Unweighted Pair Group Method Of Arithmetic Means Research Articles

Genetic diversity of the bacterial wilt pathogen Ralstonia solanacearum using a RAPD marker

Bacterial wilt caused by Ralstonia solanacearum is a destructive disease of many economically important crop species. A significant variation in wilt incidence and severity in eggplant and potato was observed among the growing areas surveyed. R. solanacearum isolates obtained both from eggplant and potato belong to biovar III, while isolates from eggplant belong to race 1 and isolates obtained from potato belong to race 3. Random amplified polymorphic DNA (RAPD) technique was used as a tool for assessing genetic variation and relationship among seven isolate groups of R. solanacearum viz., RsB-1, RsB-2, RsB-3, RsP-1, RsP-2, RsP-3 and RsP-4, consisting in a total of 28 isolates. Out of the RAPD markers used, amplification with four decamer primers produced 70 bands with sizes ranging from 100 to 1400bp. Out of 70 bands, 68 bands (97.06%) were polymorphic and two bands (2.94%) were monomorphic amongst the seven R. solanacearum isolates group. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei's genetic distance produced two main clusters of the seven isolates of R. solanacearum. The isolates RsB-1, RsB-2, RsB-3 and R-4 grouped in cluster І, while RsP-2, RsP-3 and RsP-4 grouped in cluster ІІ. The highest intra-variety similarity index (Si) was found in RsB-1 isolate (86.35%) and the lowest one in RsP-2 (56.59%). The results indicated that relatively higher and lower levels of genetic variation were found in RsP-3 and RsB-3, respectively. The coefficient of gene differentiation (Gst) was 0.5487, reflecting the existence of a high level of genetic variations among seven isolates of R. solanacearum. Comparatively higher genetic distance (0.4293) and lower genetic identity (0.6510) were observed between RsB-2 and RsP-4 combinations. The lowest genetic distance (0.0357) and highest genetic identity (0.9650) were found in RsB-1 vs. RsB-2 pair. Thus, RAPD offers a potentially simple, rapid and reliable method to evaluate genetic diversity analysis in R. solanacearum.

Genetic Variability Assay of Different Natural and Hatchery Populations of Rohu (Labeo rohita) in Bangladesh

The level of genetic variation determines the genetic status and provides the raw material for selective improvement of a stock. Randomly amplified polymorphic DNA (RAPD) technique was used to assess the genetic variability of 7 different natural (2) and hatchery (5) populations of Indian Major Carp, Labeo rohita (Rohu) in Bangladsh. In total, 140 fish samples were collected (20 from each of the populations). Genomic DNA was extracted from the muscle tissue, and 5 different oligonucleotide primers were used which revealed 80% polymorphic DNA bands. The polymorphic loci proportions were 0.71, 0.75, 0.75, 0.85, 0.84, 0.86 and 0.89 for Ma-Fatema hatchery, Chowdhuri hatchery, Niribili hatchery, Sonali hatchery, Kapotakha hatchery, the Halda river and the Baluhor Baor populations respectively. The pair-wise population differentiation (FST) values indicated a high level of genetic variation between different populations. The Unweighted Pair Group Method of Arithmetic Mean (UPGMA) dendogram based on Nei’s genetic distances also revealed high level of inter-population genetic variation among the populations. The populations were segregated into two groups: the Halda River and Baluhar Baor hatchery in one group and Kapotakha, Ma-Fatema, Chowdhuri, Niribili and Sonali hatcheries in another group. Overall, RAPD results clearly indicate the reduced genetic quality of the hatchery seeds.DOI: http://dx.doi.org/10.3126/ijls.v9i1.11923 International Journal of Life Sciences Vol.9(1) 2015 30-36

