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Incorporating GWAS-derived prior information enhances genomic prediction for body size traits in the mud crab (Scylla paramamosain).

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Updated: Sep 16, 2025

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

Lin Chen1, Yaodong Zhang1, Peitan Jia1

  • 1State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen 361021, China.

Animals : an Open Access Journal From MDPI
|July 12, 2025
PubMed
Summary

This study identified genetic markers for weight traits in mud crabs (Scylla paramamosain) using whole-genome resequencing and GWAS. Findings reveal key genes influencing growth, metabolism, and immunity, aiding sustainable breeding strategies.

Keywords:
GWASScylla paramamosainweight-related traitswhole-genome resequencing

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Area of Science:

  • Genomics and Aquaculture
  • Animal Genetics
  • Crustacean Biology

Background:

  • Weight traits are crucial economic indicators for mud crab (Scylla paramamosain) aquaculture.
  • The genetic basis of weight traits in S. paramamosain is not well understood.
  • Understanding these genetic factors is vital for improving breeding programs.

Purpose of the Study:

  • To identify genetic variations associated with weight-related traits in S. paramamosain.
  • To explore the genetic architecture underlying body and appendage weight.
  • To provide insights for enhancing growth performance and commercial quality through selective breeding.

Main Methods:

  • Whole-genome resequencing of 323 S. paramamosain individuals.
  • Genome-wide association studies (GWAS) for five weight-related traits (body weight, trunk weight, weight excluding chelae, appendage weight, cheliped weight).
  • Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses.

Main Results:

  • Significant SNPs were identified on chromosomes 15, 22, 25, and 36.
  • Common candidate genes associated with body-related traits (175 genes) and appendage-related traits (229 genes) were found.
  • Shared genes across all five traits (49 genes) are involved in metabolism, development, and immunity, including growth-related genes like NVD and CYP307A1, and immune-related gene RGS10.

Conclusions:

  • Genetic factors influencing body and appendage weight in S. paramamosain are complex, involving metabolism, development, and immunity pathways.
  • Specific genes like CCHa1R, DCX-EMA, and MSTO1 are linked to feeding, movement, and muscle development, respectively.
  • The study provides a foundation for marker-assisted selection to improve economically important weight traits in S. paramamosain breeding programs.