RAPD fingerprinting of the ornamental fish Badis badis (Hamilton 1822) and Dario dario (Kullander and Britz 2002) (Perciformes, Badidae) from West Bengal, India (original) (raw)
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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.
Rendiconti lincei. Scienze fisiche e naturali, 2016
The knowledge of molecular genetics is a key to understand biodiversity, evolutionary relationship, conservation programs, and genetic structure of species of an ecosystem. To study genetic polymorphism in morphological variants of five species of Indus River carps, namely, Labeo gonius, Labeo rohita, Labeo calbasu, Catla catla, and Cirrhinus mrigala, random amplified polymorphic DNA (RAPD) analysis was used. Using eight primers, a total of 719 loci were amplified comprising of 389 polymorphic loci (53.7%) and 330 monomorphic loci (45.3%). The mean value of observed number of alleles (na), effective number of alleles (ne), Nei gene diversity (h), and Shannon's information index were 2, 1.65, 0.38, and 0.56, respectively. The mean value of Nei total gene diversity (Ht), gene diversity within the population (Hs), relative magnitude of differentiation among population (Gst), and gene flow (Nm) were 0.38, 0.26, 0.28, and 3.98, respectively. The mean value of Hs and Gst suggests moderate gene flow between these fish populations. This study revealed that C. catla is more close to L. gonius, L. rohita, and L. calbasu than C. mrigala. We have presented the first detailed study of genetic variation within and among five fish species of Indus River carps in Pakistan.
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 Applied Ichthyology, 2004
The level of genetic variation provides the raw material for selective improvement of a stock. Random amplified polymorphic DNA (RAPD) assay was used to assess the genetic variation in three rivers: the Halda, the Jamuna and the Padma as well as in one hatchery population of the commercially important Indian major carp, Labeo rohita. RAPD markers were amplified from DNA samples of 35 fish from each of the four populations using six decamer random primers. The polymorphic loci proportions were 0.33, 0.28, 0.28 and 0.26 and Nei's gene diversity values were 0.06, 0.07, 0.06 and 0.05 for the Halda, the Jamuna, the Padma and the hatchery populations, respectively. The pairwise population differentiation (FST) values indicated a low level of genetic differentiation between the population pairs. From the unweighted pair group method of arithmetic mean (UPGMA) dendrogram based on Nei's genetic distances a correlation between genetic affinities and geographical area was found. The populations were segregated into two groups: the Halda in one group and the Jamuna, the Padma and the hatchery in another group. Overall, the RAPD technique can be introduced as a tool in the population genetics of the rohu fish to provide information on their genetic stock structure.
Study of the Genetic Diversity of Ornamental fish Badis badis IJBD 2014
Dwarf chameleon fish or Badis badis, a lesser known ornamental freshwater fish, has recently been included in the Indian threatened category of fish list. There are insufficient studies with regard to the assessment of genetic background of this ichthyofauna, especially in the western sub-Himalayan region of West Bengal, India, popularly known as the Terai. The present study is the first attempt to investigate the present status of the genetic background of this species in the Mahananda and Balason rivers, major streams of this region. Twenty-one selective RAPD primers generated 53 and 60 polymorphic fragments in the Mahananda and Balason populations, respectively. The proportion of polymorphic loci, Nei's genetic diversity (H), and Shannon's index ( ) were 0.4416, 0.1654 ± 0.2023, and 0.2450 ± 0.2907, respectively, in Mahananda river population and were 0.5041, 0.1983 ± 0.2126, and 0.2901 ± 0.3037, respectively, in Balason river population. Inbreeding coefficient and degree of gene differentiation were also calculated. The H and were found to be 0.1601±0.1944 and 0.2363±0.2782, respectively, in overall Mahananda-Balason river system. Our study revealed considerable lack of genetic variation among the individuals of Badis badis. The genetic data obtained from the present study lend support to the view that there is a scope of stock improvement for this ichthyofauna.
DNA barcoding identified selected ornamental fishes in Murti river of East India
Mitochondrial DNA Part B
Nomenclature for the nameless is one of the successful events after the invention of the DNA barcoding technique in biodiversity research. The ornamental fish species are frequently hunted from the east and northeast India and trafficked with various elusive names and high demanding values. Such illegitimate trading stimulated the severe threats on the native freshwater ecosystems and their indigenous biodiversity. Both traditional taxonomy and DNA barcoding technique successfully identified 11 ornamental fish species from a small riverine system, Murti river; linked up with three protected areas in the northern part of West Bengal. To test the efficacy of DNA barcode data for species identification, the generated sequences were subjected to similarity search results, and Neighbour-Joining tree clustering and genetic divergences. The mean genetic divergence was 21.3% and the interspecific genetic distance was ranging from 17.8% to 28.7% in the studied dataset. The detected high intraspecific genetic divergence in Opsarius barna (14.1%) and Channa gachua (6.4%) in the present dataset suggested further genetic investigation from their known distributions.
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..
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.
International Journal of Biodiversity, 2014
Dwarf chameleon fish or Badis badis, a lesser known ornamental freshwater fish, has recently been included in the Indian threatened category of fish list. There are insufficient studies with regard to the assessment of genetic background of this ichthyofauna, especially in the western sub-Himalayan region of West Bengal, India, popularly known as the Terai. The present study is the first attempt to investigate the present status of the genetic background of this species in the Mahananda and Balason rivers, major streams of this region. Twenty-one selective RAPD primers generated 53 and 60 polymorphic fragments in the Mahananda and Balason populations, respectively. The proportion of polymorphic loci, Nei's genetic diversity (H), and Shannon's index ( ) were 0.4416, 0.1654 ± 0.2023, and 0.2450 ± 0.2907, respectively, in Mahananda river population and were 0.5041, 0.1983 ± 0.2126, and 0.2901 ± 0.3037, respectively, in Balason river population. Inbreeding coefficient and degree of gene differentiation were also calculated. The H and were found to be 0.1601±0.1944 and 0.2363±0.2782, respectively, in overall Mahananda-Balason river system. Our study revealed considerable lack of genetic variation among the individuals of Badis badis. The genetic data obtained from the present study lend support to the view that there is a scope of stock improvement for this ichthyofauna.