Molecular Genetic Variations among Some Punjab Sheep Breeds Using RAPD Analysis

The present study was carried out on seven sheep breeds (Thalli, Lohi, Salt Range, Kajli, Sipli, Buchi and Hissradale) by Random Amplified Polymorphic DNA (RAPD) analysis using 21 random decamer primers. Blood samples were collected from different numbers of animals per breed, of both sexes. After DNA extraction PCR was carried out by using 25 µL reaction mixture containing 3 mM MgCl2, 100 µM each of dATP, dCTP, dGTP, dTTP, 0.2 µM primer, 15 ng of genomic DNA, and 5 unit of Taq polymerase, through programmable thermal cycler (Crea Con, TCY, USA).Out of 21 decamer primers 16 primers yielded easily scorable bright DNA bands while other five yielded smeared and nonspecific fragments. The genetic similarities of seven sheep breeds were high, ranging from 74.42% to 94.29 %. Thalli and Latti had greatest similarity (94.29%). The lowest genetic similarity was between Lohi and Hissardale (74.42%). The unweighted pair group method of arithmetic means (UPGMA) dendrogram obtained from the cluster analysis revealed two clusters. The study confirms that the molecular genetic techniques such as RAPD-PCR can economically and efficiently be used to establish genetic distances and similarities among and within breeds as well as to find out breed specific genetic markers. The seven sheep breeds in the study could be identified by using one breed specific RAPD marker or a combination of two or more markers. Primer GLB-08 can identify Lohi breed and primer GLA-14 can identify Hissardale. Primer GLA-19 can identify both Kajli and Sipli breeds simultaneously.

Genetic Variations and Cultivar Purity within the G. <i>hirsutum</i> Cultivars via RAPD Marker

To assess genetic variation within a cultivar, four commercial varieties with five individual G. hirsutum genotypes and their bulk were assayed with selected forty 10-mer RAPDs per cultivar via PCR. CIM-473 cultivar showed amplification of 321 bands in total per primer with an average of 8 bands. A range of similarity i.e.; 80% - 100% within the cultivar has been observed for minimum and maximum respectively. CIM-448 showed amplification of 300 bands in total per primer with an average of 7.5 bands. Maximum similarity of 95% and minimum similarity of 84% was observed within the cultivar. In CIM-1100 the total numbers of fragments amplified are 304, with the average of 7.6 bands per primer and are 12% - 20% polymorphic. Similarly, in NIAB-78 the total numbers of fragments amplified were 310, with the average of 7.7 bands per primer. The reliability of RAPD technique for finding genetic resemblances is indicated by the mentioned results. Numerous groups within 5 individual genotypes bulk among 4 cultivars of G. hirsutum L. have been through cluster analysis which was by the unweighted pair group method of arithmetic means (UPGMA). Dendrograms have been used for showing cultivar relationship.

Molecular Diversity Analysis in Potato (Solanum tuberosum L.) through RAPD Markers

Random Amplified Polymorphic DNA (RAPD) markers were used to study the molecular diversity of 12 popular potato varieties in Bangladesh. DNA was extracted from tender leaf sample for PCR amplification. The PCR amplified DNA profile was visualized on 2% agarose gel, staining with ethidium bromide. Eight RAPD primers were used to evaluate the genetic diversity of potato varieties. Some total of 36 DNA fragments were amplified and out of them 24 were polymorphic. Those primers generated 61.53% of polymorphic DNA band. The primer OPX 04 produced highest (9) number of DNA band and out of 9 amplicon 6 were polymorphic. Lowest number of amplification was observed in the primer OPA-17 and it was only 3. The highest Nei’s genetic distance (0.9701) was noticed between the variety Granola and Provinto. The highest (0.8205) number of genetic identity/similarity was observed between the varieties Cardinal and Diamant. The unweighted pair group method of arithmetic mean (UPGMA) dendrogram based on Nei’s genetic distance revealed that the 12 varieties followed into two main clusters. The present finding showed that there was high level of genetic diversity among the varieties which can be used for parental selection in potato breeding program. DOI: http://dx.doi.org/10.3329/sja.v11i2.18405 SAARC J. Agri., 11(2): 95-102 (2013)

Assessment of genetic diversity of brinjal (Solanum melongenaL.) germplasm by RAPD markers

Assessment of genetic diversity in a crop species is prerequisite to its improvement. The use of germplasm with distinct DNA profiles helps to generate genetically diversified breeding populations. The present study was carried out to investigate the genetic diversity in brinjal or eggplant (Solanum melongena L.) using random amplified polymorphic DNA (RAPD). Fifteen brinjal germplasm and three decamer primers were used for random polymorphic DNA assay. A total of 17 fragments were obtained, out of which 12 (70.59%) were polymorphic. Each primer generated 4 to 8 amplified fragments with an average of 5.67 fragments per primer. The highest genetic distance (0.8873) and the lowest genetic identity (0.4118) were observed in Laffa (Elongated) versus Jessore L and Dharola combinations. The lowest genetic distance (0.1525) was observed in several cultivars. The unweighted pair-group method of arithmetic means (UPGMA) dendrogram was constructed from genetic distance and all brinjal cultivars were grouped into five clusters. The genetic diversity of brinjal cultivars reported in this study will be useful when planning future crosses amongst these cultivars.

