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1.
PLoS One ; 19(5): e0302584, 2024.
Article in English | MEDLINE | ID: mdl-38709757

ABSTRACT

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.


Subject(s)
Catfishes , DNA, Mitochondrial , Genetic Variation , Inbreeding , Microsatellite Repeats , Animals , Catfishes/genetics , Thailand , Microsatellite Repeats/genetics , DNA, Mitochondrial/genetics , Genotype , Aquaculture , North African People
2.
Genes Genomics ; 2024 Apr 30.
Article in English | MEDLINE | ID: mdl-38687435

ABSTRACT

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.

3.
PLoS One ; 19(3): e0298745, 2024.
Article in English | MEDLINE | ID: mdl-38536889

ABSTRACT

Aeromonas spp. are the opportunistic pathogens that infect both aquatic and terrestrial homeotherms. They were commonly present in aquatic environments, including effluent, tap water, marine, river, and lake, where they are often isolated from aquatic animals, including fish, molluscs, and crustaceans. The Aeromonas infections can cause sepsis, ulcer, and other symptoms, resulting in the death of massive aquatic animals. Therefore, the prevention and control of Aeromonas is of great significance for the healthy development of aquaculture. In this study, we used modern molecular methods to enhance disease control of Aeromonas isolates from freshwater fish in Hebei Province. A total of 130 Aeromonas spp. isolates were isolated from freshwater fish farms in Hengshui, Handan, and Shijiazhuang and all 130 Aeromonas spp. isolates were sequenced for species identification. Of the 130 Aeromonas spp. isolates, 104 isolates were successfully sequenced, and BLAST analysis showed that Aeromonas veronii was predominant in freshwater fish farms in Hebei Province. In addition, 26 antibiotic resistance profiles were obtained from 102 fully cultured isolates among the 104 Aeromonas spp. isolates whose species was primarily identified, and 44 multidrug-resistant bacteria among the 102 isolates were identified using an antibiotic susceptibility test. Using the Multilocus Sequence Typing (MLST) method, 33 out of 44 multidrug-resistant isolates with 14 non-Aeromonas reference strains were selected for phylogenetic and MLST analysis, and all 33 multidrug-resistant isolates were A. veronii. A total of 30 new Sequence Types (STs) were obtained by comparing concatenated sequences (gyrB-groL-gltA-metG-ppsA-recA) on PubMLST website. Furthermore, recombination event analysis detected using RDP5 and ClonalFrameML software 42 and 49 recombination events, respectively, and 22 recombination events were validated by four or more algorithms. Since mutation and recombination events increase clonal diversity and single housekeeping gene sequence alignments are limited for identifying species, we propose the use of multiple concatenated sequence loci to increase discriminatory power. In addition, we propose that the MLST method is an appropriate technique to study and develop the resistance mechanisms of multidrug-resistant Aeromonas and to identify Aeromonas systematically in complex samples obtained from the environment.


Subject(s)
Aeromonas , Animals , Multilocus Sequence Typing , Anti-Bacterial Agents/pharmacology , Phylogeny , Fishes/genetics , Drug Resistance, Multiple, Bacterial/genetics , Fresh Water
4.
Cytogenet Genome Res ; 2024 Mar 07.
Article in English | MEDLINE | ID: mdl-38452741

ABSTRACT

Backgound The synaptonemal complex (SC) is a protein axis formed along chromosomes during meiotic prophase to ensure proper pairing and crossing over. SC analysis has been widely used to study the chromosomes of mammals, and less frequently of birds, reptiles, and fish. It is a promising method to investigate the evolution of fish genomes and chromosomes as a part of complex approach. Summary Compared with conventional metaphase chromosomes, pachytene chromosomes are less condensed and exhibit pairing between homologous chromosomes. These features of SCs facilitate the study of the small chromosomes that are typical in fish. Moreover, it allows the study of heteromorphisms in sex chromosomes and supernumerary chromosomes. In addition, it enables the investigation of the pairing between orthologous chromosomes in hybrids, which is crucial for uncovering the causes of hybrid sterility and asexual reproduction, such as gynogenesis or hybridogenesis. However, the application of SC analysis to fish chromosomes is limited by the associated complications. First, in most fish, meiosis does not occur during every season and life stage. Second, different SC preparation methods are optimal for different fish species. Third, commercial antibodies targeting meiotic proteins have been primarily developed against mammalian antigens, and not all of them are suitable for fish chromosomes. Key messages In the present review, we provide an overview of the methods for preparing fish SCs and highlight important studies using SC analysis in fish. This study will be valuable for planning and designing research that applies SC analysis to fish cytogenetics and genomics.

