Three vibrio-resistance related EST-SSR markers revealed by selective genotyping in the clam Meretrix meretrix

The clam Meretrix meretrix is an important commercial bivalve distributed in the coastal areas of South and Southeast Asia. In this study, marker-trait association analyses were performed based on the stock materials of M. meretrix with different vibrio-resistance profile obtained by selective breeding. Forty-eight EST-SSR markers were screened and 27 polymorphic SSRs of them were genotyped in the clam stocks with different resistance to Vibrio parahaemolyticus (11-R and 11-S) and to Vibrio harveyi (09-R and 09-C). Allele frequency distributions of the SSRs among different stocks were compared using Pearson's Chi-square test, and three functional EST-SSR markers (MM959, MM4765 and MM8364) were found to be associated with vibrio-resistance trait. The 140-bp allele of MM959 and 128-bp allele of MM4765 had significantly higher frequencies in resistant groups (11-R and 09-R) than in susceptive/control groups (11-S and 09-C) (P < 0.01), which suggested that the clams carrying these two alleles have stronger resistance against vibrio. Clam individuals of 11-S were divided into three subgroups based on the survival time post-challenge, and the multi-dimensional scaling (MDS) analysis showed that clusters generated by genetic similarity revealed by the three SSR markers were consistent with the three subgroups distinctions. The putative functions of contig959, contig4765 and contig8364 also suggested that the three SSR-involved genes might play important roles in immunity of M. meretrix. All these results supported that EST-SSR markers MM959, MM4765 and MM8364 were associated with vibrio-resistance and would be useful for marker-assisted selection (MAS) in M. meretrix genetic breeding.