Assessment of Genetic Variability of Prawn (<i>Macrobrachium rosenbergii</i>) Post Larvae (PL) from the Broods Stocked under Different Sex Ratios

The giant freshwater prawn ( Macrobrachium rosenbergii ) culture in Bangladesh is now at stake due to slower growth performance. The aim of the present study was to assay the impact of sex ratio on the genetic variability of larvae produced from the broods stocked under different sex ratios by analyzing Randomly Amplified Polymorphic DNA (RAPD) of M. rosenbergii . Broods were stocked under 3 different sex ratios viz., 1♂: 1♀, 1♂: 2♀ and 2♂: 1♀. A control population was also kept that involved the larvae production from the broods of natural source. The RAPD analysis generated 88 distinct bands of which 36 (41%) bands were polymorphic. The percentages of polymorphic loci were found to be 32%, 48%, 24% and 52% for the sex ratios 1♂: 2♀, 1♂: 1♀, 2♂: 1♀ and Control respectively. The pair wise genetic distances were 0.010, 0.007, 0.021, 0.016, 0.026 and 0.008 for 1♂: 1♀ vs. 1♂: 2♀, 1♂: 1♀ vs. Control, 1♂: 1♀ vs. 2♂: 1♀, 1♂: 2♀ vs. Control, 2♂: 1♀ vs. Control and 1♂: 2♀ vs. 2♂: 1♀ respectively. Overall gene diversity for all loci was 0.10. The unweighted pair group method of arithmetic mean (UPGMA) dendrogram based on Nei’s genetic distances clearly showed the severance of four different experimental groups into two clusters: 1♂: 1♀ and control in one and 1♂: 2♀ and 2♂: 1♀ in the other cluster. Results of the present study revealed that 1♂: 1♀ sex ratio is appropriate to establish the brood banks and for maintaining genetic variation in the offspring.

Genetic Determination of Potential Trichoderma Species Using ISSR (Microsatellite) Marker in Uttar Pradesh, India

Seven Trichoderma sp. were collected from different locations of Uttar Pradesh, India for evaluating their bioefficiency by determining their genetic variations. PCR-based Inter Simple Sequence Regions (ISSR) Marker employing 6 primers produced 30 scorable bands out of which 27 bands were polymorphic. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei’s [14] genetic distance produced 2 main clusters (1 isolates in cluster 1 and 6 isolates in cluster 2). The result indicating their genetic diversity has opened new possibility of using the most efficient and more isolates of Trichoderma in the preparation of effective biopesticide.

Analyzed the Toxicity of Ganaxolide on <i>Phanerochaete chrysosporium</i> by AFLP

Galaxolide (1,3,4,6,7,8-hexahydro-4,6,6,7,8,8-hexamethyl-cyclopenta-γ-2- benzopyran, HHCB) is recognized as a novel contaminant in water and has potential adverse impacts on aquatic organisms. The toxic effect of HHCB on Phanerochaete chrysosporium was investigated by exposure of the fungus in nitrogen-limited culture medium to various concentrations of HHCB. DNA damage of P. chrysosporium by HHCB was detected. Comparing with that in the control, the percent polymorphism under different concentrations of HHCB increased, from 21.4% to 42.9%. In addition, the result of UPGMA (un-weighted pair group method of arithmetic means) dendrogram showed that the Simple Matching Coefficient (SM) was decreased with an increase in the concentrations of HHCB. Thus, as an environmental pollutant, HHCB has the toxic effect on P. chrysosporium at molecular level.

Analyzed the Toxicity of Dyes on <i>Phanerochaete chrysosporium</i> by AFLP

In this paper, the toxic effect of the dye wastewater onPhanerochaete chrysosporiumwas investigated. The DNA damage of the dye onP. chrysosporiumwas analyzed using the AFLP method. Comparing with that in the control, the percent polymorphism under different concentrations of the dye increased, from 17.54% to 53.49%. In addition, the result of UPGMA (un-weighted pair group method of arithmetic means) dendrogram showed that the Simple Matching Coefficient (SM) was decreased with an increase in the concentrations of dyes. Results suggested that the dyes have toxic effect onP. chrysosporiumat molecular level as environmental pollutants.

