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Background: Fighting cock breeds have considerable historical and cultural place in Thailand. Breeds such as Lueng Hang Khao (LHK) and Pradu Hang Dam (PDH) are known for their impressive plumage and unique meat quality, suggesting selection for fighting and other purposes. However, information regarding the genetic diversity and clustering in indigenous and local Thai chickens used for cockfighting is unclear. Objective: To investigates the genetic diversity and differentiation in Thai fighting cock breeds, including populations for cockfighting, ornamental aspects, and consumption. Methods: Thai fighting cook breeds, including LHK and PDH chickens were analyzed using genotyping with 28 microsatellite loci. Data were compared to a gene pool library from "The Siam Chicken Bioresource Project" to understand the impact of human selection on genetic differentiation. Fighting cock strains from different breeds may cluster owing to shared breeding goals. Result: The analysis of several chicken breeds showed subpopulation differentiation driven by artificial selection and genetic drift, affecting the genetic landscape and causing genetic hitchhiking. Eleven of 28 microsatellite loci showed hitchhiking selection, indicating directional selection in fighting cocks. Additionally, analyses revealed admixture with domestic chicken breeds and minimal influence of red junglefowl in the gene pool of Thai fighting chickens. These findings inform breed improvement, selection strategies, genetic resource management, and maintaining genetic diversity in fighting cocks. Conclusion: Analysis of Thai Fighting chicken breeds revealed a correlation between utilization and subpopulation differentiation. Specifically, selection for cockfighting and ornamental traits appears to explain the observed genetic structure within these breeds. [ABSTRACT FROM AUTHOR]

Objective: The remarkable adaptability to the environment, high growth rate, meat with good taste and aroma, and ornamental appearance of the Pradu Hang Dam (PDH) and Samae Dam (SD) chickens make them valuable for improvement of poultry production to enhance food security. However, despite their close phenotypic similarity, distinct classification of PDH and SD chickens remains controversial. Thus, this study aimed to clarify genetic origins and variation between PDH and SD chickens, genetic diversity and structures of PDH and SD chickens. Methods: This study analyzed 5 populations of PDH and 2 populations of SD chickens using 28 microsatellite markers and compared with those of other indigenous and local chicken breeds using Thailand's "The Siam Chicken Bioresource Project" database. Results: Considerably high genetic variability was observed within PDH (370 total alleles; 4.086±0.312 alleles/locus) and SD chickens (179 total alleles; 3.607±0.349 alleles/locus). A partial overlap of gene pools was observed between SD chickens from the Department of Livestock, Uthai Thani (SD1) and PDH chickens, suggesting a potentially close relationship between the two chicken breeds. A gene pool that partially overlapped with that of the red junglefowl was observed in the SD chicken population from the Sanhawat Farm Uthai Thani population (SD2). Distinct subclusters were observed within SD chickens, indicating the possibility that genetic differentiation occurred early in the process of establishment of SD chickens. Conclusion: These findings could offer valuable insights into genetic verification of Thai local chicken breeds and their sustainable conservation and utilization. [ABSTRACT FROM AUTHOR]

Background: The Bangkaew dog is an indigenous dog breed in the Phitsanulok province of Thailand. This breed is recognized by the Fédération Cynologique Internationale (FCI), a global canine organization. The unique traits of the Bangkaew breed lead to purebred selection for breeding, while only their traits and pedigree from parental history are recorded. Determination of the risk of inbreeding depression and the origin of unknown DNA profiles is essential due to the challenges in predicting puppy characteristics, which are crucial for breed management and conservation. Objective: This study aimed to emphasize that current allelic frequency data for the Bangkaew dog breed must be considered for precise individual identification. Methods: Approximately 82 Bangkaew dogs from various Thai localities were studied using 15 microsatellite markers for genotypic monitoring and individual identification. Maternal genetic inheritance was assessed via mtDNA D-loop analysis. Results: The results revealed high genetic diversity in the Bangkaew breed, indicating low potential for inbreeding. We also found that using a 15 loci microsatellite panel was effective for the identification of Bangkaew dogs. The optimized 10 loci microsatellite genotyping panel developed in this study presents improved identification testing efficiency, promoting both time- and cost-effectiveness. Conclusion: Analysis of microsatellite DNA markers in Bangkaew dogs using an optimized panel of 10 loci selected from 15 loci effectively facilitated individual identification. This approach not only enhances time and cost efficiency, but also provides accurate allelic frequency estimates, which are crucial for the realistic evaluation of DNA evidence. [ABSTRACT FROM AUTHOR]

