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This study aimed to provide information about the reproductive biology of moonlight gourami (Trichopodus microlepsis) distributed in U Minh National Parks. Fish samples were collected monthly from January to October 2019 at two locations: U Minh Ha (UMH, Ca Mau, n=462) and U Minh Thuong (UMT, Kien Giang, n=635). Results showed that the maturation-stage ratios of females were similar between the two fish populations. Mature females (with stage IV-ovaries) and the increase in their gonadal somatic index (GIS) were found from June to October, indicating that this period is their spawning season. GSI reached the highest values in August with 8.04% in UMH and 6.44% in UMT. Female fish of the UMH population showed higher average fecundity (7,483±3,008 eggs/female) and larger egg diameter (762±55 µm) than those of UMT (6,898±2,952 eggs/female and 754±43 µm, respectively), but these differences were not significant (p>0.05).

Selective programs associated with domestication can improve fish production but also can have an impact on broodstock’s genetic diversity. In this study, the genetic diversity of original sources (G0) from wild and cultured bighead catfish populations, as well as the two successive generations (G1 and G2) subjected to selection experiments, was assessed. G0 wild adults were collected in Ca Mau conservation area and G0 cultured fish were from a hatchery in Can Tho. The G1 fish included pure crosses and crossbreeds of G0, while G2 was the offspring of the selected G1. Fin clips from 27 to 29 individuals of each fish group were randomly sampled for genetic analysis. The amplification results using six ISSR primers showed that the genetic diversity was relatively higher in G0 (effective number of alleles Ne from 1.43 to 1.49; heterozygosity He from 0.265 to 0.290) than in G1 (Ne = 1.32±0.04; He = 0.201±0.023) and G2 (Ne = 1.34±0.04; He = 0.216±0.023). Genetic differences increased between the original populations and the descending generations. To reduce the detrimental impacts of low genetic diversity in domesticated bighead catfish in the Mekong Delta, it is recommended that broodstock in later generations should be produced in a larger...

The development of bighead catfish (Clarias macrocephalus) aquaculture in Viet Nam has been constrained by the slow growth performance in the domesticated strain. Crossbreeding can be a solution to improve fish production. This study was aimed to evaluate the growth and survival performance of the second generation (G2) fingerlings crossbreeds (CMCT and CTCM) from two bighead catfish strains (wild Ca Mau, CM, and domesticated Can Tho, CT) compared to offspring from their original strains (G0-CT and G0-CM) and G1 crossbreeds (♀CM × ♂CT and ♀CT × ♂CM). The larvae were reared in 50-L tanks (3 to 5 replications) with the density of 1,000 individuals/tank and fed with Moina and artificial feed (40% protein). After 40 days of rearing, the fish grew differently among crosses (P0.05). The performance of these crossbreeds should be investigated further at the grow-out stage to see whether crossbreeding between wild and cultured strains of bighead catfish may be used in practice to increase bighead catfish production.

Euthynnus (family Scombridae) is a genus of marine pelagic fish species with a worldwide distribution that comprises three allopatric species: E. alletteratus, E. affinis and E. lineatus. All of them targeted by artisanal and commercial fisheries. We analyzed 263 individuals from Atlantic and Pacific Oceans using two genetic markers, the mtDNA Control Region (350 bp) and nuclear calmodulin (341 bp). The results obtained challenge the phylogeny of this group. We found a deep genetic divergence, probably at species level, within E. alletteratus, between the North Atlantic-Mediterranean and the Tropical East Atlantic. This deep genetic divergence was tested with several species delimitation methods. This complete phylogeographic association between the North Atlantic and the Tropical East Atlantic support the hypothesis of two cryptic species. In addition, population genetic heterogeneity was detected between the North East Atlantic–Mediterranean and North West Atlantic regions. Our results indicate two scales of differentiation in what is currently considered a single population. Accordingly, for management purposes, the populations of E. alletteratus, should be divided into a minimum of three management units. On the other hand, the high level of differentiation found in E. alletteratus contrasts with the shallow genetic divergence of E. affinis and E. lineatus.