DIFFERENTIATION AMONG FLAX CULTIVARS BY RAPD ANALYSIS AND SUSCEPTIBILITY TO SOME PATHOGENIC FUNGI

Random amplified polymorphic DNA (RAPD) analysis was used to evaluate the genetic diversity of 10 flax cultivars. Flax cultivars showed varying levels of susceptibility to a set of pathogenic fungi. The tested cultivars were analyzed with four random decamer primers using the polymerase chain reaction (PCR). All the primers detected varying levels of polymorphism in all the tested cultivars. Cluster analysis by the unweighted pair-group method of arithmetic means (UPGMA) placed cultivars in several groups based on their RAPD-PCR banding patterns with overall similarity levels ranged from 4.05 to 94.72%. UPGMA also placed studied cultivars in several groups based on the patterns of susceptibility to a set of pathogenic fungi. The present study demonstrated that flax cultivars could be identified by their RAPD-PCR banding patterns, combined with their patterns of susceptibility to a set of pathogenic fungi. These results could be practical value for cultivar identification or for seed purity tests.

Molecular Diversity Analysis of Lentil (Lens culinaris Medik.) through RAPD Markers

Random Amplified Polymorphic DNA (RAPD) markers were used to study the molecular genetic diversity analysis among six BARI released lentil varieties viz. BARI masur-1, BARI masur-2, BARI masur-3, BARI masur-4, BARI masur-5 and BARI masur-6. PCR amplified products were visualized on 1.0% agarose gel and the band for each primer were scored. Ten RAPD markers were used in this study. Out of them 7 primers showed amplification of 53 DNA fragments with 60.37% of them being polymorphic. The highest number of polymorphic loci was noticed in the variety BARI masur-3. The same variety also showed maximum Nei’s gene diversity value (0.0552). The highest Nei’s genetic distance (0.5002) was observed in BARI masur-1 vs. BARI masur-5 whereas, the lowest genetic distance (0.0692) was found in BARI masur-1 vs. BARI masur-2. The unweighted pair group method of arithmetic mean (UPGMA) dendrogram based on Nei’s genetic distance grouped the six cultivars into two main clusters. BARI masur-1, BARI masur-2 and BARI masur-3 were in cluster I and BARI masur-4, BARI masur-5 and BARI masur-6 were in cluster II. The cultivar BARI masur-4 was closest to the cultivar BARI masur-6 with the lowest genetic distance (0.0972) and the highest genetic distance (0.5002) was found between BARI masur-1 and BARI masur-5. The RAPD markers were found to be useful in molecular characterization of lentil varieties which could be utilized by the breeders for the improvement of lentil cultivars. DOI: http://dx.doi.org/10.3329/ptcb.v22i1.11260 Plant Tissue Cult. & Biotech. 22(1): 51-58, 2012 (June)

Rapd Analysis of Trichoderma Isolates for Superior Selection for Biopesticide Preparation

Thirty five isolates of Trichoderma species collected from seven different locations of Bangladesh were studied for morphological characters and molecular variation. Mycelial diameters of the isolates varied from 8.28 cm to 9.00 cm. Based on colony colour, isolates were grouped into five such as dark green, green, light green, yellowish green and whitish green. Maximum isolates were green and light green. On the basis of growth habit and colony consistency, the isolates were categorized into three groups, in which most species had fast growth and were compact in appearance. PCR-based Random Amplified Polymorphic DNA (RAPD) technique employing 3 decamer primers produced 36 scorable bands of which all (100%) were polymorphic. The co-efficient of gene differentiation (Gst) was 1.0000 reflecting the existence of high level of genetic diversity among the isolates. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei's (1972) genetic distance produced 2 main clusters (13 isolates in cluster 1 and 22 isolates in cluster 2). The result indicating their genetic diversity has opened new possibility of using the most efficient and more isolates of Trichoderma in the preparation of biopesticide and decomposition of municipality waste.