The North African catfish (Clarias gariepinus) is a significant species in aquaculture, which is crucial for ensuring food and nutrition security. Their high adaptability to diverse environments has led to an increase in the number of farms that are available for their production. However, long-term closed breeding adversely affects their reproductive performance, leading to a decrease in production efficiency. This is possibly caused by inbreeding depression. To investigate the root cause of this issue, the genetic diversity of captive North African catfish populations was assessed in this study. Microsatellite genotyping and mitochondrial DNA D-loop sequencing were applied to 136 catfish specimens, collected from three populations captured for breeding in Thailand. Interestingly, extremely low inbreeding coefficients were obtained within each population, and distinct genetic diversity was observed among the three populations, indicating that their genetic origins are markedly different. This suggests that outbreeding depression by genetic admixture among currently captured populations of different origins may account for the low productivity of the North African catfish in Thailand. Genetic improvement of the North African catfish populations is required by introducing new populations whose origins are clearly known. This strategy should be systematically integrated into breeding programs to establish an ideal founder stock for selective breeding. [ABSTRACT FROM AUTHOR]

Simple Summary: Hybrids between the critically endangered Siamese crocodile (Crocodylus siamensis) and least-concern saltwater crocodile (C. porosus) pose a significant challenge to conservation efforts due to human activities. Previous studies used microsatellite and mitochondrial DNA data to identify these hybrids, but potential biases and genetic drift within the populations could influence the results. To address these limitations and gain a clearer understanding of the genetic dynamics, we employed DArT sequencing to identify genome-wide single nucleotide polymorphisms (SNPs) in both species and confirm hybrid scenarios. We compared a population of Australian saltwater crocodiles to assess species-specific SNP distribution. Various analytical approaches were used to diagnose hybridization levels, especially in cases with potential backcrossing. Approximately 17.00–26.00% of loci were shared between Siamese and saltwater crocodile genomes. We identified 8051 species-specific SNP loci for Siamese crocodiles and 1288 for saltwater crocodiles. Using a PCR-based approach, three SNP loci were developed as markers, successfully enabling the distinction between species and various levels of hybridization. By combining mitochondrial and nuclear genetic information with species-diagnostic DNA markers, we developed a novel method for conservation prioritization, aiding long-term species survival through reintroduction and management programs. Hybrids between the critically endangered Siamese crocodile (Crocodylus siamensis) and least-concern saltwater crocodile (C. porosus) in captive populations represent a serious challenge for conservation and reintroduction programs due to the impact of anthropogenic activities. A previous study used microsatellite and mitochondrial DNA data to establish the criteria for identifying species and their hybrids; however, the results may have been influenced by biased allelic frequencies and genetic drift within the examined population. To overcome these limitations and identify the true signals of selection, alternative DNA markers and a diverse set of populations should be employed. Therefore, this study used DArT sequencing to identify genome-wide single nucleotide polymorphisms (SNPs) in both species and confirm the genetic scenario of the parental species and their hybrids. A population of saltwater crocodiles from Australia was used to compare the distribution of species-diagnostic SNPs. Different analytical approaches were compared to diagnose the level of hybridization when an admixture was present, wherein three individuals had potential backcrossing. Approximately 17.00–26.00% of loci were conserved between the Siamese and saltwater crocodile genomes. Species-diagnostic SNP loci for Siamese and saltwater crocodiles were identified as 8051 loci and 1288 loci, respectively. To validate the species-diagnostic SNP loci, a PCR-based approach was used by selecting 20 SNP loci for PCR primer design, among which 3 loci were successfully able to differentiate the actual species and different hybridization levels. Mitochondrial and nuclear genetic information, including microsatellite genotyping and species-diagnostic DNA markers, were combined as a novel method that can compensate for the limitations of each method. This method enables conservation prioritization before release into the wild, thereby ensuring sustainable genetic integrity for long-term species survival through reintroduction and management programs. [ABSTRACT FROM AUTHOR]

