Association analysis reveals SNP markers associated with growth traits in swimming crabs (Portunus trituberculatus)

The swimming crab (Portunus trituberculatus) is an economically important species in mariculture, widely distributed along the coastal areas of China. Due to its rapid growth and high nutritional value, it is a key target for selective breeding to enhance production efficiency and reduce costs. In this study, we conducted an association analysis between 233 high-quality SNPs and seven growth traits of 244 P. trituberculatus individuals: full carapace width (FCW), carapace width (CW), carapace length (CL), fixed length of the claw (FLC), meropodit length of the claw (MLC), body height (BH), and body weight (BW). The analysis identified 11 SNPs significantly associated with growth, which are distributed across multiple chromosomes, underscoring the polygenic nature of these traits. Multiple comparisons of diplotypes revealed that the diplotype D1 (AA-AT) exhibited a significant advantage for all seven growth-related traits. Additionally, we annotated 33 candidate genes located near these significant SNPs, including cytochrome c oxidase subunit (COX), NADH dehydrogenase subunit (ND), cytochrome b (CYTB), and 15-hydroxyprostaglandin dehydrogenase (15-PGDH). These genes play key roles in oxidative phosphorylation, ATP synthesis, and energy metabolism-key processes for cellular function and growth. These findings enhance our understanding of the genetic architecture underlying growth-related traits in P. trituberculatus and provide valuable SNP markers for marker-assisted selection to improve breeding efficiency in this economically important species.