Genetic diversity of walking catfish, Clarias macrocephalus, in Thailand and evidence of genetic introgression from introduced farmed C. gariepinus

The Thai walking catfish, Clarias macrocephalus Günther, 1864, is economically important to Thailand. It occupies marshes and swamps that are severely endangered due to population expansion and natural populations are thought to be suffering from massive back-crossing with the C. macrocephalus×C. gariepinus hybrids. Therefore, a study on genetic diversity of this species is required to enable efficient conservation and management plans. In this study, 25 natural populations were collected throughout the country, 12 populations from provinces locate in the Chaophraya river basin in the center of the country, 5 from the Mekong river basin, 1 from the east and 7 from the south. One population of hatchery origin was obtained from the Department of Aquaculture, Kasetsart University in Bangkok.

Twelve isozymes and one protein system were analyzed. Among 18 loci resolved, 8 were polymorphic. The number of alleles per locus, average polymorphism and individual polymorphism were significantly higher in collections from the Chaophraya river basin than from the Mekong, east and south. The hatchery population also had relative high genetic variation. Six out of twenty-six populations differed significantly from Hardy-Weinberg equilibrium after Bonferroni correction. None of loci pairs showed significant linkage disequilibrium after Bonferroni correction. The F_st value across loci was highly significant from zero. A neighbor-joining tree reveals that populations from the south were genetically distinct from the remaining populations.

Alleles peculiar to the African catfish [C. gariepinus (Burchell, 1822)] genome were observed in 12 of the natural populations and the hatchery population. This is evidence of genetic introgression which has probably persisted for several generations, since there was no significant genotype disequilibrium between the macrocephalus and gariepinus alleles at three diagnostic loci.     

Genetic diversity of wild mekong giant catfish Pangasianodon gigas collected from Thailand and Cambodia

The Mekong giant catfish Pangasianodon gigas is endemic to the Mekong River and is a critically endangered species. The genotypes of the microsatellite DNA (msDNA) and mitochondrial DNA (mtDNA) markers (right domain of the control region) were detected to evaluate the present status of genetic divergence of this species from the Mekong River in Thailand and Cambodia. The observed and expected heterozygosity values of Mekong giant catfish in Thailand and Cambodia were relatively low in comparison with those of other nonendangered freshwater fish species. These two populations from Thailand and Cambodia showed similar levels of genetic diversity, as evaluated by the 384 nucleotides of the mtDNA control region with 13 haplotypes. The pairwise F _ST value between the two populations based on the genotype frequencies of msDNA and mtDNA markers suggested a close genetic relationship between the populations in Thailand and Cambodia. The results of this study support the conclusion that the Mekong giant catfish is critically endangered. Care should be taken to sustain the genetic diversity of this species, as the level of genetic variability has already decreased in the wild population. This species is a target species for an ongoing stock enhancement program in the Mekong River in Thailand. It is proposed to apply these markers for proper broodstock management, such as for minimal kinship selective breeding in the hatchery.     

Heritability for growth traits in giant freshwater prawn,Macrobrachium rosenbergii (de Mann 1879) based on best linear unbiased prediction methodology

In this study, heritability was estimated for growth‐related traits of giant freshwater prawn (Macrobrachium rosenbergii) before and after morphological sexual differentiation. Estimation was made on data from 16 full‐sib and eight half‐sib families. The variance estimation was performed using a univariate mixed linear animal model and variance components were analysed following an animal model using restricted maximum likelihood procedure using average information algorithm. Heritability estimates (h²) varied considerably with ages. At 2 months old, h²for carapace length (CL; 0.35±0.15) and body weight (BW; 0.26±0.13) were higher than those estimated at 5 months old, based on mixed sex data. However, when data were sorted by sex, h² calculated from data of females were higher than those of males for CL (0.26±0.16 vs. 0.10±0.06), BW (0.28±0.17 vs. 0.12±0.08), body length (0.40±0.17 vs. 0.11±0.07), total length (0.47±0.18 vs. 0.11±0.07) and claw length (0.29±0.16 vs. 0.03±0.04). The same trend was observed for traits at 6 months old in both bulk and individual rearing.     

