchus contortus infection in goats

Mahmuda Bilkis Bintee Alam,Zhenyang Wu,David Russell Notter,Jianhua Cao,Md Jalal Uddin Sarder,Xiaoyong Du,Md Shamsuddin,Kathiravan Periasamy,Shuhong Zhao,Md Motahar Hussain Mondal,Abdullah Ibne Omar,Md Omar Faruque

doi:10.1186/s40104-019-0327-8

Abstract

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

Highlights

Haemonchosis is a major economic problem in goat production in humid, tropical and subtropical regions
Goats are susceptible to gastrointestinal nematode (GIN) parasites in humid, tropical and subtropical regions where goats are reared under natural grazing conditions and are especially affected by Haemonchus contortus (H. contortus), haematophagous abomasal nematode parasite [3, 4]
Descriptive statistics Based on fecal egg counts (FEC), 237 out of 507 goats were infected with H. contortus, resulting in an overall infection rate as 46.75%

Summary

Introduction

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. Goats are susceptible to gastrointestinal nematode (GIN) parasites in humid, tropical and subtropical regions where goats are reared under natural grazing conditions and are especially affected by Haemonchus contortus (H. contortus), haematophagous abomasal nematode parasite [3, 4]. Several candidate genes associated with parasite susceptibility have been identified and partially characterized in different farm animal species. Only a few studies have addressed candidate genes and polymorphisms associated with resistance to GIN in goat [6, 12, 13]

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