Weight traits serve as key economic indicators for assessing growth performance and commercial quality in the mud crab Scylla paramamosain, yet the genetic basis of these traits remains poorly characterized. Here, we performed whole-genome resequencing on 323 individuals and conducted genome-wide association studies (GWAS) on five weight-related traits: (1) body-related traits, including body weight (BW), trunk weight (TruW), and weight excluding chelae (WEC); (2) appendage-related traits, containing appendage weight (AppW) and cheliped weight (CheW). Significantly associated SNPs were primarily enriched on chromosomes 15, 22, 25, and 36. For body-related traits, we identified 45 shared candidate SNPs and 175 common candidate genes; appendage-related traits revealed 71 shared candidate SNPs, and 229 common genes were identified; and across all five traits, there were 9 shared candidate SNPs and 49 common genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that shared functional terms/pathways among the five traits were mainly related to metabolism, development, and immunity. Body-related traits exhibited more unique GO terms and KEGG pathways associated with metabolism and immunity, whereas appendage-related traits showed some unique GO terms and KEGG pathways involved in development and morphogenesis. Among the candidate genes, we identified multiple genes associated with growth and development, metabolism, and immune responses. For example, the CCHa1R gene, common to carapace-related traits, is linked to feeding; the DCX-EMA gene, which is common to appendage-related traits, is connected to movement, and the MSTO1 gene is pertinent to muscle development. Among the candidate genes shared by all five traits, there are a series of genes concerning growth and development (such as NVD, CYP307A1, FGF1, NF2, ANKRD52) and immune responses (RGS10). These findings advance our understanding of the genetic architecture underlying decapod crustacean growth and provide valuable insights for optimizing sustainable breeding strategies in S. paramamosain.

Chanodichthys mongolicus, a carnivorous fish belonging to the Cyprinidae family (Erythroculter), is widely distributed in reservoirs and lakes across China. However, the lack of research on whole genome assembly has impeded advancements in genetic studies for this species. In this study, we employed PacBio sequencing and Hi-C technology to assemble high-quality genomes for both female and male Chanodichthys mongolicus at the chromosome level. The assembly results revealed a male genome size of 1.10 GB with a scaffold N50 of 43 Mb, while the female genome was 1.09 GB with a scaffold N50 of 42 Mb. Both assemblies consist of 24 chromosomes and demonstrate an average genome integrity of 98.5%, as assessed by BUSCO. We annotated the male genome using a combination of ab initio predictions, protein homology comparisons, and RNAseq data, resulting in the identification of 33,581 genes, of which 88.15% were predicted to have functional roles. These findings provide a valuable resource for future research on the genetic breeding and genome evolution of Chanodichthys mongolicus.

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.