Genetic variation, population structure and identification of yellow catfish, Mystus nemurus (C&V) in Thailand using RAPD, ISSR and SCAR marker (original) (raw)
Related papers
Molecular Biology Reports, 2012
Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were used to investigate the genetic structure of four subpopulations of Mystus nemurus in Thailand. The 7 RAPD and 7 ISSR primers were selected. Of 83 total RAPD fragments, 80 (96.39%) were polymorphic loci, and of 81 total ISSR fragments, 75 (92.59%) were polymorphic loci. Genetic variation and genetic differentiation obtained from RAPD fragments or ISSR fragments showed similar results. Percentage of polymorphic loci (%P), observed number of alleles, effective number of alleles, Nei's gene diversity (H) and Shannon's information index revealed moderate to high level of genetic variations within each M. nemurus subpopulation and overall population. High levels of genetic differentiations were received from pairwise unbiased genetic distance (D) and coefficient of differentiation. Mantel test between D or gene flow and geographical distance showed a low to moderate correlation. Analysis of molecular variance indicated that variations among subpopulations were higher than those within subpopulations. The UPGMA dendrograms, based on RAPD and ISSR, showing the genetic relationship among subpopulations are grouped into three clusters; Songkhla (SK) subpopulation was separated from the other subpopulations. The candidate species-specific and subpopulation-specific RAPD fragments were sequenced and used to design sequencecharacterized amplified region primers which distinguished M. nemurus from other species and divided SK subpopulation from the other subpopulations. The markers used in this study should be useful for breeding programs and future aquacultural development of this species in Thailand.
Journal of Biosciences, 2001
Genetic similarity and diversity of cultured catfishSilurus asotus populations collected from two areas in western Korea were examined using randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR). Out of 20 random primers tested, 5 produced 1344 RAPD bands ranging from 8.2 to 13.6 polymorphic bands per primer. The polymorphic bands in these populations ranged from 56.4% to 59.6%. Polymorphic bands per lane within populations ranged from 4.9% to 5.3%. The similarity within the Kunsan population varied from 0.39 to 0.82 with a mean (± SD) of 0.56 ± 0.08. The level of bandsharing values was 0.59 ± 007 within the catfish population from Yesan. The genetic similarity in cultured catfish populations may have been caused because individuals from two populations were reared in the same environmental conditions or by inbreeding during several generations. However, in view of bandsharing values, polymorphic bands and also the specific major bands that were inter-population-specific, significant genetic differentiation between these populations were present even if bandsharing (BS) values were somewhat numerically different. Therefore, the number of RAPD polymorphisms identified in this study may be sufficient to permit estimating genetic similarity and diversity. However, in future, additional populations, sampling sites and individuals will be necessary to make up for these weak points.
This study was conducted to provide baseline information on the genetic population structure of Ompok bimaculatus, an endangered catfish of Bangladesh. Random amplified polymorphic DNA (RAPD) fingerprinting analysis was performed to assess the genetic variation in two wild (Chalan beel and Tola haor) and one hatchery (Brahmmaputra Fish Seed Complex-BFSC) populations of O. bimaculatus,. Five selected decamer random primers amplified a total of 34 RAPD bands among which 24 were found to be polymorphic. The percentage of polymorphic loci, intra-population similarity indices, gene diversity and Shannon's information indidex values were 64.71%, 77.57% , 0.249±0.216 and 0.365±0.303 for Chalan beel, 58.82%, 75.45%, 0.219±0.215 and 0.322±0.304 for Tola haor population and 52.94%, 86.49%, 0.214±0.219 and 0.311±0.312 for the hatchery, BFSC, respectively. The coefficient of population differentiation (PhiPT) between the Chalan beel-BFSC and Tola haor-BFSC pairs were found to be significant. The gene flow (Nm) between the population pairs ranged from 1.899 to 5.052. The highest inter-population similarity (Sij) was found between Chalan beel-BFSC populations. Among the three populations, the highest genetic distance (0.157) was found between Tola haor and the BFSC population. The results of the present study indicated a substantial level of genetic variation in the enangerd O. bimaculatus populations in Bangladesh and significant differentiation among the populations..
Int. J. Integ. Biol, 2009
The present study has focused on the genetic diversity between two feral populations of Aorichthys seenghala (Skyes) of Madhya Pradesh, India. Ten RAPD primers were primarily screened of which five primers gave polymorphism, were selected for the final RAPD analysis. Using these five primers, 659 scorable DNA fragments were found, of which 513 (77.85%) were polymorphic, 140 (21.24%) were monomorphic and 6 (0.91%) were unique. By comparing RAPD banding patterns, variations were found between and within the populations. The unweighted pair group method with averages (UPGMA) dendrogram showed two clusters, the Mohinisagar reservoir (Gwalior) population formed one cluster and the other cluster was represented by the population of Bhadwada reservoir (Bhopal). Although the morphological differences were negligible, using these techniques a little but significant difference was detected in genetic diversity among two populations of Ariochthys seenghala.