Molecular Characterization of 12 Mango Germplasm Using RAPD markers

Randomly amplified polymorphic DNA (RAPD) markers were used for the genetic variation and relationship analysis among 12 Mango (Mangifera indica L.) germplasm. Five oligonucleotide primers were employed to amplify DNA from 12 cultivars. PCR amplification with five primers generated 45 reproducible, clear and distinct bands, out of which 41 bands are considered polymorphic and the remaining four fragments (8.88%) monomorphic. The size of amplified product ranged from 200 (RPI-5) to 3000 base pairs (RPI-1) with an average of nine bands per primer. The average polymorphism in all the 12 cultivars using the five primers was found to be 91.91%. Among all the primers RPI-2 and RPI-4 have shown 100% polymorphism while RPI-5 was found to be least polymorphism (81.81%). One specific band, namely was found with RPI-5, in a particular variety, Chiratpuri. The UPGMA (Unweighted Pair Group Method of Arithmetic Mean) dendrogram based on Jaccard’s similarity coefficient segregated the 12 mango germplasm into two clusters. Langra, Chiratpuri, Pravasankar, Alphanso, Sindhu and Kesar formed one cluster and rest six mango germplasm grouped together into another cluster. Sindhu and Alphanso cultivar pair was very close to each other with highest similarity coefficient (0.78), which was comparatively higher than all other cultivar pairs. On the other hand, Pravasankar and Neelam cultivar pair was more distinct to each other with the lowest intervarietal similarity coefficient 0.38. This study showed clearly that cultivars from Orissa unveiled maximum diversity and indicated the potential of RAPD markers for the identification of management of mango germplasm for breeding purposes. Key words: Molecular characterization, Mango germplasm, Dversity D.O.I. 10.3329/ptcb.v20i1.5972 Plant Tissue Cult. & Biotech. 20(1): 91-99, 2010 (June)

Genetic diversity analysis of the species of Gossypium by using RAPD markers

Random Amplified Polymorphic DNAs (RAPDs), a DNA polymorphism assay based on the amplification of random DNA segments with single primers of arbitrary nucleotide sequence, was utilized to measure the genetic distance among the species of Gossypium . Variations among 20 different species of Gossypium were analyzed with 63 random 10-mer primers using the polymerase chain reaction (PCR). Out of a total of 370 RAPD bands generated from the 20 wild species, 310 were perceived polymorphic. The study detected a high level of genomic variability of the species of Gossypium . The maximum similarity of 64% was observed between Gossypium arboreum and Gossypium herbaceum and minimum similarity of 3% was observed between Gossypium stocksii and Gossypium longicalyx . Cluster analysis by the unweighted pair group method of arithmetic means (UPGMA) showed that 20 wild species can be divided into several groups, although it is believed that Gossypium is a very widely distributed, wild species having being discovered in all the continents of the world which extends into the subtropical region. The relationship among the species is presented in the dendrogram.

Developing EST-Derived Microsatellites in Sesame ( Sesamum indicum L.)

To accelerate the application of molecular markers in sesame ( Sesamum indicum L.), expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed using publicly available sesame EST data. A total of 1785 nonredundant EST sets were assembled among the 3328 identified sesame ESTs. One hundred and forty-eight microsatellite sequences containing 155 EST-SSRs were detected from these ESTs. The total length of the nonredundant EST sequences was 774.27 kb with an average of 4.99 kb. Among these EST-SSRs, dinucleotide AG/TC was the most abundant (occurring 58 times) with a frequency of 37.42%. Based on these EST sequences containing SSRs, 50 primer pairs were designed and tested with 36 sesame accessions, 2 cotton ( Gossypium barbadense L. and G. hirsutum L.) accessions, 2 soybean ( Glycine max Merr.) accessions, and 2 oil sunflower accessions ( Helianthus annuus L.) to detect their polymorphism and transferability. A few SSRs were able to be transferred to PCR markers, including 2 for cotton, to PCR markers, including 2 for cotton, 3for soybean, and 4 for oil sunflower. Using 44 EST-SSRs, 108 loci were successfully amplified in sesame with an average of 2.45 loci per primer pair. Twenty-seven out of the 44 primer pairs, 27 (61.4%) were polymorphic in the 36 sesame accessions. Their average polymorphism information content (PIC) was 0.390, ranging from 0.105 to 0.844. In the Unweighted Pair Group Method of Arithmetic Mean (UPGMA) dendrogram based on genetic similarity coefficient from 91 polymorphic loci, 36 accessions were classified into 4 groups. No geographic distribution was observed in these accessions. The EST-SSRs developed from sesame are valuable for genetic analysis, linkage mapping, and transferability study among oil plants.