Lao Pa Koi (LPK) chicken is a popular fighting breed in Thailand, prized for (its unique characteristics acquired by selective breeding), and a valuable model for exploring the genetic diversity and admixture of red junglefowls and domestic chickens. In this study, genetic structure and diversity of LPK chicken were assessed using 28 microsatellite markers and mitochondrial DNA (mtDNA) D-loop sequences, and the findings were compared to a gene pool library from "The Siam Chicken Bioresource Project". High genetic variability was observed in LPK chickens using mtDNA D-loop haplotype analysis, and six haplotypes were identified. Microsatellite data revealed 182 alleles, with an average of 6.5 alleles per locus. These results confirmed the occurrence of genetic admixture of red junglefowl and Thai domestic chickens in LPK chicken breed. A maximum entropy modeling approach was used to analyze the spatial suitability and to assess the adaptive evolution of LPK chickens in diverse local environments. The model identified 82.52% of the area studied as unsuitable, and 9.34%, 7.11%, and 2.02% of the area indicated moderate, low, and high suitability, respectively. The highest contribution rate to land suitability for LPK chickens was found at an elevation of 100–250 m, suggesting the importance of elevation for their potential distribution. The results of this study provide valuable insights into the genetic origin of LPK chicken breed and identify resources for future genetic improvement. [ABSTRACT FROM AUTHOR]

Simple Summary: Mae Hong Son chicken is a local breed of North Thai domestic chicken widely distributed in Mae Hong Son; however, its genetic characterization, origin, and diversity remain unclear. Here, we studied the socio–cultural, environmental, and genetic aspects of the Mae Hong Son chicken breed, and we investigated its genetic diversity and footprint using the genotyping of 28 microsatellite markers and analyzed mitochondrial D-loop sequencing data. Genetic diversity analysis indicated that the Mae Hong Son chicken population is genetically highly diverse, with 35 haplotypes clustered into haplogroups A, B, E, and F, mostly in the North ecotype. Allelic gene pool patterns showed a unique DNA fingerprint of the Mae Hong Son chicken, as compared to other breeds and red junglefowl. A genetic introgression of some parts of the gene pool of red junglefowl and other indigenous breeds was identified in the Mae Hong Son chicken, supporting the hypothesis of the origin of the Mae Hong Son chicken as a crossbreed between red junglefowl and Thai indigenous village chickens that adapted to the environmental, social, and cultural conditions in its habitat. These findings enrich our understanding of the genetic blueprint, origin, and evolutionary process of the Mae Hong Son chickens and lay the foundation for future studies to improve domestic chickens using this indigenous chicken breed. Understanding the genetic diversity of domestic chicken breeds under the impact of socio–cultural and ecological dynamics is vital for the conservation of natural resources. Mae Hong Son chicken is a local breed of North Thai domestic chicken widely distributed in Mae Hong Son Province, Thailand; however, its genetic characterization, origin, and diversity remain poorly understood. Here, we studied the socio–cultural, environmental, and genetic aspects of the Mae Hong Son chicken breed and investigated its diversity and allelic gene pool. We genotyped 28 microsatellite markers and analyzed mitochondrial D-loop sequencing data to evaluate genetic diversity and assessed spatial habitat suitability using maximum entropy modeling. Sequence diversity analysis revealed a total of 188 genotyped alleles, with overall nucleotide diversity of 0.014 ± 0.007, indicating that the Mae Hong Son chicken population is genetically highly diverse, with 35 (M1–M35) haplotypes clustered into haplogroups A, B, E, and F, mostly in the North ecotype. Allelic gene pool patterns showed a unique DNA fingerprint of the Mae Hong Son chicken, as compared to other breeds and red junglefowl. A genetic introgression of some parts of the gene pool of red junglefowl and other indigenous breeds was identified in the Mae Hong Son chicken, supporting the hypothesis of the origin of the Mae Hong Son chicken. During domestication in the past 200–300 years after the crossing of indigenous chickens and red junglefowl, the Mae Hong Son chicken has adapted to the highland environment and played a significant socio–cultural role in the Northern Thai community. The unique genetic fingerprint of the Mae Hong Son chicken, retaining a high level of genetic variability that includes a dynamic demographic and domestication history, as well as a range of ecological factors, might reshape the adaptation of this breed under selective pressure. [ABSTRACT FROM AUTHOR]