Understanding inter-population variation and sexual differences in morphology is a fundamental part of taxonomic and biological research. External morphology of swamp barb (Puntius brevis) was compared between sexes and among three populations in the Mekong Delta, including O Mon-Can Tho (n=86), U Minh Thuong-Kien Giang (n=49) and U Minh Ha-Ca Mau (n=77). The results illustrate that color and countable parameters are similar in all populations. Nonetheless, 9 out of 20 morphometric indices are significantly different among three populations (P

The bighead catfish (Clarias macrocephalus) and channel catfish (Ictalurus punctatus) are freshwater species in the Siluriformes order. C. macrocephalus has both gills and modified gill structures serving as an air-breathing organ (ABO), while I. punctatus does not possess such an organ, and cannot breathe in air, providing an excellent model for studying the molecular basis of ABO development in teleost fish. To investigate the critical time window for the development of air-breathing function, seven development stages were selected based on hypoxia challenge results, and RNA-seq was performed upon C. macrocephalus to compare with the non-air-breathing I. punctatus. Five-hundred million reads were generated and 25,239 expressed genes were annotated in C. macrocephalus. Among those, 8675 genes were differentially expressed across developmental stages. Comparative genomic analysis identified 1458 C. macrocephalus specific genes, which were absent in I. punctatus. Gene network and protein-protein interaction analyses identified 26 key hub genes involved in the air-breathing function. Three top candidate genes, mb, ngb, hbae, are mainly associated with oxygen carrying, oxygen binding, and heme binding activities. Our study provides a rich data set for exploring the genomic basis of air-breathing function in C. macrocephalus and offers insights into the adaption to hypoxic environments.

Simple Summary The mahseer, particularly the Tor species, is of significant cultural and economic importance as a high-value freshwater food fish in the Southeast (SE) Asian region. However, overexploitation of natural stocks because of high demand and their deteriorating habitat has resulted in a marked decline of Tor species in the wild. There are 13 Tor species that inhabit SE Asian rivers. All these species share distinct morphology, which is the presence of the median lobe. The unique characteristics, including body color, mouth position, and number of lateral scales, distinguish one species from another. Nonetheless, the taxonomy of the Tor species remains unstable and confusing, with contradictory data presented by different authors from different countries for a single Tor species. Therefore, in this review, we have gathered data for the SE Asian Tor species, outlining their distribution, morphology, and genetic identification. In addition, the present review also proposes a list of valid Tor species in the SE Asian region. The proposed list will serve as a standard and template for improving SE Asia’s Tor taxonomy, enhancing the study’s continuity, and a better understanding of specific Tor species. Abstract The king of rivers or mahseer comprises three genera: Tor, Neolissochilus, and Naziritor, under the Cyprinidae family. The Tor genus has been classified as the true mahseer due to the presence of a median lobe among the three genera. The Tor species are widely distributed across Southeast (SE) Asia, and 13 Tor species have been reported previously: Tor ater, Tor dongnaiensis, Tor douronensis, Tor laterivittatus, Tor mosal, Tor mekongensis, Tor putitora, Tor sinensis, Tor soro, Tor tambra, Tor tambroides, Tor tor and Tor yingjiangensis. However, the exact number of valid Tor species remains debatable. Different and unstandardized approaches of applying genetic markers in taxonomic identification and morphology variation within the same species have further widened the gap and ameliorated the instability of Tor species taxonomy. Therefore, synchronized and strategized research among Tor species researchers is urgently required to improve and fill the knowledge gap. This review is a current update of SE Asia’s Tor species, outlining their distribution, morphology, and genetic identification. In addition, the present review proposes that there are ten valid Tor species in the SE Asian region. This list will serve as a template and standard to improve the taxonomy of the SE Asian Tor species, which could serve as a basis to open new directions in Tor research.

Freshwater catfish of the genus Clarias, known as the airbreathing catfish, are widespread and important for food security through small scale inland fisheries and aquaculture. Limited genomic data are available for this important group of fishes. The bighead catfish (Clarias macrocephalus) is a commercial aquaculture species in southeast Asia used for aquaculture and threatened in its natural environment through habitat destruction, over-exploitation and competition from other introduced species of Clarias. Despite its commercial importance and threats to natural populations, public databases do not include any genomic data for C. macrocephalus. We present the first genomic data for the bighead catfish from Illumina sequencing. A total of 128 Gb of sequence data in paired-end 150 bp reads were assembled de novo, generating a final assembly of 883 Mbp contained in 27,833 scaffolds (N50 length: 80.8 kbp) with BUSCO completeness assessments of 96.3% and 87.6% based on metazoan and Actinopterygii ortholog datasets, respectively. Annotation of the genome predicted 21,124 gene sequences, which were assigned putative functions based on homology to existing protein sequences in public databases. Raw fastq reads and the final version of the genome assembly have been deposited in the NCBI (BioProject: PRJNA604477, WGS: JAAGKR000000000, SRA: SRR11188453). The complete C. macrocephalus mitochondrial genome was also recovered from the same sequence read dataset and is available on NCBI (accession: MT109097), representing the first mitogenome for this species. Lastly, we find an expansion of the mb and ora1 genes thought to be associated with adaptations to air-breathing and a semi-terrestrial life style in this genus of catfish.

