Animal Genomics and Bioresource Research Center KU

20/01/2026

Now available online in Genes.

https://www.mdpi.com/2073-4425/17/1/112

Comparative Chromosomal Analysis of the Z Chromosome in South American Bird Species Shows a High Rate of Intrachromosomal Rearrangements

Background: Intrachromosomal rearrangements in birds play a subtle but important role in shaping genomic evolution, phenotypic diversity and speciation. However, the avian s*x chromosome system (homogametic ZZ males; heterogametic ZW females) remains relatively understudied, and evolutionary rearrangements of the Z chromosome have not been mapped in most species. To address this, we employed universally hybridizing avian Z chromosome probes to metaphases of 11 avian species from South America. Methods: Chromosome preparations were obtained from fibroblast cell cultures of 11 birds representing nine different orders; four bacterial artificial chromosome (BAC) probes were used in our interspecies fluorescence in situ hybridization (FISH) experiments. We identified chromosomal rearrangements in the species investigated, tracing the evolution of the Z chromosome in these species through comparison with reptiles from Southeast Asia (three snake species used as an outgroup), along with two reference species: chicken (Galliformes) and zebra finch (Passeriformes). Results: We observed high rates of intrachromosomal rearrangements in the avian Z chromosome, with most species showing different patterns from chicken and zebra finch. Nannopterum brasilianum (Suliformes) and Jacana jacana (Charadriiformes) showed the same BAC order as chicken, but centromere repositioning was evident. Apart from Piciformes, all other species exhibited a conserved Z chromosome size. The corresponding Z chromosome sequences were homologous to regions of the long arms of Chromosome 2 and W in snakes but not on the Z chromosomes. Conclusions: Comparative analysis of the Z chromosome across avian orders provides important insights into the dynamics of avian s*x chromosomes and the evolution of s*x chromosome systems in general.

07/01/2026

ขอแสดงความยินดีกับ
Ms. Marie Roselle Enguito (PhD student, School of Biosciences, University of Kent)
ภายใต้การดูแลของ ศ. ดร.ครศร ศรีกุลนาถ และ Prof. Dr.Darren K Griffin (หน่วยวิจัยด้านจีโนมิกส์และทรัพยากรชีวภาพสัตว์ คณะวิทยาศาสตร์ มหาวิทยาลัยเกษตรศาสตร์)
ในโอกาสที่ผลงานวิจัยได้รับการตีพิมพ์ในวารสาร Genes (Impact Factor 2.😎 ในหัวข้อ “Comparative Chromosomic Analysis of the Z Chromosome in South American Bird Species Shows a High Rate of Intrachromosomal Rearrangements”

06/01/2026

Our article "Chromosome-scale, haplotype-resolved genome of Bighead catfish for conservation and aquaculture"
The first haplotype-resolved chromosome-scale genome assembly for the bighead catfish (Clarias macrocephalus), a freshwater species native to Thailand and Vietnam, which has importance in aquaculture and conservation, is presented here. The 880 Mb genome was assembled using high-fidelity long-read sequencing from Pacific Biosciences and Oxford Nanopore Technologies, which was scaffolded using high-throughput chromosome conformation capture data, and polished with Illumina short-read sequencing. The assembly, which spans 27 pseudo-chromosomes, demonstrates high completeness and continuity, with a scaffold N50 of 33.48 Mb, 95.5% completeness based on Benchmarking Universal Single-Copy Orthologs (BUSCO), and a quality value (QV) of 50. This genomic resource provides a foundation for studying aquaculture traits, genetic diversity, and structural variation of the bighead catfish and supports efforts in their selective breeding, conservation, and sustainable aquaculture in Southeast Asia.

Website: https://www.nature.com/articles/s41597-025-06325-6

29/12/2025

🎉🎉🎉
หน่วยวิจัยด้านจีโนมิกส์และทรัพยากรชีวภาพสัตว์ คณะวิทยาศาสตร์ มหาวิทยาลัยเกษตรศาสตร์
ขอแสดงความยินดีกับ ดร.ฐิติพงศ์ พันทุม
ที่ได้รับ "ทุนพัฒนาเส้นทางอาชีพนักวิจัยรุ่นใหม่" ประจำปีงบประมาณ พ.ศ. 2569 จากสำนักงานการวิจัยแห่งชาติ (วช.)
🎉🎉🎉

23/12/2025

Our article "High-Accuracy Chicken Breed
Identification Using Microsatellite Genotype Data and AutoGluon Framework" is available online in Biology