Current status & prospects of farming the giant river prawn (Macrobrachium rosenbergii de Man 1879) in Thailand

Thailand was second only to P.R.China in annual production of giant river prawn. This article briefly describes the seed production of giant river prawn technology in Thailand and notes that broodstock management has paid scant attention to genetic issues. There are, however, ongoing selective breeding programmes on giant river prawn aimed to improve growth and disease resistance. In the conventional culture technology, postlarvae are stocked at a high density and prawns are harvested partially. The cropping period is long and the practice has led to disease outbreaks and deteriorated pond bottoms that result in frequent detection of antibiotic residue. The improved culture technology involves manual sexing of the prawns at 3 months and restocking only the male prawns into new ponds at low density. The technique gives higher yield and reduces incidence of disease and thus the need for prophylactics. The constraints to giant river prawn culture business in Thailand include low yield and a limited export market. The article describes three ways to expand and sustain the business of giant river prawn farming in the country: development of more genetically improved strains; culture of all‐male stock, and new culture techniques.     

Temporal genetic heterogeneity of juvenile orange-spotted grouper (Epinephelus coioides, Pisces: Serranidae)

Juveniles of orange-spotted grouper ( Epinephelus coioides ), a tropical serranid species, are heavily harvested for aquaculture seeds from nursing grounds in several Southeast Asian countries. Because juveniles of similar sizes are present in a nursery area throughout the year, we aimed to determine whether more than one genetically distinct population contributes to juvenile aggregations. We examined the temporal genetic heterogeneity of juvenile aggregations collected at four different times of the year at a nursery area in coastal waters of the Andaman Sea in Trang province, Thailand. Also, we examined the differences between these temporal samples and an outgroup collected from the Gulf of Thailand (Chantaburi). The genetic variation at six polymorphic microsatellite loci within each sample was moderate, with observed heterozygosities across all loci ranging from 0.551 to 0.629 and number of alleles per locus ranging from 7.0 to 8.33. Results indicated substantial genetic differences between the two geographically distant samples, Trang and Chantaburi (F_st=0.040–0.050, P <0.005), and between the July sample and the remaining samples from Trang (F_st=0.096–0.106, P <0.005). The observed temporal genetic heterogeneity of E. coioides juveniles may reflect high variability in the reproductive success of each spawning event and the existence of spatially isolated groups of spawners.     

Isolation and characterization of microsatellite DNA markers in endangered Mekong giant catfish Pangasianodon gigas

ABSTRACT:   The Mekong giant catfish is one of the largest freshwater fish in the world, and is endemic to the Mekong basin. Recently, the number of Mekong giant catfish has drastically decreased. In this study, seven microsatellite DNA markers of the Mekong giant catfish were developed for evaluation of the species' genetic diversity. Mendelian inheritance of four of seven markers was confirmed using offspring (F1) produced from one pair. Number of alleles per locus in the founder population ranged 1–4 with a mean of 2.8, and that in F1 ranged 1–2 with a mean of 1.6. The expected heterozygosity in the founder population ranged 0–0.66 with a mean of 0.38, and that in F1 ranged 0–0.5 with a mean of 0.28. The mean expected heterozygosity in the founder population is apparently lower than that in Pangasius bocourti and other freshwater species, but higher than that in endangered species. In the future, the microsatellite data in this study will be used in minimal kinship approaches, because these individuals constitute the basic seed for release into wild in an effort to conserve the native population of Mekong giant catfish.     

No AFLP sex-specific markers detected in Pangasianodon gigas and P. hypophthalmus

Sex-specific DNA markers are useful for hatchery management. Sex identification at early ages can reduce broodstock rearing costs. This study employed the Amplified Fragment Length Polymorphism (AFLP) approach for the identification of sex-linked markers in Pangasianodon gigas and P. hypophthalmus. Eight DNA pools (4 females, 4 males) each from P. gigas and P. hypophthalmus were screened using a total of 570 and 102 different primer combinations, respectively. None of the 570 primer combinations gave sex-associated amplification for P. gigas while 31 of the 102 primer combinations gave apparent sex-associated amplification across the pooled DNA samples of P. hypophthalmus. However, none of the 45 SCAR markers derived from the presumed sex-specific fragments showed sex specificity when tested using DNA of individual P. hypophthalmus males and females.     

