Piangjai Chalermwong

Background/Objectives: North African catfish (Clarias gariepinus) and bighead catfish (Clarias macrocephalus) play crucial roles in Thai aquaculture. Although significant growth disparities exist among these species, the genetic factors underlying these differences are still unknown. This study aimed to identify GH1 gene polymorphisms, in North African and bighead catfish populations across Thailand and Laos. Methods: Sequencing, phylogenetic, and clustering analyses were performed to assess genetic diversity, selection patterns, and lineage differentiation of catfish partial GH1 fragment. Results: Six alleles of the studied fragment of GH1 gene were identified; they differed at 33 variable sites within intron 2, located between the conserved regions at the 3′ end of exon 2 and the 5′ end of exon 3. At the population-level, GH1 exhibited low heterozygosity (mean H_o = 0.043 ± 0.023; H_e = 0.059 ± 0.028). Bayesian clustering analyses identified two distinct genetic clusters, corresponding to North African and bighead catfish, apart from the bighead population in Laos, indicating their distinct genetic origins. Evidence of purifying selection was observed in both species. Phylogenetic analysis indicated the presence of lineage-specific alleles in the GH1 gene. Conclusions: These findings provide valuable insights into GH1 polymorphisms in commercially important catfish species and may help to develop future breeding programs aimed at enhancing aquaculture productivity.

Background/Objectives: Understanding variabilities in the Major Histocompatibility Complex class I (MHC I) gene is essential for evaluating immunogenetic diversity in clariid catfish. MHC 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 MHC I alleles in three important clariid catfish species (Clarias gariepinus, Clarias macrocephalus, and Clarias batrachus) across wild and hatchery populations in Thailand. Methods: Targeted next-generation sequencing of a 174 bp fragment partial exon 6 of MHC I-UAA gene was performed, along with phylogenetic analyses, neutrality tests and dN/dS analyses. Results: 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 dN/dS 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. Conclusions: These findings provide critical insights into immune adaptation and highlight the potential of MHC I as a functional marker for genetic monitoring. Although a causal relationship between MHC 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.