Triangle sail mussel (Hyriopsis cumingii, Lea 1852) is the most important freshwater pearl mussel in China. Growth traits of host mussels and inner shell color traits of donor mussels are critical determinants for pearl size and color. In this study, we performed GWAS analysis to explore the genetic architecture of growth and inner shell color traits. Using genotype by sequencing (GBS) technique, we obtained 80,562 SNPs from a total dataset of 463 mussels, based on these data, we found weak genetic relationship (−0.1–0.4) and rapid LD decay rate among the population. Moreover, GWAS analysis identified 12 growth-related significant SNPs and 29 inner shell color related significant SNPs. Five of the 12 SNPs linked to growth traits were validated to be credible SNPs in a new population. Cyclin, SNF, PMP22, CPED1, F-box and APC/C genes were found to be significantly associated with growth traits, which may influence the growth and development of H. cumingii by regulating cell mitosis, mantle epithelial tissue activity, and Ca2+ absorption and transport capacity. Notably, redness a* showed an obvious aggregation peak in chromosome 17, indicating that this region may be closely related to the inner shell color. Furthermore, three causal genes in chromosome 17, HSP78, MAS and PKS are inferred to be the key genes on color formation of purple inner shell. These results provide some new insights into the genetic basis and physiological regulation mechanism of growth and inner shell color traits in H. cumingii. However, detailed functional identification and regulation mechanism analysis merits more investigation.
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