Genome-Wide Association Study and Genomic Prediction for Swimming Leg Dactyl Traits in the Mud Crab Scylla paramamosain Based on Whole-Genome Resequencing

The paddle-shaped dactyl of the fifth pereiopod in the mud crab Scylla paramamosain is a specialized appendage, but the genetic basis and genomic prediction potential of its traits remain poorly understood. Using whole-genome resequencing data from 323 individuals, we performed a genome-wide association study (GWAS) and genomic prediction analyses for bilateral dactyl length, width, area and first principal component (PC1). Heritability estimates ranged from 0.184 to 0.538. GWAS identified 116 and 70 significant SNPs for left and right dactyl length, 73 and 68 for the corresponding width traits, 102 and 76 for the corresponding area traits, and 91 for PC1. Major signals occurred on chromosomes 19 and 28 for length, chromosomes 19 and 23 for width, and chromosomes 19, 21 and 30 for composite traits. Two SNPs, Chr16:23074328 and Chr30:357279, were shared across all seven phenotypes and showed consistent additive effects on bilateral length and width. Chr30:357279 was annotated as a missense variant in an SRSF6-like gene. GBLUP based on GWAS-prioritized SNP subsets improved accuracy over whole-genome SNPs, with the FDR = 0.05 subset performing best (0.39–0.47). These results provide new insights into the genetic dissection and genomic prediction of functional morphological traits in S. paramamosain.