Genetic Diversity and Selection of MHC I-UAA in Clariid Catfish from Thailand: Implications for Breeding and Conservation

<b>Background/Objectives:</b> Understanding variabilities in the Major Histocompatibility Complex class I (<i>MHC I</i>) gene is essential for evaluating immunogenetic diversity in clariid catfish. <i>MHC I</i> plays a critical role in immune defense by presenting endogenous antigens to cytotoxic T cells. Therefore, we aimed to investigate the genetic diversity, selection patterns, and phylogenetic relationships of <i>MHC I</i> alleles in three important clariid catfish species (<i>Clarias gariepinus</i>, <i>Clarias macrocephalus</i>, and <i>Clarias batrachus</i>) across wild and hatchery populations in Thailand. <b>Methods:</b> Targeted next-generation sequencing of a 174 bp fragment partial exon 6 of <i>MHC I-UAA</i> gene was performed, along with phylogenetic analyses, neutrality tests and <i>dN</i>/<i>dS</i> analyses. <b>Results:</b> Overall, 91 novel alleles were identified in 674 individuals, all of which were novel (100% novelty), with none matching existing reference sequences, thereby revealing extensive variation in population-specific variants. Phylogenetic analyses revealed allele sharing among species, which was consistent with balanced selection. Neutrality tests and <i>dN</i>/<i>dS</i> analyses provided evidence of both purifying and diversifying selection, with episodic positive selection detected at multiple codon sites associated with the antigen-binding α1 domain. Distinct selection patterns among populations, influenced by local environmental conditions and human pressures, along with high allele richness, are reflected in the diversity of immunogenetic variations. <b>Conclusions:</b> These findings provide critical insights into immune adaptation and highlight the potential of <i>MHC I</i> as a functional marker for genetic monitoring. Although a causal relationship between <i>MHC I</i> polymorphism and disease resistance is debated, studies suggest associations with pathogen survival, indicating future implications for aquaculture breeding and conservation, particularly in marker-assisted selection for broodstock management in Thailand.