Knowledge of the genetic characteristics, origin, and local adaptation of chickens is essential to identify the traits required for chicken breeding programs. Chee Fah and Fah Luang are black-boned chicken breeds reared in Chiang Rai, Thailand. Chickens are an important part of the local economy and socio-culture; however, the genetic diversity, characteristics, and origins of these two breeds have been poorly studied. Here, we investigated the genetic diversity, gene pool, and origin of the Chee Fah and Fah Luang chickens using mitochondrial DNA D-loop (mtDNA D-loop) sequencing and microsatellite genotyping, as well as habitat suitability analysis using maximum entropy modeling. The MtDNA D-loop sequencing and microsatellite genotype analyses indicated that the Chee Fah and Fah Luang chickens shared haplogroups A, B, and CD with Chinese black-boned chickens. Gene pool analysis revealed that the Chee Fah and Fah Luang chickens have distinct genetic patterns compared to Thai domestic chickens and red junglefowl. Some gene pools of red junglefowl and other Thai domestic chickens were observed within the Chee Fah and Fah Luang chicken gene pool structures, suggesting genetic exchange. The data indicate that the Chee Fah and Fah Luang chickens originated from Chinese indigenous black-boned chicken breeds and experienced crossbreeding/hybridization and introgression with red junglefowl and other domestic breeds during domestication. Interestingly, the Chee Fah and Fah Luang chickens from Chiang Rai shared the same allelic gene pool, which was not shared with the Chee Fah and Fah Luang chickens from Mae Hong Son, suggesting at least two gene pool origins in the Chee Fah and Fah Luang chicken populations. Alternatively, different gene pools in the Chee Fah and Fah Luang chickens from different localities might be caused by differences in environmental factors, especially elevation. [ABSTRACT FROM AUTHOR]

Simple Summary: Morphological divergence between Siamese and other crocodiles has been identified by size, number of scales, and patterns of cervical squamation with post-occipital scutes (P.O.). However, a large variation of P.O. has been observed in captive Siamese crocodiles in Thailand, leading to questions about possible crocodile hybrids. The genetic diversity and population structure of Siamese crocodiles were studied using mitochondrial DNA D-loop and microsatellite genotyping. The STRUCTURE plot revealed numerous distinct gene pools, indicating that the crocodiles in each farm descended from distinct lineages. Researchers also discovered evidence of introgression in several individual crocodiles, implying that Siamese and saltwater crocodiles may have hybridized. A schematic protocol for screening hybrids was proposed based on patterns observed in phenotypic and molecular data. Populations of Siamese crocodiles (Crocodylus siamensis) have severely declined because of hunting and habitat fragmentation, necessitating a reintroduction plan involving commercial captive-bred populations. However, hybridization between Siamese and saltwater crocodiles (C. porosus) has occurred in captivity. Siamese crocodiles commonly have post-occipital scutes (P.O.) with 4–6 scales, but 2–6 P.O. scales were found in captives on Thai farms. Here, the genetic diversity and population structure of Siamese crocodiles with large P.O. variations and saltwater crocodiles were analyzed using mitochondrial DNA D-loop and microsatellite genotyping. Possible crocodile hybrids or phenotypic variations were ascertained by comparison with our previous library from the Siam Crocodile Bioresource Project. Siamese crocodiles with <4 P.O. scales in a row exhibit normal species-level phenotypic variation. This evidence encourages the revised description of Siamese crocodiles. Moreover, the STRUCTURE plot revealed large distinct gene pools, suggesting crocodiles in each farm were derived from distinct lineages. However, combining both genetic approaches provides evidence of introgression for several individual crocodiles, suggesting possible hybridization between Siamese and saltwater crocodiles. We proposed a schematic protocol with patterns observed in phenotypic and molecular data to screen hybrids. Identifying non-hybrid and hybrid individuals is important for long-term in situ/ex situ conservation. [ABSTRACT FROM AUTHOR]

