Genome-Wide Association Study for Weight-Related Traits in Scylla paramamosain Using Whole-Genome Resequencing

Abstract

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.

Keywords: GWAS; Scylla paramamosain; weight-related traits; whole-genome resequencing.

Figure 1

Statistics of phenotypic and sequencing data. (A) Five weight-related traits of S. paramamosain. The abbreviations BW, WEC, TruW, AppW, and CheW correspond to body weight, weight excluding chelae, trunk weight, appendage weight, and cheliped weight, respectively. (B) Correlation among the five traits. *** indicates a p-value less than 0.001. (C) Density plot of SNP distribution across chromosomes based on sequencing data, generated using the R package CMplot (v4.5.1) [23]. (D) Distribution plot of the minor allele frequency (MAF) counts for SNPs. (E) Classification information of SNPs after annotation.

Figure 2

Population genetic structure analysis. (A) Principal component analysis; red and blue dots represent female and male individuals, respectively; (B) heatmap of the genetic relationship matrix for the tested population.

Figure 3

Manhattan plots from genome-wide association studies. (A) Body weight (BW); (B) trunk weight (TruW); (C) weight excluding chelae (WEC); (D) appendage weight (AppW); (E) cheliped weight (CheW). Red dashed lines indicate the significance threshold (p = 10⁻⁵). Chromosome 6 (highlighted in red) corresponds to the sex chromosome as previously reported [21].

Figure 4

Venn diagram analysis of GWAS results. (A) Shared significant SNP loci across five traits. Numerical values within intersection areas denote the quantity of shared SNPs, with the central overlap indicating nine SNPs common to all five traits. (B) Shared candidate genes across five traits. Numerical values within intersection areas denote the quantity of shared genes, with the central overlap indicating 49 candidate genes common to all five traits. The full names corresponding to the five phenotypic abbreviations can be found in Table 1.

Figure 5

Functional enrichment analysis of candidate genes. The top 10 significant GO terms for biological process (BP), cellular component (CC), and molecular and function (MF) categories are presented for common candidate genes in the (A) BTW group, (B) AC group, and (C) the genes common to both BTW and AC groups. Additionally, the top 20 significant KEGG pathways are displayed for shared candidate genes in the (D) BTW group, (E) AC group, and (F) the genes common to both BTW and AC groups.

Figure 6

Genome-wide association analyses reveal pleiotropic loci for growth-related traits in mud crab. Manhattan plots highlighting significant genomic regions associated with phenotypic traits: (A) chromosome 25 (11.40–12.40 Mb), shared association with BW, TruW, and WEC; (B) chromosome 36 (5.60–5.80 Mb), shared association with BW, TruW, and WEC; (C) chromosome 18 (7.48–7.90 Mb), shared association with AppW and CheW; (D) chromosome 22 (8.70–9.44 Mb), shared association with AppW and CheW; (E) chromosome 3 (40.26–40.47 Mb), pleiotropic region influencing all five traits; (F) chromosome 36 (2.60–3.00 Mb), pleiotropic region influencing all five traits. Red dashed line indicates the significance threshold (p = 1 × 10⁻⁵). The full names corresponding to the five phenotypic abbreviations can be found in Table 1. Blue dashed lines demarcate the physical position interval in the Manhattan plot (upper panel), which directly corresponds to the physical position range displayed in the lower panel.