Polymorphisms at Three Introns in the Manila Clam (Ruditapes philippinarum) and the Grooved Carpet-Shell Clam (R. Decussatus)

Abstract

Abstract We have designed a set of exon-primed intron-crossing (EPIC) PCR primers to amplify introns at the genes TBP and SRP54 in the Manila clam (Ruditapes philippinarum) and the grooved carpet-shell clam (R. decussatus), and also one intron at a histone 3 homologous gene in the Manila clam. The primers were developed by using “universal” EPIC primers available in the literature and by searching for intron locations in cDNA sequences taken from public databases. The identity of the amplified products was checked by sequencing. The three introns of the Manila clam, and one in the carpet shell clam (TBP), exhibited length polymorphisms. The number of alleles was two at the TBP locus of the grooved carpet-shell clam, and ranged from three to five in the three loci of the Manila clam. The locus without length polymorphism in the carpet-shell clam exhibited polymorphism when digested with the restriction enzyme EcoR I (4 haplotypes). The variability of the markers was examined in two population samples in ea...