Genome-Wide Association Study Identifies Loci and Candidate Genes Associated with Body Shape and Muscle Texture in Rice Field Eel (Monopterus albus)

The rice field eel (Monopterus albus) is an economically important aquaculture species widely distributed in Southeast Asia. However, the lack of nationally approved varieties and the increasing demand for high-quality eel products have highlighted the necessity of developing improved germplasm resources for aquaculture production. In this study, morphometric morphology and muscle texture traits were evaluated in 367 wild eel individuals, and a genome-wide association study (GWAS) based on whole-genome resequencing was conducted to identify genetic variants and candidate genes associated with economically important traits, including body length (BL), tail length (TL), tail height (TH), head length (HL), head width (HW), head height (HH), hardness, chewiness, springiness, and resilience. The GWAS identified three significant and seventeen suggestive SNPs associated with body shape traits, with most loci located on chromosome 4. Candidate gene analysis of the associated genomic regions revealed several candidate genes potentially associated with growth regulation, nutrient metabolism, and skeletal development, including b4galnt4a, tmem86a, cpt1b, mrpl23, lama1, gcm2, wnt3a, thrab, and bmpr1a. Additionally, four suggestive SNPs associated with muscle texture traits were detected, and candidate genes related to muscle development and extracellular matrix regulation, including fstl1b, col5a3a, and pnn, were identified. These findings provide new insights into the genetic basis underlying morphometric variation and muscle texture diversity in M. albus. The identified SNP markers and candidate genes provide potential molecular resources for understanding the genetic basis of body morphology and muscle texture variation in rice field eel.