The practical applications of breed identification are numerous and diverse, and they include breed conservation and breeding program design. However, distinguishing between breeds remains challenging and costly, especially for phenotypically similar chicken populations. Continued research is necessary to develop more accessible and optimized methodologies. To address these challenges, machine learning (ML) offers promising tools for analyzing complex genetic data. The capabilities of machine learning, especially the random forest (RF) model, to enhance various fields, including bioinformatics, have recently been demonstrated. In this study, microsatellite genotype data from 651 individuals across 30 chicken populations filtered from a larger initial dataset for consistency were used to classify breeds using an RF model. Cross-validation techniques, including 10-fold cross-validation and leave-one-out cross-validation, were employed to assess the performance of the model. The model performance was evaluated using metrics such as accuracy, Cohen’s Kappa, 95% confidence interval, and F1-score. Results showed that the RF model achieved a 95.38% accuracy on the testing dataset. Accuracies of 91.44% and 90.99% were observed for 10-fold cross-validation and leave-one-out cross-validation, respectively. It is believed that larger datasets will significantly improve outcomes for other breeds. Because of its generalizability, the trained model can serve as a straightforward and modern method for chicken breed determination using machine learning. This study demonstrates that ML, particularly automated approaches like AutoGluon, provides a robust and accessible framework for chicken breed identification using cost-effective microsatellite data.

Website: https://www.mdpi.com/2079-7737/15/1/21
PDF Version: https://www.mdpi.com/2079-7737/15/1/21/pdf

19/12/2025

17/12/2025

Now available online in Genes & Genomics
Clariid catfish hybridization in aquaculture: a comprehensive review of strategies, challenges, and future directions

https://doi.org/10.1007/s13258-025-01709-9

Abstract
Background
Hybridization within the family Clariidae has been recognized as a crucial strategy for genetic improvement in aquaculture, particularly in Asia and Africa, due to its potential to enhance growth, feed efficiency, tolerance, and disease resistance.
Objective
This review synthesizes information on the biological, genetic, and technological aspects of clariid catfish hybridization, explaining its benefits and highlighting the ecological and regulatory challenges in aquaculture.
Methods
Published information on reproductive biology, hybrid performance, induced breeding, and genomic resources of clariid catfish was examined and summarized.
Results
The reproductive biology of clariid catfish, including external fertilization, overlapping spawning periods, and premating barriers, was described, which shows that viability is promoted. Notable crosses such as Clarias gariepinus × Heterobranchus longifilis and Clarias gariepinus × Clarias macrocephalus were reported, which demonstrated heterosis with higher growth, feed efficiency, and survival rate. Breeding using hormonal agents such as luteinizing hormone-releasing hormone analog, human chorionic gonadotropin, and Ovaprim has facilitated the production of hybrids. Challenges such as partial sterility, phenotypic variability, and decline of vigor in the F1 generation were identified. Ecological concerns related to hybrid escape, genetic introgression, and biodiversity loss, which pose a risk to native species, were highlighted. The absence of harmonized regulations, limited genomic resources, and insufficient traceability protocols worsens these issues.
Conclusions
Sustainability of clariid catfish hybridization depends on the integration of genomic tools into breeding programs, deployment of sterile hybrids, reinforcement of biosafety systems, and establishment of regional policies. A balance between productivity and conservation is necessary; Clarias hybridization supports aquaculture development but requires careful consideration to protect biodiversity.

17/12/2025

▪️ สาระสัตว์
เสียงขันจากป่า... ไก่ป่า มรดกพันธุกรรมกับความมั่นคงทางอาหารของชาติ
โดย AGB Research Unit Team, KU

#นิตยสารสาระวิทย์ โดย สวทช. ฉบับที่ 153 เดือนธันวาคม 2568
⚛ เรื่องจากปก
พระราชินีผู้สร้างกำไรให้แผ่นดิน
โดย สำนักสนองงานพระราชดำริ กรมอุทยานแห่งชาติ สัตว์ป่า และพันธุ์พืช

⏬ ดาวน์โหลดฟรี นิตยสารสาระวิทย์
https://www.nstda.or.th/sci2pub/sarawit/

12/12/2025

Online available in BMC Microbiology

Genetic insights into antimicrobial resistance and virulence characteristics of Salmonella enterica isolated from Nile tilapia sourced from retail markets in Thailand

https://doi.org/10.1186/s12866-025-04451-0

Background
Antimicrobial-resistant Salmonella enterica in aquaculture represents a significant public health concern due to its potential transmission through the food chain. Despite these concerns, there is a notable lack of comprehensive genomic characterization of S. enterica isolates from Nile tilapia in Thailand. This study aimed to evaluate the prevalence, antimicrobial resistance (AMR) profiles, and genetic diversity of S. enterica isolated from retail-sourced Nile tilapia (Oreochromis niloticus) between May and October 2023.

