Purifying Selection and Interspecific Differentiation at the Myf5 Locus Inform Hybrid Identification and Genetic Management of Thai Clariid Resources

Background/Objectives: Clariid catfishes are a cornerstone of Southeast Asian aquaculture, where intensive breeding and interspecific hybridization have significantly decreased genetic diversity. To address the limited understanding of growth-governing molecular determinants, we characterized the genomic architecture and evolutionary dynamics of the myogenic factor 5 (Myf5) gene, a master regulator of myogenesis, in 511 individuals from 17 catfish populations in Thailand. Methods: A total of 511 individuals representing 17 catfish populations were analyzed. A 334-bp fragment of exon 1 of the Myf5 gene was sequenced using Illumina short-read technology. Genetic diversity indices were calculated to evaluate sequence variation, population structure, and selective constraints acting on the locus. Results: Sequence analysis of a 334-bp segment of exon 1 using Illumina short-read technology identified 17 haplotypes and 92 variable sites, which revealed moderate allelic richness despite low overall nucleotide diversity (π ≈ 0.008). Evolutionary analyses indicated that the Myf5 locus is governed by stringent purifying selection (ω = 0.063), wherein site-specific constraints preserve the stability of the α-helix folding architecture, which is essential for myogenic regulation. Population genetic analyses revealed substantial differentiation among taxa (56% among-population variation), while Bayesian clustering successfully resolved a hierarchical structure (K = 2) that distinguished Clarias gariepinus, Clarias macrocephalus, and Clarias batrachus. These findings demonstrate that species-specific Myf5 haplotypes serve as diagnostic markers for identifying parental species and assisting in the identification of F1 hybrid stocks. Conclusions: Overall, this study provides the molecular markers for species identification, broodstock authentication, hybrid detection, and sustainable genetic management of Thai Clariid resources, which are critical for balancing production efficiency with the conservation of native biodiversity in Southeast Asia.