The bighead catfish (Clarias macrocephalus) and channel catfish (Ictalurus punctatus) are freshwater species in the Siluriformes order. C. macrocephalus has both gills and modified gill structures serving as an air-breathing organ (ABO), while I. punctatus does not possess such an organ, and cannot breathe in air, providing an excellent model for studying the molecular basis of ABO development in teleost fish. To investigate the critical time window for the development of air-breathing function, seven development stages were selected based on hypoxia challenge results, and RNA-seq was performed upon C. macrocephalus to compare with the non-air-breathing I. punctatus. Five-hundred million reads were generated and 25,239 expressed genes were annotated in C. macrocephalus. Among those, 8675 genes were differentially expressed across developmental stages. Comparative genomic analysis identified 1458 C. macrocephalus specific genes, which were absent in I. punctatus. Gene network and protein-protein interaction analyses identified 26 key hub genes involved in the air-breathing function. Three top candidate genes, mb, ngb, hbae, are mainly associated with oxygen carrying, oxygen binding, and heme binding activities. Our study provides a rich data set for exploring the genomic basis of air-breathing function in C. macrocephalus and offers insights into the adaption to hypoxic environments.

The transition from fertilized egg to larva in fish is accompanied with various biological processes. We selected seven early developmental stages in channel catfish, Ictalurus punctatus, for transcriptome analysis, and covered 22,635 genes with 590 million high-quality RNA-sequencing (seq) reads. Differential expression analysis between neighboring developmental timepoints revealed significantly enriched biological categories associated with growth, development and morphogenesis, which was most evident at 2 vs. 5 days post fertilization (dpf) and 5 vs. 6 dpf. A gene co-expression network was constructed using the Weighted Gene Co-expression Network Analysis (WGCNA) approach and four critical modules were identified. Among candidate hub genes, GDF10, FOXA2, HCEA and SYCE3 were involved in head formation, egg development and the transverse central element of synaptonemal complexes. CK1, OAZ2, DARS1 and UBE2V2 were mainly associated with regulation of cell cycle, growth, brain development, differentiation and proliferation of enterocytes. IFI44L and ZIP10 were critical for the regulation of immune activity and ion transport. Additionally, TCK1 and TGFB1 were related to phosphate transport and regulating cell proliferation. All these genes play vital roles in embryogenesis and regulation of early development. These results serve as a rich dataset for functional genomic studies. Our work reveals new insights of the underlying mechanisms in channel catfish early development.

Bighead catfish (Clarias macrocephalus) is an important freshwater species for aquaculture and fisheries in Southeast Asia. The species has been domesticated for more than 30 generations in hatcheries, but wild population numbers have declined to “threatened” levels. In this study, genetic diversity was quantified in areas of intensive catfish culture and natural areas of the Mekong Delta, Viet Nam to inform hatchery genetic improvement programs and conservation actions. Fish were collected from three hatcheries and four wild populations in conservation parks (wild-conservation) and seven wild populations in rice fields of aquaculture-intensive areas (wild-farming). Results based on six microsatellite loci showed all populations had relatively high levels of genetic diversity for allelic richness (range 8.10– 10.18), and observed heterozygosity (range 0.708– 0.819). However, genetic diversity was lower in hatchery fish and wild farming populations as evidenced by significantly lower (P ≤ 0.03) allelic richness (9.16 ± 0.27 and 9.27 ± 0.66, respectively) than wild conserved populations (10.01 ± 0.19). Pairwise individuals’ genetic relatedness within three cultured populations (0.013–0.028) and five wild farming populations (0.016–0.039) indicated low potential for inbreeding in the immediate future. Genetic differentiation among populations (FST = 0.017 ± 0.002) indicated a modest level of gene flow, likely due to the expansive river network, straying of hatchery fish, and large-scale transport of wild fish to hatcheries.

