GH1 Gene Polymorphisms Reveal Population-Level Allele Variation in North African (Clarias gariepinus) and Bighead Catfish (Clarias macrocephalus)

Thammachak, Phonemany; Chalermwong, Piangjai; Patta, Chananya; Jaito, Wattanawan; Singchat, Worapong; Panthum, Thitipong; Budi, Trifan; Sriphairoj, Kednapat; Hatachote, Sittichai; Srisapoome, Prapansak; Muangmai, Narongrit; Sawatdichaikul, Orathai; Griffin, Darren K.; Antunes, Agostinho; Duengkae, Prateep; Na-Nakorn, Uthairat; Matsuda, Yoichi; Srikulnath, Kornsorn

doi:10.3390/genes16111266

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GH1 Gene Polymorphisms Reveal Population-Level Allele Variation in North African (Clarias gariepinus) and Bighead Catfish (Clarias macrocephalus)

by

Phonemany Thammachak

^1,2,†,

Piangjai Chalermwong

¹,

Chananya Patta

¹,

Wattanawan Jaito

¹

,

Worapong Singchat

^1,3,*,

Thitipong Panthum

^1,3

,

Trifan Budi

^1,†

,

Kednapat Sriphairoj

⁴,

Sittichai Hatachote

⁴

,

Prapansak Srisapoome

^1,5

,

Narongrit Muangmai

^1,6

,

Orathai Sawatdichaikul

⁷

,

Darren K. Griffin

^1,8

,

Agostinho Antunes

^9,10

,

Prateep Duengkae

^1,3,

Uthairat Na-Nakorn

⁵

,

Yoichi Matsuda

¹ and

Kornsorn Srikulnath

^1,2,3,11,*

¹

Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand

²

Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand

³

Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand

⁴

Faculty of Natural Resources and Agro-Industry, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon 47000, Thailand

⁵

Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand

⁶

Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand

⁷

Department of Nutrition and Health, Institute of Food Research and Product Development, Kasetsart University, Bangkok 10900, Thailand

⁸

School of Biosciences, University of Kent, Canterbury, Kent CT2 7 NJ, UK

⁹

CIIMAR/CIMAR, Terminal de Cruzeiros do Portode Leixões, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal

¹⁰

Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal

¹¹

Biodiversity Center, Kasetsart University (BDCKU), Bangkok 10900, Thailand

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^*

Authors to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Genes 2025, 16(11), 1266; https://doi.org/10.3390/genes16111266

Submission received: 25 September 2025 / Revised: 17 October 2025 / Accepted: 23 October 2025 / Published: 27 October 2025

(This article belongs to the Section Animal Genetics and Genomics)

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Abstract

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.

Keywords: allele; bighead catfish; GH1 gene; North African catfish; purifying selection

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MDPI and ACS Style

Thammachak, P.; Chalermwong, P.; Patta, C.; Jaito, W.; Singchat, W.; Panthum, T.; Budi, T.; Sriphairoj, K.; Hatachote, S.; Srisapoome, P.; et al. GH1 Gene Polymorphisms Reveal Population-Level Allele Variation in North African (Clarias gariepinus) and Bighead Catfish (Clarias macrocephalus). Genes 2025, 16, 1266. https://doi.org/10.3390/genes16111266

AMA Style

Thammachak P, Chalermwong P, Patta C, Jaito W, Singchat W, Panthum T, Budi T, Sriphairoj K, Hatachote S, Srisapoome P, et al. GH1 Gene Polymorphisms Reveal Population-Level Allele Variation in North African (Clarias gariepinus) and Bighead Catfish (Clarias macrocephalus). Genes. 2025; 16(11):1266. https://doi.org/10.3390/genes16111266

Chicago/Turabian Style

Thammachak, Phonemany, Piangjai Chalermwong, Chananya Patta, Wattanawan Jaito, Worapong Singchat, Thitipong Panthum, Trifan Budi, Kednapat Sriphairoj, Sittichai Hatachote, Prapansak Srisapoome, and et al. 2025. "GH1 Gene Polymorphisms Reveal Population-Level Allele Variation in North African (Clarias gariepinus) and Bighead Catfish (Clarias macrocephalus)" Genes 16, no. 11: 1266. https://doi.org/10.3390/genes16111266

APA Style

Thammachak, P., Chalermwong, P., Patta, C., Jaito, W., Singchat, W., Panthum, T., Budi, T., Sriphairoj, K., Hatachote, S., Srisapoome, P., Muangmai, N., Sawatdichaikul, O., Griffin, D. K., Antunes, A., Duengkae, P., Na-Nakorn, U., Matsuda, Y., & Srikulnath, K. (2025). GH1 Gene Polymorphisms Reveal Population-Level Allele Variation in North African (Clarias gariepinus) and Bighead Catfish (Clarias macrocephalus). Genes, 16(11), 1266. https://doi.org/10.3390/genes16111266

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GH1 Gene Polymorphisms Reveal Population-Level Allele Variation in North African (Clarias gariepinus) and Bighead Catfish (Clarias macrocephalus)

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