5.
Poult Sci ; 103(4): 103503, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38330888

ABSTRACT

The thermal stress caused by global climate change adversely affects the welfare, productivity, and reproductive performance of farm animals, including chickens, and causes substantial economic losses. However, the understanding of the genetic basis of the indigenous chicken adaptation to high ambient temperatures is limited. Hence, to reveal the genetic basis of thermal stress adaptation in chickens, this study investigated polymorphisms in the heat shock protein 70 (HSP70) and HSP90 genes, known mechanisms of cellular defense against thermal stress in indigenous and local chicken breeds and red junglefowls in Thailand. The result revealed seven alleles of the HSP70 gene. One allele exhibited a missense mutation, where an amino acid changed from Asn to His in the substrate-binding and peptide-binding domains, which is exclusive to the Lao Pa Koi chicken breed. Twenty new alleles with silent mutations in the HSP90 gene highlighted its greater complexity. Despite this diversity, distinct population structures were not found for either HSP70 or HSP90, which suggests incomplete impact on the domestication process and selection. The low genetic diversity, shown by the sharing of alleles between red junglefowls and Thai indigenous and local chicken breeds, aligns with the hypothesis that these alleles have undergone selection in tropical regions, such as Thailand. Selection signature analysis suggests the purifying selection of HSP70 for thermotolerance. This study provides valuable insights for enhancing the conservation of genetic resources with thermotolerant traits, which are essential for developing breeding programs to increase poultry production in the context of global climate change.


Subject(s)
Chickens , HSP70 Heat-Shock Proteins , Animals , Chickens/genetics , HSP70 Heat-Shock Proteins/genetics , Genetic Variation , Thailand , Polymorphism, Genetic , HSP90 Heat-Shock Proteins/genetics
6.
Genes Genomics ; 46(1): 113-119, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37985546

ABSTRACT

The location of female-specific/linked loci identified in Siamese cobra (Naja kaouthia) previously has been determined through in silico chromosome mapping of the Indian cobra genome (N. naja) as a reference genome. In the present study, we used in silico chromosome mapping to identify sex-specific and linked loci in Siamese cobra. Many sex-specific and sex-linked loci were successfully mapped on the Z sex chromosome, with 227 of the 475 specific loci frequently mapped in a region covering 57 Mb and positioned at 38,992,675-95,561,177 bp of the Indian cobra genome (N. naja). This suggested the existence of a putative sex-determining region (SDR), with one specific locus (PA100000600) homologous to the TOPBP1 gene. The involvement of TOPBP1 gene may lead to abnormal synaptonemal complexes and meiotic chromosomal defects, resulting in male infertility. These findings offer valuable insights into the genetic basis and functional aspects of sex-specific traits in the Siamese cobra, which will contribute to our understanding of snake genetics and evolutionary biology.


Subject(s)
Elapidae , Naja naja , Animals , Male , Female , Elapidae/genetics , Naja naja/genetics , Elapid Venoms/genetics , Antivenins/genetics , Sex Chromosomes/genetics
7.
Genes Genomics ; 46(1): 95-112, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37985545

ABSTRACT

BACKGROUND: In nucleotide public repositories, studies discovered data errors which resulted in incorrect species identification of several accipitrid raptors considered for conservation. Mislabeling, particularly in cases of cryptic species complexes and closely related species, which were identified based on morphological characteristics, was discovered. Prioritizing accurate species labeling, morphological taxonomy, and voucher documentation is crucial to rectify spurious data. OBJECTIVE: Our study aimed to identify an effective DNA barcoding tool that accurately reflects the efficiency status of barcodes in raptor species (Accipitridae). METHODS: Barcode sequences, including 889 sequences from the mitochondrial cytochrome c oxidase I (COI) gene and 1052 sequences from cytochrome b (Cytb), from 150 raptor species within the Accipitridae family were analyzed. RESULTS: The highest percentage of intraspecific nearest neighbors from the nearest neighbor test was 88.05% for COI and 95.00% for Cytb, suggesting that the Cytb gene is a more suitable marker for accurately identifying raptor species and can serve as a standard region for DNA barcoding. In both datasets, a positive barcoding gap representing the difference between inter-and intra-specific sequence divergences was observed. For COI and Cytb, the cut-off score sequence divergences for species identification were 4.00% and 3.00%, respectively. CONCLUSION: Greater accuracy was demonstrated for the Cytb gene, making it the preferred primary DNA barcoding marker for raptors.