Molecular Characterization of Mulberry Accessions in Turkey by AFLP Markers

Mulberries (Morus L.) show a great deal of genetic variability and adaptability to various environments. There are more than 24 species of mulberries in cultivated and wild forms. In Turkey, three Morus species, M. alba L., M. nigra L., and M. rubra L., are grown. In this study, we attempted to characterize 43 Morus accessions originating from distinct regions of Turkey using fluorescent dye amplified fragment length polymorphism (AFLP) markers and capillary electrophoresis. The accessions belonged to M. alba, M. nigra, and M. rubra; M. alba consisted of white- and purple-fruited samples. Eight primer combinations generated a total of 416 bands, 337 of which were polymorphic (80.5%). Resolving powers of the AFLP primers ranged from 0.410 to 0.942 making a total of 5.015, whereas the polymorphic information content ranged from 0.662 to 0.898 with an average of 0.812. Unweighted pair-group method of arithmetic mean (UPGMA) clustering of the accessions showed three major groups representing M. nigra, M. rubra, and M. alba accessions. The M. alba group had two subgroups that were not correlated with fruit color. The UPGMA dendrogram of average taxonomic differences confirmed these results. The principle coordinate analysis demonstrated that M. nigra accessions had limited genetic variation. In conclusion, our study indicated that M. nigra and M. rubra are molecularly distinct from M. alba. Our results also suggest that M. nigra accessions having a low level of morphological variation are molecularly similar.

Diversity of Macrophomina phaseolina from cotton in Egypt: Analysis of pathogenicity, chlorate phenotypes, and molecular characterization

Pathogenicity of 21 isolates of Macrophomina phaseolina was tested on three cotton cultivars under greenhouse conditions. Analysis of variance (ANOVA) showed that the main effects of both isolates (P= 0.000) and cultivars (P= 0.000) were very highly significant sources of variation in postemergence dampingoff and survival. Isolate x cultivar interaction was also a significant source of variation in postemergence damping-off (P= 0.03) and survival (P= 0.04). Statistically significant isolate, cultivar, and isolate x cultivar interaction suggest that physiologic specialization exists within M. phaseolina isolates pathogenic on cotton. It also implies that the resistance of the tested cultivars is a mixture of both vertical and horizontal resistance and there are significant differences among cultivars in both types of resistance. Cluster analysis of the isolates, based on their virulence patterns on different cultivars, differentiated the isolates reasonably well and grouped them into three pathotypes. The isolates were distinguished phenotypically by using a defined medium containing 120 mM potassium chlorate. Chlorate-resistant isolates (33.3%) grew densely on chlorate medium, while the remaining isolates (66.7%) were chlorate sensitive and showed either a restricted (23.8%) or feathery (42.9%) growth. No associations were observed between grouping the isolates based on their virulence patterns and their chlorate phenotypes. Random amplified polymorphic DNA (RAPD) analysis was used to evaluate the genetic diversity of the isolates. In this analysis, polymerase chain reaction was performed by using four random decamer primers. All the primers detected polymorphisms in all the tested isolates. Cluster analysis by the unweighted pairgroup method of arithmetic mean (UPGMA) placed the isolates in three distinct groups. Grouping the isolates based on cluster analysis of their virulence patterns did not match that based on cluster analysis of their RAPD profiles while, grouping the isolates based on cluster analysis of their RAPD profile exhibited clear correlation with their chlorate phenotypes.

Relationship among acidophilic bacteria from diverse environments as determined by randomly amplified polymorphic DNA analysis (RAPD)

Random amplification of polymorphic DNA (RAPD), a PCR-based technique was applied to evaluate genomic diversity among three strains of Acidithiobacillus thiooxidans, five strains of Acidithiobacillus ferrooxidans and one acidophilic moderate thermophile strain, using 45 random primers of five different series. More than 2200 bands were observed, with an average of 45 bands per primer. Primer OPC-3 produced the maximum number of fragments whereas minimum numbers of fragments were produced with primer OPA-5. A dendrogram was generated using cluster analysis by the unweighted pair group method of arithmetic means (UPGMA). The dendrogram showed three groups with similarity ranging from 29 to 85%. The maximum similarity (85%) was observed between the strains T.t1 and T.t2 of Acidithiobacillus thiooxidans.

Randomly amplified polymorphic DNA analysis of four different populations of the Indian major carp, Labeo rohita (Hamilton)

Summary 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.