title: Genome-wide SNP analysis using 2b-RAD sequencing identifies the candidate genes putatively associated with resistance to ivermectin in Haemonchus contortus.
abstract: The excessive and uncontrolled use of anthelmintics, e.g. ivermectin (IVM) for the treatment of livestock parasites has led to widespread resistance in gastrointestinal nematodes, such as Haemonchus contortus. There is an urgent need for better management of drug-use in nematode control and development of novel anthelmintics. Discovery and identification of anthelmintic resistance-associate molecules/markers can provide a basis for rational anthelmintics-use and development of novel drugs. Recent studies have shown that ivermectin resistance in H. contortus is likely to be multi-genic in nature except for several genes coding for IVM target and efflux pump. However, no other IVM resistance-associated genes were characterized by conventional methods or strategies. In the present study we adopted a new strategy, i.e. using genome-wide single nucleotide polymorphism (SNP) analysis based on 2b-RAD sequencing, for discovering SNPs markers across the genomes in both IVM susceptible and resistant isolates of H. contortus and identifying potential IVM resistance-associated genes.
  
  
  
  We discovered 2962 and 2667 SNPs within both susceptible and resistant strains of H. contortus, respectively. A relative lower and similar genetic variations were observed within both resistant and susceptible strains (average π values were equal to 0.1883 and 0.1953, respectively); whereas a high genetic variation was found across both strains (average π value was equal to 0.3899). A significant differentiation across 2b-RAD tags nucleotide sites was also observed between the two strains (average FSTvalue was equal to 0.3076); the larger differences in average FSTwere observed at SNPs loci between coding and noncoding (including intronic) regions. Comparison between resistant and susceptible strains revealed that 208 SNPs loci exhibited significantly elevated FSTvalues, 24 SNPs of those loci were located in the CDS regions of the nine genes and were likely to have signature of IVM directional selection. Seven of the nine candidate genes were predicted to code for some functional proteins such as potential IVM target and/or efflux pump proteins, component proteins of receptor complex in membrane on neuromuscular cells, and transcriptional regulation proteins. Those genes might be involved in resistance to IVM.
  
  
  
  Our data suggest that candidate genes putatively associated with resistance to IVM in H. contortus may be identified by genome-wide SNP analysis using 2b-RAD sequencing.
authors.affiliation: Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, 200241, People's Republic of China.|College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, 010010, Inner Mongolia Nationality Autonomous, People's Republic of China.
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Luo
authors.affiliation: Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, 200241, People's Republic of China.|College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 250014, People's Republic of China.
authors.forename: Xiaona
authors.initials: X
authors.lastname: Shi
authors.affiliation: Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, 200241, People's Republic of China.|Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, Jiangsu Province, People's Republic of China.
authors.forename: Chunxiu
authors.initials: C
authors.lastname: Yuan
authors.affiliation: Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, 200241, People's Republic of China.
authors.forename: Min
authors.initials: M
authors.lastname: Ai
authors.affiliation: Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, 200241, People's Republic of China.|College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 250014, People's Republic of China.
authors.forename: Cheng
authors.initials: C
authors.lastname: Ge
authors.affiliation: State Key Laboratory of Agricultural Microbiology, Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, 430070, Hubei Province, People's Republic of China.
authors.forename: Min
authors.initials: M
authors.lastname: Hu
authors.affiliation: Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, 200241, People's Republic of China. xingangf62@aliyun.com.
authors.forename: Xingang
authors.initials: X
authors.lastname: Feng
authors.affiliation: College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, 010010, Inner Mongolia Nationality Autonomous, People's Republic of China. xiaoyeyang122@sohu.com.
authors.forename: Xiaoye
authors.initials: X
authors.lastname: Yang
mesh_terms: D000818:Animals; D000871:Anthelmintics / Q000494:pharmacology; D018509:DNA, Helminth / Q000235:genetics*; D004351:Drug Resistance / Q000235:genetics*; D055106:Genome-Wide Association Study; D006189:Haemonchus / Q000187:drug effects* / Q000235:genetics; D007559:Ivermectin / Q000494:pharmacology*; D020641:Polymorphism, Single Nucleotide
chemical_list: D000871:Anthelmintics; D018509:DNA, Helminth; D007559:Ivermectin
keywords: 2b-RAD sequencing; Candidate ivermectin resistance-associate genes; Genome-wide SNP analysis; Haemonchus contortus