Methods
A total of 714 Nile tilapia specimens comprising liver, kidney, meat, gill, mucus, lung, and intestine tissues were collected from fish purchased at retail markets in Thailand. Salmonella isolation and identification were performed using standard microbiological methods following ISO 6579-1:2017, and serotyping was conducted using the Kauffmann–White scheme. Antimicrobial susceptibility testing was carried out using the agar dilution method in accordance with CLSI guidelines. The whole genome sequencing was performed on 14 multidrug-resistant isolates using Illumina short-read technology to characterize their genetic resistance and virulence profiles.

Results
The prevalence of S. enterica was 15.4%, with the highest rates observed in gill (40.9%) and mucus (26.5%) samples. Thirty-five serovars were identified, with Escanaba, Kentucky, and Othmarschen being the most frequently detected. Resistance to oxytetracycline (33.6%), tetracycline (16.0%), and ampicillin (12.8%) were prevalent, and 19.2% of isolates exhibited multidrug resistance (MDR). Although extended-spectrum beta-lactamase (ESBL)-producing isolates accounted for only 2.4%, concerns persist regarding their increasing global prevalence. WGS of 14 MDR isolates identified over 20 resistance genes, including blaTEM−1B, blaCTX−M−55, qnrS1, and tet(A), as well as efflux pump systems (mdsABC and mdtK) and various virulence factors.

Conclusions
These isolates were classified into nine sequence types (STs), several of which have been associated with human infections. The findings underscore the necessity of stringent antimicrobial regulations and improved aquaculture practices to mitigate AMR transmission and enhance food safety.

12/12/2025

Our article "High Amplification of CLA-SAT-149 Satellite DNA in Bighead Catfish: Insights into Satellite DNA Evolution in Clariid Lineages" has been published online in Cytogenet Genome Res.

https://doi.org/10.1159/000548841

Introduction: Satellite DNA (satDNA) is an important component of eukaryotic genomes that influences chromosomal organization and evolution. This study investigates the sequence diversity, chromosomal distribution, and copy number variation of the CLA-SAT-149 satDNA family (149 bp) in four clariid catfish species, Clarias macrocephalus, C. gariepinus, C. batrachus, and C. nieuhofii, as well as in F1 hybrids and backcross (BC) progeny. Methods: Fluorescence in situ hybridization (FISH) was used to map CLA-SAT-149 on metaphase chromosomes. Quantitative PCR (qPCR) quantified copy number variation. Amplicon sequencing was applied to characterize sequence variants, and Bayesian clustering analysis was used to assess genetic relationships among subfamilies. Results: Chromosome mapping showed species-specific signals present in C. macrocephalus and F1 hybrids but absent in C. gariepinus and C. nieuhofii. qPCR revealed significantly higher copy numbers in C. macrocephalus. Two sequence variants were identified: the canonical 149-bp (subfamily A) and an 85-bp derivative (subfamily B). Bayesian analysis indicated multiple genetically distinct subgroups among species. F1 hybrids and BC progeny exhibited unique sequence profiles and copy number patterns, while C. nieuhofii lacked CLA-SAT-149 entirely. Conclusion: The results support lineage-specific expansion, amplification, and loss of CLA-SAT-149 in clariid catfish, consistent with the satDNA library model. These patterns provide insights into satDNA evolution and have potential applications in aquaculture genetics, hybrid identification, and species differentiation.

25/11/2025

ขอแสดงความยินดีกับ
ดร.วรพงศ์ สิงห์ชาติ
Dr. Trifan Budi
ศ. ดร.ครศร ศรีกุลนาถ
หน่วยวิจัยด้านจีโนมิกส์และทรัพยากรชีวภาพสัตว์
คณะวิทยาศาสตร์ มหาวิทยาลัยเกษตรศาสตร์
และ
ศ. ดร.สุจินดา มาลัยวิจิตรนนท์
ศูนย์วิจัยไพรเมทแห่งชาติ จุฬาลงกรณ์มหาวิทยาลัย

ในโอกาสที่ผลงานวิจัยได้รับการตีพิมพ์ในวารสาร
Journal of Heredity (Impact Factor 2.5) ระดับ Q1

ในหัวข้อ
“Low genetic diversity of major histocompatibility complex class II DQB gene in wild rhesus and long-tailed macaques in Thailand reflects purifying selection and poses risks to population health”

25/11/2025

📘 Newly published research article in the journal Genes (Impact Factor 3.5, Q2)
Genes 2025, 16, 1266
🔗 https://doi.org/10.3390/genes1611266

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

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
Ho = 0.043 ±0.023; He = 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