Journal of Aquaculture Research and Development, 2015
Mystus vittatus is a small indigenous fish species having higher nutritional value in terms of protein, micronutrients, vitamins and minerals. But the catfish aquaculture including Mystus sp has not been developed extensively for its aquaculture potential even though the demand of catfishes in the Indian domestic markets are very high. Therefore for good aquacultural practices and to maintain a healthy gene pool, detailed knowledge on the population structure of Mystus sp. is needed. In the present study molecular and morphological analysis of a population of Mystus vittatus caught from four different freshwater bodies of Assam about 100-400 km away from each other was done using RAPD markers. Total 412 RAPD fragments were generated using nine decamer primers of arbitrary nucleotide sequences. In the experiment 322 polymorphic bands and 90 monomorphic bands were produced which shows 78.15% of polymorphism and 21.84% of monomorphism. UPGMA dendrogram constructed on the basis of genet...
Journal of Advanced …, 2011
DNA fingerprinting has assumed an important role in aquaculture and fisheries management. Molecular genetic markers have been developed into powerful tools to analyze genetic diversity and relationships among different aquatic species. Besides the varied techniques using polymorphic DNA markers, Random Amplified Polymorphic DNA (RAPD) markers generated by Arbitrarily Primed Polymerase Chain Reaction (AP-PCR) have become ubiquitous and essential in aquaculture genetics. Single 9-20 base oligonucleotide primers with G+C contents ranging between 40-80% were randomly chosen for PCR to generate useful genomic fingerprints. DNA amplification products were resolved by denaturing polyacrylamide gel electrophoresis (dSDS-PAGE). Subsequent detection by silver staining could easily allow the visualization of fragments below 3.5 kb. The spectrum of amplified products varied with each primer-template combination but was consistent and reproducible under similar PCR conditions. The primers could detect polymorphisms in the absence of specific nucleotide sequence information of the fishes. Such DNA polymorphisms are especially useful for genotyping, taxonomic identification, population studies and genetic mapping. This approach is also applicable for assessing inbreeding levels and population structure within wild and cultivated fish and shrimp stocks. Here, we review the development, applications and advances of AP-PCR in elucidating DNA polymorphisms in tropical ornamental fishes. Genetic differences among species and strains, sexes, species-and phenotype-specific DNA polymorphisms, and applications of DNA marker-based approaches in fish breeding and management programmes are discussed.
RAPD Probe on Genetic Variation in Damselfishes (Family Pomacentridae) in Gulf of Mannar Region
Tamil Nadu (INDIA) -600 119 Information on the genetic structure of cultivable finfish and shellfish species is useful for the identification of real stocks, stock enhancement, breeding programs, management for sustainable yield and preservation of genetic diversity . Damsel fishes are the most required group in the ornamental fish trade. The family pomacentridae a member of the perciform is composed of four subfamilies of damsel fishes: Amphiprioninae, Chrominae, Lepidozginae, and Pomacentrinae . Based on gene sequence data, Tang [3] stated that the subfamily Pomacentrinae is polyphyletic and Neopomacentrus is a sister group to Pomacentrus. However, information on genetic relationships and diversities at the molecular level in Indian damsel fish species is not yet available. Random amplified polymorphic DNA (RAPD) analysis is a technique based on the polymerase chain reaction (PCR) amplification of discrete regions of genome with short oligonucleotide primers of arbitrary sequence . The method is simple and rapid for determining the genetic diversity and no prior knowledge of the genome under study is required . This technique has been used extensively to detect genetic diversity in plants , animals [8] and microbes [9] for a long period. RAPD analysis also has been used to evaluate genetic diversity in species and subspecies identification in guppy [10], tilapia , brown trout and Atlantic salmon [13], largemouth bass [14], Ictalurid catfishes and Indian major carps . But in Indian damsels, it has not been used so far. The Gulf of Mannar of India is one of the biodiversity hot spots with a good coral bed which support a variety of damsel fishes. The phylogenetic relationship and molecular identification of most Indian damsel fish is still untraced. The objectives of the present study is to evaluate the RAPD assay as a source of genetic markers to generate speciesspecific RAPD profiles these damsel fishes collected from Gulf of Mannar and estimate genetic variation among them.
International Journal of Fisheries and Aquatic Studies, 2015
In the present study molecular and morphological analysis of a population of Mystus cavasius caught from four different freshwater bodies of Assam, India about 100-400 km away from each other was done using RAPD markers. Total 578 RAPD fragments were generated using nine decamer primers of arbitrary nucleotide sequences. In the experiment 448 polymorphic bands and 130 monomorphic bands were produced which shows 77.50% of polymorphism and 22.49% of monomorphism. UPGMA dendrogram constructed on the basis of genetic distance formed four distinct clusters, indicating comparatively higher level of genetic variations in the studied M. cavasius populations in Assam. The genetic diversity data can be applied in the areas of research on evolution, conservation and management of cat fish resources and genetic improvement programmes. RAPD analysis for genetic diversity study provides a basis to obtain genetic variation within and among populations.