title: Development of Vibrio spp. infection resistance related SNP markers using multiplex SNaPshot genotyping method in the clam Meretrix meretrix.
abstract: The clam Meretrix meretrix is a commercially important mollusc species in the coastal areas of South and Southeast Asia. In the present study, large-scale SNPs were genotyped by the Multiplex SNaPshot genotyping method among the stocks of M. meretrix with different Vibrio spp. infection resistance profile. Firstly, the AUTOSNP software was applied to mine SNPs from M. meretrix transcriptome, and 323 SNP loci (including 120 indels) located on 64 contigs were selected based on Uniprot-GO associations. Then, 38 polymorphic SNP loci located on 15 contigs were genotyped successfully in the clam stocks with different resistance to Vibrio parahaemolyticus infection (11-R and 11-S groups). Pearson's Chi-square test was applied to compare the allele and genotype frequency distributions of the SNPs between the different stocks, and seven SNP markers located on three contigs were found to be associated with V. parahaemolyticus infection resistance trait. Haplotype-association analysis showed that six haplotypes had significantly different frequency distributions in 11-S and 11-R (P < 0.05). With selective genotyping between 09-R and 09-C populations, which had different resistance to Vibrio harveyi infection, four out of the seven selected SNPs had significantly different distributions (P < 0.05) and therefore they were considered to be associated with Vibrio spp. infection resistance. Sequence alignments and annotations indicated that the contigs containing the associated SNPs had high similarity to the immune related genes. All these results would be useful for the future marker-assisted selection of M. meretrix strains with high Vibrio spp. infection resistance.
authors: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100039, China.
authors: Qing
authors: Q
authors: Nie
authors: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
authors: Xin
authors: X
authors: Yue
authors: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China. Electronic address: bzliu@qdio.ac.cn.
authors: Baozhong
authors: B
authors: Liu
mesh_terms: D000818:Animals; D049872:Bivalvia / Q000235:genetics* / Q000276:immunology / Q000382:microbiology*; D016009:Chi-Square Distribution; D020451:Contig Mapping; D005819:Genetic Markers / Q000235:genetics; D006239:Haplotypes; D007113:Immunity, Innate / Q000235:genetics*; D058977:Molecular Sequence Annotation; D060885:Multiplex Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D014733:Vibrio / Q000502:physiology*; D014736:Vibrio parahaemolyticus / Q000502:physiology
chemical_list: D005819:Genetic Markers
keywords: Marker-trait association analysis; Meretrix meretrix; Selective genotyping; Single nucleotide polymorphism (SNP); Vibrio spp. infection resistance