General flowchart for SNP identification and association analysis.

Abbreviations: N, the northern subspecies of bay scallop; S, the southern subspecies of bay scallop; QHD, Qinhuangdao, Hebei Province, China; QD, Qingdao, Shandong Province, China; YT, Yantai, Shandong Province, China; ZJ, Zhanjiang, Guangdong Province, China; Z, hybrids of the two subspecies; ZZ, a descendant of the cross between Z (♂) and Z (♀); ZN, a descendant of the cross between Z (♂) and N (♀).