Genetic relatedness and differentiation of hatchery populations of Asian seabass (Lates calcarifer) (Bloch, 1790) broodstock in Thailand inferred from microsatellite genetic markers

After more than 20 years of hatchery production of Asian seabass in Thailand, genetic information is still lacking for effective genetic management and a selective breeding programme. This study aimed to evaluate genetic status of existing hatchery populations and genetic consequences of a selective breeding attempt. We examined genetic relatedness in seven hatchery samples, including a selectively bred population (RACF‐F1), compared with three wild samples using 11 microsatellite loci. Genetic diversity and relatedness values within most hatchery samples, except for RACF‐F1, did not differ from those of wild populations (P > 0.05). RACF‐F1 had the lowest allelic diversity and effective population size (A_r = 6.99; N_e = 7.8) and highest relatedness values (mean r_xy = 0.075–0.204). Pairwise Φ_ST values, principal component analysis and model‐based cluster analyses revealed three genetically distinct hatchery groups: Eastern Thailand (CHN, RACF, NSCF and SKCF), Southern Thailand (NICA) and the Andaman Sea (STCF). Results suggest that exiting domestic populations capture reasonable amount of genetic variation and can be useful for a base population for genetic improvement programmes. In addition, given the rapid increase in relatedness that we observed in one selectively bred population, we recommend using selection methods and hatchery practices that reduce variability in family contribution in the subsequent generations.     

Preliminary study on performance of triploid Thai silver barb, Puntius gonionotus

The triploid chromosome condition was induced in Thai silver barb (Puntius gonionotus) by application of cold shock (2°C) to eggs at time intervals after activation of 0.5 min with a duration of 10 min which resulted in mean triploidy yield of 72.5% at 9 months of age. Growth rate of the 2–9-month-old, cold shock group (0.1–6.2 g/month) did not differ from that of the control (0.1–5.7 g/month). Gonadal somatic indices (GSI) of presumed triploid males and females were lower than that of control (GSI values of the presumed triploids were 35.0–60.2% and 28.7–75.9% of control males and females, respectively). Spermatogenesis and oogenesis were retarded in triploids. However, all stages of spermatogenic cells were observed in triploid males, including few spermatozoa. Oocytes of triploid females did not undergo vitellogenesis while normal oogenesis was observed in diploids. Nuclear volume of red blood cells (RBCs) of triploid fish was 1.63 times larger than that of diploids.     

Evaluation of genetic diversity of eight grouper species <Emphasis Type="Italic">Epinephelus</Emphasis> spp. based on microsatellite variations

ABSTRACT:   Genetic diversity among eight species of grouper, Epinephelus bleekeri , E. coioides , E. malabaricus , E. ongus , E. akaara , E. maculatus , E. merra and E. fuscoguttatus , was studied using six microsatellite loci, Em-01 *, Em-03 *, Em-07 *, Em-08 *, Em-10 *, and CA-07 *, with the aim of exploring the feasibility of using microsatellite data for species identification. The results showed high levels of genetic differentiation among species ( F _ST  = 0.4403 and R _ST  = 0.4954). Species identification based on fixed allelic differences was possible between E. coioides , E. ongus , and E. fuscoguttatus at Em-01 * and between E. fuscoguttatus and E. ongus at Em-08 *. Private alleles were found in all species, except for E. ongus . Pairwise F _ST ranged 0.238–0.578 ( P  < 0.008 Bonferroni correction), and Nei's genetic distance ranged 0.433–2.710. Size homoplasy was observed at Em-03 * 157 allele, which was characterized by a T–C transition at the 119th nucleotide site of PCR products. The genetic assignment test unambiguously assigned each individual to the correct species. Thus, this test can be used for species identification of unknown individuals when the multilocus genotypes of the six microsatellite loci are available. The phylogenetic (neighbor-joining) tree, which was constructed based on the genetic distance matrix, separated the eight grouper species into two main groups.