Subject(s)
DNA Barcoding, Taxonomic , DNA , DNA Barcoding, Taxonomic/methods , Base Sequence , Genes, Mitochondrial , Electron Transport Complex IV/genetics , Cytochromes b/genetics
8.
Biology (Basel) ; 12(11)2023 Nov 13.
Article in English | MEDLINE | ID: mdl-37998027

ABSTRACT

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.

9.
Chromosome Res ; 31(4): 34, 2023 11 29.
Article in English | MEDLINE | ID: mdl-38017297

ABSTRACT

Eukaryotes have varying numbers and structures of characteristic chromosomes across lineages or species. The evolutionary trajectory of species may have been affected by spontaneous genome rearrangements. Chromosome fusion drastically alters karyotypes. However, the mechanisms and consequences of chromosome fusions, particularly in muntjac species, are poorly understood. Recent research-based advancements in three-dimensional (3D) genomics, particularly high-throughput chromatin conformation capture (Hi-C) sequencing, have allowed for the identification of chromosome fusions and provided mechanistic insights into three muntjac species: Muntiacus muntjak, M. reevesi, and M. crinifrons. This study aimed to uncover potential genome rearrangement patterns in the threatened species Fea's muntjac (Muntiacus feae), which have not been previously examined for such characteristics. Deep Hi-C sequencing (31.42 × coverage) was performed to reveal the 3D chromatin architecture of the Fea's muntjac genome. Patterns of repeated chromosome fusions that were potentially mediated by high-abundance transposable elements were identified. Comparative Hi-C maps demonstrated linkage homology between the sex chromosomes in Fea's muntjac and autosomes in M. reevesi, indicating that fusions may have played a crucial role in the evolution of the sex chromosomes of the lineage. The species-level dynamics of topologically associated domains (TADs) suggest that TAD organization could be altered by differential chromosome interactions owing to repeated chromosome fusions. However, research on the effect of TADs on muntjac genome evolution is insufficient. This study generated Hi-C data for the Fea's muntjac, providing a genomic resource for future investigations of the evolutionary patterns of chromatin conformation at the chromosomal level.


Subject(s)
Chromatin , Muntjacs , Animals , Muntjacs/genetics , Chromatin/genetics , Chromosome Mapping/methods , Genome , Sex Chromosomes
10.
Virology ; 588: 109911, 2023 11.
Article in English | MEDLINE | ID: mdl-37918186

ABSTRACT

The walbRep megasatellite DNA found in the red-necked wallaby was formed from the walb endogenous retrovirus. Our previous PCR experiments suggested the presence of walb and absence of walbRep in the genome of the tammar wallaby, which diverged from the red-necked wallaby 2-3 Mya. The results failed to exclude the possibility that certain walbRep sequences might have remained undetected owing to variation in the primer-annealing regions; therefore, the aforementioned suggestion was not confirmed. To obtain conclusive evidence, we analyzed the structure of walb sequences drawn from the tammar wallaby genome database recently updated to a chromosome-level assembly. All walb copies existed as separate DNA segments, not constituting tandem repeats. We concluded that walbRep was formed in the red-necked wallaby lineage after its divergence from the tammar wallaby. We also confirm the presence of a walb copy with an anomalistic, complex structure and propose a simple model for its generation mechanism.


Subject(s)
Endogenous Retroviruses , Macropodidae , Animals , Macropodidae/genetics , DNA, Satellite/genetics , Endogenous Retroviruses/genetics , DNA
11.
Biology (Basel) ; 12(10)2023 Sep 25.
Article in English | MEDLINE | ID: mdl-37886990

ABSTRACT

Microsatellites are polymorphic and cost-effective. Optimizing reduced microsatellite panels using heuristic algorithms eases budget constraints in genetic diversity and population genetic assessments. Microsatellite marker efficiency is strongly associated with its polymorphism and is quantified as the polymorphic information content (PIC). Nevertheless, marker selection cannot rely solely on PIC. In this study, the ant colony optimization (ACO) algorithm, a widely recognized optimization method, was adopted to create an enhanced selection scheme for refining microsatellite marker panels, called the PIC-ACO selection scheme. The algorithm was fine-tuned and validated using extensive datasets of chicken (Gallus gallus) and Chinese gorals (Naemorhedus griseus) from our previous studies. In contrast to basic optimization algorithms that stochastically initialize potential outputs, our selection algorithm utilizes the PIC values of markers to prime the ACO process. This increases the global solution discovery speed while reducing the likelihood of becoming trapped in local solutions. This process facilitated the acquisition of a cost-efficient and optimized microsatellite marker panel for studying genetic diversity and population genetic datasets. The established microsatellite efficiency metrics such as PIC, allele richness, and heterozygosity were correlated with the actual effectiveness of the microsatellite marker panel. This approach could substantially reduce budgetary barriers to population genetic assessments, breeding, and conservation programs.

