Selecting fast-growing strains is the most common objective of genetic breeding programs. In this study, we sought to mine the growth-associated single nucleotide polymorphisms (SNPs) in the commercially cultured clam Meretrix meretrix by candidate gene association analysis. Fifty potentially growth-associated contigs based on their functional annotation were chosen as candidates from our EST database, and 240 SNPs were predicted from these contigs. Seventy-one predicted SNPs and five novel SNPs were identified by pooled DNA sequencing in both a fast-growing population (09SPSB) and a control population (09G(3)SB). Among these SNPs, 24 were also identified in an independent population (CP). Through multiplex SNaPshot genotyping, 16 of the 24 SNPs were used in the marker-trait association analysis between 09SPSB and 09G(3)SB. The results showed that seven SNPs in five contigs were significantly associated with clam shell length (P < 0.05). With bidirectional selective genotyping in the CP, three of the seven growth-associated SNPs were further confirmed. Annotations of these SNP-containing contigs provided some clues of these genes functioning in growth. After a haplotype association analysis, we found four haplotypes with significantly different frequencies between 09SPSB and 09G(3)SB (P < 0.001). Through a generalized multifactor dimensionality reduction (GMDR) analysis, we found several gene-gene interaction models, of which the two-factor model (SNPg5/SNPg16) was the best one. These obtained markers will be useful in further quantitative trait loci identification and marker-assisted selection in M. meretrix.
1.Chinese Acad Fishery Sci, Key Lab Sustainable Utilizat Marine Fisheries Res, Minist Agr, Yellow Sea Fisheries Res Inst, Qingdao 266071, Peoples R China 2.Chinese Acad Sci, Key Lab Expt Marine Biol, Inst Oceanol, Qingdao 266071, Peoples R China 3.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Peoples R China
Recommended Citation:
Dai, Ping,Wang, Hongxia,Liu, Baozhong. Mining and identification of SNP markers associated with growth traits in the clam Meretrix meretrix[J]. AQUACULTURE INTERNATIONAL,2017,25(3):1185-1196.
