High-density single nucleotide polymorphisms linkage and quantitative trait locus mapping of the pearl oyster, Pinctada fucata martensii Dunker

The pearl oyster, Pinctada fucata martensii, is an important aquaculture species  in the production of free marine pearls in China and Japan; likewise, it is an ideal animal model for the study of biomineralization. A high-density genetic linkage map was constructed for P. fucata martensii with 3,117 SNP markers. The map spanned 990.74 cM whereas the genome coverage was 99.1% with an average interval of 0.39 cM, a resolution that was the highest in pearl oyster and even higher than that of any other mollusc. QTL mapping and association analysis suggested that six growth-related QTLs were identified, including two QTLs related with total weight and one QTL related with shell length, hinge line length, inner non-nacre covered shell length and shell nacre thickness. One marker, f394, was located at scaffold21710.1|size9744 and 117 bp away from the highly homologous region with intron 2 of N16, a matrix protein gene involved in nacreous layer formation. Taken together, our study generates, for the first time, a high-density genetic linkage map for P. fucata martensii, which enables us to fine-map a gene potentially crucial for pearl formation, thus providing a target gene for selective breeding of P. fucata martensii to improve pearl production.