12.
Genomics Inform ; 21(3): e39, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37813635

ABSTRACT

DNA barcoding without assessing reliability and validity causes taxonomic errors of species identification, which is responsible for disruptions of their conservation and aquaculture industry. Although DNA barcoding facilitates molecular identification and phylogenetic analysis of species, its availability in clariid catfish lineage remains uncertain. In this study, DNA barcoding was developed and validated for clariid catfish. 2,970 barcode sequences from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes and D-loop sequences were analyzed for 37 clariid catfish species. The highest intraspecific nearest neighbor distances were 85.47%, 98.03%, and 89.10% for COI, Cytb, and D-loop sequences, respectively. This suggests that the Cytb gene is the most appropriate for identifying clariid catfish and can serve as a standard region for DNA barcoding. A positive barcoding gap between interspecific and intraspecific sequence divergence was observed in the Cytb dataset but not in the COI and D-loop datasets. Intraspecific variation was typically less than 4.4%, whereas interspecific variation was generally more than 66.9%. However, a species complex was detected in walking catfish and significant intraspecific sequence divergence was observed in North African catfish. These findings suggest the need to focus on developing a DNA barcoding system for classifying clariid catfish properly and to validate its efficacy for a wider range of clariid catfish. With an enriched database of multiple sequences from a target species and its genus, species identification can be more accurate and biodiversity assessment of the species can be facilitated.

13.
PLoS One ; 18(10): e0289983, 2023.
Article in English | MEDLINE | ID: mdl-37792798

ABSTRACT

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.


Subject(s)
Chickens , Genetic Variation , Animals , Chickens/genetics , DNA, Mitochondrial/genetics , Haplotypes , Phylogeny , Thailand
14.
Chromosome Res ; 31(4): 29, 2023 09 30.
Article in English | MEDLINE | ID: mdl-37775555

ABSTRACT

Microsatellites are short tandem DNA repeats, ubiquitous in genomes. They are believed to be under selection pressure, considering their high distribution and abundance beyond chance or random accumulation. However, limited analysis of microsatellites in single taxonomic groups makes it challenging to understand their evolutionary significance across taxonomic boundaries. Despite abundant genomic information, microsatellites have been studied in limited contexts and within a few species, warranting an unbiased examination of their genome-wide distribution in distinct versus closely related-clades. Large-scale comparisons have revealed relevant trends, especially in vertebrates. Here, "MicrosatNavigator", a new tool that allows quick and reliable investigation of perfect microsatellites in DNA sequences, was developed. This tool can identify microsatellites across the entire genome sequences. Using this tool, microsatellite repeat motifs were identified in the genome sequences of 186 vertebrates. A significant positive correlation was noted between the abundance, density, length, and GC bias of microsatellites and specific lineages. The (AC)n motif is the most prevalent in vertebrate genomes, showing distinct patterns in closely related species. Longer microsatellites were observed on sex chromosomes in birds and mammals but not on autosomes. Microsatellites on sex chromosomes of non-fish vertebrates have the lowest GC content, whereas high-GC microsatellites (≥ 50 M% GC) are preferred in bony and cartilaginous fishes. Thus, similar selective forces and mutational processes may constrain GC-rich microsatellites to different clades. These findings should facilitate investigations into the roles of microsatellites in sex chromosome differentiation and provide candidate microsatellites for functional analysis across the vertebrate evolutionary spectrum.


Subject(s)
Genome , Vertebrates , Animals , Vertebrates/genetics , Microsatellite Repeats , Sex Chromosomes/genetics , Genomics , Mammals/genetics
15.
Genomics Inform ; 21(2): e24, 2023 Jun.
Article in English | MEDLINE | ID: mdl-37704210

ABSTRACT

Assays of clinical diagnosis and species identification using molecular markers are performed according to a quantitative method in consideration of sensitivity, cost, speed, convenience, and specificity. However, typical polymerase chain reaction (PCR) assay is difficult to quantify and have various limitations. In addition, to perform quantitative analysis with the quantitative real-time PCR (qRT-PCR) equipment, a standard curve or normalization using reference genes is essential. Within the last a decade, previous studies have reported that the digital PCR (dPCR) assay, a third-generation PCR, can be applied in various fields by overcoming the shortcomings of typical PCR and qRT-PCR assays. We selected Stilla Naica System (Stilla Technologies), Droplet Digital PCR Technology (Bio-Rad), and Lab on an Array Digital Real-Time PCR analyzer system (OPTOLANE) for comparative analysis among the various droplet digital PCR platforms currently in use commercially. Our previous study discovered a molecular marker that can distinguish Hanwoo species (Korean native cattle) using Hanwoo-specific genomic structural variation. Here, we report the pros and cons of the operation of each dPCR platform from various perspectives using this species identification marker. In conclusion, we hope that this study will help researchers to select suitable dPCR platforms according to their purpose and resources.