Members of the freshwater halfbeak genus Dermogenys are hard to identify to the species level, despite several previous attempts to isolate fixed meristic, morphometric and colour pattern differences. This has led to ongoing confusion in scientific literature, records of species occurrence, and entries in museum collections. Here, a DNA barcoding study was conducted on the genus to gain further understanding of its taxonomic status across the Southeast Asian region. Fish were collected from 33 localities, spanning freshwater and brackish habitats in Malaysia, Western Indonesia, Thailand and Vietnam. In total, 290 samples of Dermogenys spp. were amplified for a 651 base pair fragment of the mitochondrial cytochrome oxidase c subunit I (COI) gene. Analysis was able to successfully differentiate the three species: D. collettei, D. siamensis, D. sumatrana; reveal the presence of a new putative species, Dermogenys sp., that was sampled in sympatry with D. collettei at three locations; as well as uncovering two genetic lineages of a fifth species, D. bispina, that display non-overlapping geographical distributions in drainages of northern Borneo; Kudat and Sandakan. This study expands the barcode library for Zenarchopteridae, demonstrates the efficacy of DNA barcoding techniques for differentiating Dermogenys species, and the potential thereof in species discovery.

Crossbreeding between wild and domesticated strains of important aquaculture species to determine potential for heterosis and heterobeltiosis is of interest to aquaculturists. The present study was aimed to evaluate broodstock strain effects and heterosis for growth and survival rates from larvae to grow out stages of bighead catfish (Clarias macrocephalus) crossed from one domesticated (Can Tho, CT) and two wild (Ca Mau, CM and Hau Giang, HG) populations. Nine crossbreeds were reared for 40 days at the larval stage in static tanks, 60 days for juveniles, and 90 days for grow out in recirculating systems. At harvest, pure CT exhibited the highest growth (final body weight BW = 154.1 ± 61.3 g), while HG × CT and HG × CM crossbreeds had the lowest (57.0 ± 17.0 g and 68.0 ± 28.5 g, respectively) and the other crossbreeds had intermediate values (mean BW ranged from 93.4 g to 113.1 g) (P = 0.01). The three stages showed consistently that the domestic CT strain grew faster than wild CM and HG strains. The growth performance of offspring was affected by dam strains, but not sire strains. Parental crosses generally had better growth rates compared to crossbreeds of the same dam source. However, crossbreeds did not differ in feed conversion ratios and survival rates from parental crosses. None of the crossbreeds had better growth than the better parent (heterobeltiosis), suggesting that crossbreeding among strains in the Mekong Delta may not be an effective genetic improvement program for bighead catfish.

The widespread farming of catfish (genus Clarias ) hybrids between bighead catfish ( C. macrocephalus , Cm ) and the introduced North African Catfish ( C. gariepinus , Cg ) in the Mekong Delta, where flooding is common, has raised concerns of introgression of Cg into the native catfish due to backcrossing by escaped hybrids with wild Cm . This study employed novel PCR-RFLP analyses of a mitochondrial ( Cytochrome c oxidase subunit I , COI) and two nuclear ( Rhodopsin and Tropomyosin ) markers and six microsatellite loci to differentiate hybrid individuals from their parental species, and evaluate whether introgression has occurred in wild and cultured Cm populations in the region. Results of marker screening showed that sizes and frequencies of microsatellite alleles differed between the two parental species. Four loci exhibited fixed species-specific differences in allele frequency (monomorphic in Cg and highly polymorphic in Cm ). Levels of sequence variation varied at the three genes examined, ranging from 3 to 8% (sequence length 652 bp for COI, 802 bp for Rhodopsin and 925 bp for Tropomyosin ). Based on variable sites identified that were not shared between the two species, 3 restriction enzymes ( Spe I, Xcm I and PflMI ) were selected to digest PCR products at species-specific sites within the COI, Rhodopsin and Tropomyosin genes, respectively. Results of PCR-RFLP analyses confirmed that Cm is the maternal lineage of cultured hybrids, while nuclear genes ( Rhodopsin and Tropomyosin ) and microsatellite loci revealed that hybrids possessed admixed multi-locus genotypes relative to the two parental species. Analyses of six microsatellite loci and PCR-RFLP of two nuclear genes in 473 individuals collected from 11 wild and three cultured populations revealed one F1 hybrid in the wild but no evidence of widespread introgression into native bighead catfish. These results differ from findings in Thailand where intensive catfish culture and deliberate species hybridization is practiced.