Developing successful conservation programs for genetically depleted species is challenging. Survival and adaptive potential are related to genetic and habitat factors; therefore, conservation programs are designed to minimize risks associated with inbreeding and loss of genetic diversity. The greater mouse-deer (Tragulus napu) is a true forest species that contributes to seed distribution dynamics in forests. However, with continuous demographic decline over the last century in the wild, only captive populations of the greater mouse-deer remain on the Thai mainland. A restoration program initiated 20 years ago has increased their population to more than 100 individuals but maintaining high genetic diversity in a small captive population is crucial for successful recovery. Microsatellite genotyping and mitochondrial D-loop and SRY gene sequence analyses were performed to examine the genetic diversity and population structure in 123 greater mouse-deer (64 females and 59 males). Highly reduced effective captive population size with trends of inbreeding were observed. No historical bottleneck was observed. These conditions have reduced their reproductive fitness and ability to adapt to environmental change, increasing the risk of population decline and eventual extinction. Demographic analyses suggested a recent captive population expansion due to effective animal welfare and reproduction. The results also suggested that population size at equilibrium is the main factor of allelic diversity (number of alleles). Large habitat carrying capacity, representing each fixed captive population size can support the genetic diversity of greater mouse-deer. We also identified suitable habitat areas for reintroduction and long-term in situ conservation of greater mouse-deer using maximum entropy modeling. Based on the environmental variables, species distribution modeling for greater mouse-deer indicated lowland tropical forest regions in the Khlong Saeng-Khao Sok forest complexes as most suitable and requiring urgent habitat improvement. These findings highlight the relevance of careful genetic monitoring and habitat suitability for the long-term conservation of greater mouse-deer and enhance the success of future conservation plans. [ABSTRACT FROM AUTHOR]

The domestication of wild animals represents a major milestone for human civilization. Chicken is the largest domesticated livestock species and used for both eggs and meat. Chicken originate from the red junglefowl (Gallus gallus). Its adaptability to diverse environments and ease of selective breeding provides a unique genetic resource to address the challenges of food security in a world impacted by climatic change and human population growth. Habitat loss has caused population declines of red junglefowl in Thailand. However, genetic diversity is likely to remain in captive stocks. We determine the genetic diversity using microsatellite genotyping and the mitochondrial D-loop sequencing of wild red junglefowl. We identified potential distribution areas in Thailand using maximum entropy models. Protected areas in the central and upper southern regions of Thailand are highly suitable habitats. The Bayesian clustering analysis of the microsatellite markers revealed high genetic diversity in red junglefowl populations in Thailand. Our model predicted that forest ranges are a highly suitable habitat that has enabled the persistence of a large gene pool with a nationwide natural distribution. Understanding the red junglefowl allows us to implement improved resource management, species reintroduction, and sustainable development to support food security objectives for local people. [ABSTRACT FROM AUTHOR]

Fishes provide a unique and intriguing model system for studying the genomic origin and evolutionary mechanisms underlying sex determination and high sex-chromosome turnover. In this study, the mode of sex determination was investigated in Siamese fighting fish, a species of commercial importance. Genome-wide SNP analyses were performed on 75 individuals (40 males and 35 females) across commercial populations to determine candidate sex-specific/sex-linked loci. In total, 73 male-specific loci were identified and mapped to a 5.6 kb region on chromosome 9, suggesting a putative male-determining region (pMDR) containing localized dmrt1 and znrf3 functional sex developmental genes. Repeat annotations of the pMDR revealed an abundance of transposable elements, particularly Ty3/Gypsy and novel repeats. Remarkably, two out of the 73 male-specific loci were located on chromosomes 7 and 19, implying the existence of polygenic sex determination. Besides male-specific loci, five female-specific loci on chromosome 9 were also observed in certain populations, indicating the possibility of a female-determining region and the polygenic nature of sex determination. An alternative explanation is that male-specific loci derived from other chromosomes or female-specific loci in Siamese fighting fish recently emerged as new sex-determining loci during domestication and repeated hybridization. [ABSTRACT FROM AUTHOR]