16.
Virology ; 586: 56-66, 2023 09.
Article in English | MEDLINE | ID: mdl-37487326

ABSTRACT

The kangaroo endogenous retrovirus (KERV) was previously reported to have undergone a rapid copy number increase in the red-necked wallaby; however, the mode of amplification was left to be clarified. The present study revealed that the long terminal repeat (LTR) (0.6 kb) and internal region (2.0 kb) of a provirus are repeated alternately, forming megasatellite DNA which we named kervRep. This repetition pattern was the same as that observed for walbRep, megasatellite DNA originating from another endogenous retrovirus. Their formation process can be explained using a simple model: pairing slippage followed by homologous recombination. This model features that the initial step is triggered by the presence of two identical sequences within a short distance; the possession of LTRs by endogenous retroviruses fulfills this condition. The discovery of two cases suggests that formation of this type of satellite DNA is one of non-negligible effects of endogenous retroviruses on their host genomes.


Subject(s)
Endogenous Retroviruses , Animals , Endogenous Retroviruses/genetics , Proviruses/genetics , Macropodidae/genetics , DNA , Terminal Repeat Sequences
17.
Animals (Basel) ; 13(12)2023 Jun 10.
Article in English | MEDLINE | ID: mdl-37370459

ABSTRACT

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.

18.
Biology (Basel) ; 12(4)2023 Mar 31.
Article in English | MEDLINE | ID: mdl-37106736

ABSTRACT

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.

19.
Genes Genomics ; 45(2): 169-181, 2023 Feb.
Article in English | MEDLINE | ID: mdl-36512198

ABSTRACT

BACKGROUND: The number of nucleotide sequences in public repositories has exploded recently. However, the data contain errors, leading to incorrect species identification. Several fighting fish (Betta spp.) are poorly described, with unresolved cryptic species complexes masking undescribed species. Here, DNA barcoding was used to detect erroneous sequences in public repositories. OBJECTIVE: This study reflects the current quantitative and qualitative status of DNA barcoding in fighting fish and provides a rapid and reliable identification tool. METHODS: A total of 1034 barcode sequences were analyzed from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes from 71 fighting fish species. RESULTS: The nearest neighbor test showed the highest percentage of intraspecific nearest neighbors at 93.41% for COI and 91.67% for Cytb, which can be used as reference barcodes for certain taxa. Intraspecific variation was usually less than 13%, while most species differed by more than 54%. The barcoding gap, calculated from the difference between inter- and intraspecific sequence divergences, was negative in the COI data set indicating overlapping intra- and interspecific sequence divergence. Sequence saturation was observed in the Cytb data set but not in the COI data set. CONCLUSION: The COI gene should thus be used as the main barcoding marker for fighting fish.


Subject(s)
DNA Barcoding, Taxonomic , DNA , Animals , Base Sequence , Quality Control , Mitochondria/genetics , Fishes/genetics , Cytochromes b/genetics
20.
Genomics Inform ; 21(4): e47, 2023 Dec.
Article in English | MEDLINE | ID: mdl-38224714

ABSTRACT

Silver barb (Barbonymus gonionotus) is among the most economically important freshwater fish species in Thailand. It ranks fourth in economic value and third in production weight for fisheries and culture in Thailand. An XX/XY sex-determination system based on gynogenesis was previously reported for this fish. In this study, the molecular basis underlying the sex-determination system was further investigated. Genome-wide single-nucleotide polymorphism data were generated for 32 captive-bred silver barb individuals, previously scored by phenotypic sex, to identify sex-linked regions associated with sex determination. Sixty-three male-linked loci, indicating putative XY chromosomes, were identified. Male-specific loci were not observed, which indicates that the putative Y chromosome is young and the sex determination region is cryptic. A homology search revealed that most male-linked loci were homologous to the Mariner/Tc1 and Gypsy transposable elements and are probably the remnants of an initial accumulation of repeats on the Y chromosome from the early stages of sex chromosome differentiation. This research provides convincing insights into the mechanism of sex determination and reveals the potential sex determination regions in silver barb. The study provides the basic data necessary for increasing the commercial value of silver barbs through genetic improvements.

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