The transition from fertilized egg to larva in fish is accompanied with various biological processes. We selected seven early developmental stages in channel catfish, Ictalurus punctatus, for transcriptome analysis, and covered 22,635 genes with 590 million high-quality RNA-sequencing (seq) reads. Differential expression analysis between neighboring developmental timepoints revealed significantly enriched biological categories associated with growth, development and morphogenesis, which was most evident at 2 vs. 5 days post fertilization (dpf) and 5 vs. 6 dpf. A gene co-expression network was constructed using the Weighted Gene Co-expression Network Analysis (WGCNA) approach and four critical modules were identified. Among candidate hub genes, GDF10, FOXA2, HCEA and SYCE3 were involved in head formation, egg development and the transverse central element of synaptonemal complexes. CK1, OAZ2, DARS1 and UBE2V2 were mainly associated with regulation of cell cycle, growth, brain development, differentiation and proliferation of enterocytes. IFI44L and ZIP10 were critical for the regulation of immune activity and ion transport. Additionally, TCK1 and TGFB1 were related to phosphate transport and regulating cell proliferation. All these genes play vital roles in embryogenesis and regulation of early development. These results serve as a rich dataset for functional genomic studies. Our work reveals new insights of the underlying mechanisms in channel catfish early development.

Quantifying interannual variation in effective adult breeding number (N(b)) and relationships between N(b), effective population size (N(e)), adult census size (N) and population demographic characteristics are important to predict genetic changes in populations of conservation concern. Such relationships are rarely available for long-lived iteroparous species like lake sturgeon (Acipenser fulvescens). We estimated annual N(b) and generational N(e) using genotypes from 12 microsatellite loci for lake sturgeon adults (n = 796) captured during ten spawning seasons and offspring (n = 3925) collected during larval dispersal in a closed population over 8 years. Inbreeding and variance N(b) estimated using mean and variance in individual reproductive success derived from genetically identified parentage and using linkage disequilibrium (LD) were similar within and among years (interannual range of N(b) across estimators: 41-205). Variance in reproductive success and unequal sex ratios reduced N(b) relative to N on average 36.8% and 16.3%, respectively. Interannual variation in N(b)/N ratios (0.27-0.86) resulted from stable N and low standardized variance in reproductive success due to high proportions of adults breeding and the species' polygamous mating system, despite a 40-fold difference in annual larval production across years (437-16 417). Results indicated environmental conditions and features of the species' reproductive ecology interact to affect demographic parameters and N(b)/N. Estimates of N(e) based on three single-sample estimators, including LD, approximate Bayesian computation and sibship assignment, were similar to annual estimates of N(b). Findings have important implications concerning applications of genetic monitoring in conservation planning for lake sturgeon and other species with similar life histories and mating systems.

Mortality that occurs during larval dispersal as a consequence of environmental, maternal, and genetic effects and their interactions can affect annual recruitment in fish populations. We studied larval lake sturgeon (Acipenser fulvescens) drift for two consecutive nights to examine whether larvae from different females exposed to the same environmental conditions during dispersal differed in relative levels of mortality. We estimated proportional contributions of females to larval collections and relative larval loss among females as larvae dispersed downstream between two sampling sites based on genetically determined parentage. Larval collections were composed of unequal proportions of offspring from different females that spawned at upstream and downstream locations (~0.8 km apart). Hourly dispersal patterns of larvae produced from females spawning at both locations were similar, with the largest number of larvae observed during 22:00–23:00 h. Estimated relative larval loss did not differ significantly among females as larvae were sampled at two sites approximately 0.15 and 1.5 km from the last section downstream of spawning locations. High inter- and intra-female variation in larval contributions and relative larval loss between nights may be a common feature of lake sturgeon and other migratory fish species, and likely is a source of inter-annual and intra-annual variation in fish recruitment.

Songklanakarin Journal of Science and Technology (SJST), 38, 4