Identification of BMP2 and BMP7 genes and association of their SNPs with growth traits in the hard clam (Meretrix meretrix)

The hard clam (Meretrix meretrix) is a commercially and ecologically important benthic mollusk in South and Southeast Asia. Growth is one of the most important and complex traits affecting clam breeding. Therefore, identification of key growth factor genes and their association with growth traits are the primary prerequisites for in-depth study of the mechanisms of growth regulation and molecular marker-assisted selection of the hard clam. In the present study, we generated the full-length cDNA sequences of the growth-related genes BMP2 and BMP7 in M. meretrix (MmBMP2 and MmBMP7) and then investigated their gene expression patterns and associations with growth traits. The full-length cDNA of MmBMP2 was 2641 base pairs (bp), with a 1395 bp open reading frame (ORF) encoding 464 amino acids. The full-length MmBMP7 cDNA was 3161 bp, with a 1257 bp ORF encoding 418 amino acids. In adult clams, expression of MmBMP2 and MmBMP7 were significantly higher in the mantle than in the other five tested tissues (p < 0.05). Among the seven developmental stages of M. meretrix, expression of MmBMP2 was the highest in juveniles (p < 0.05), and expression of MmBMP7 was very low in 4-cell embryo and eyespot larva stages (p < 0.05). Two hundred and sixty-three individuals from two populations were screened for MmBMP2 and MmBMP7 polymorphisms, and single nucleotide polymorphisms (SNPs) associated with growth traits in MmBMP2 was found in both populations. Subsequent analysis revealed that two SNPs in MmBMP2 were shared between the populations. One was A726G, for which individuals with genotypes AG had significantly higher growth traits than those with genotype AA (p < 0.05). The other was A732T, for which individuals with genotype AT had significantly higher growth traits than those with genotype AA (p < 0.05). These results suggest that BMP2 markers may have potential value in molecular selective breeding to improve clam growth.