Genotypic diversity in a localized population of Ralstonia solanacearum as revealed by random amplified polymorphic DNA markers

AIMS

To assess genotypic diversity within Ralstonia solanacearum isolates of a single field.

METHODS AND RESULTS

A total of 44 field isolates and 22 in vitro generated clones of R. solanacearum were studied for genotypic diversity by random amplified polymorphic DNA (RAPD) technique. Genomic DNA of these isolates and clones was extracted by proteinase-K-SDS lysis mini-prep method. RAPD analysis was done with 30 decamer primers. The data were analysed using NTSYSpc 2.02h software. Forty-two out of 44 field isolates and all the clonal isolates were identified as distinct genotypes at 70% similarity level.

CONCLUSION

Very high level of genome variability was observed within the field and clonal isolates of R. solanacearum. This might be a reason for the wide host range of this bacterium and for quick breakdown of wilt resistance in host plants.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results suggest that it would be difficult to design specific diagnostic protocol for R. solanacearum even for a localized population and to breed cultivars with broad-spectrum resistance.

Nuclear and chloroplast DNA reassessment of the origin of Indian potato varieties and its implications for the origin of the early European potato

The modern cultivated potato was first recorded in Europe in 1562, but its area(s) of exportation has long been in dispute. Two competing hypotheses have proposed an "Andean" area (somewhere from upland Venezuela to northern Argentina) or a lowland south central "Chilean" area. Potato landraces from these two areas can be distinguished, although sometimes with difficulty, by (1) cytoplasmic sterility factors, (2) morphological traits, (3) daylength adaptation, (4) microsatellite markers, and (5) co-evolved chloroplast (cp) and mitochondria (mt) DNA. The Chilean introduction hypothesis originally was proposed because of similarities among Chilean landraces and modern "European" cultivars with respect to traits 2 and 3. Alternatively, the Andean introduction hypothesis suggests that (1) traits 2 and 3 of European potato evolved rapidly, in parallel, from Andean landraces to a Chilean type through selection following import to Europe, and (2) the worldwide late blight epidemics beginning in 1845 in the United Kingdom displaced most existing European cultivars and the potato was subsequently improved by importations of Chilean landraces. We reassess these two competing hypotheses with nuclear microsatellite and cpDNA analyses of (1) 32 Indian cultivars, some of which are thought to preserve putatively remnant populations of Andean landraces, (2) 12 Andean landraces, and (3) five Chilean landraces. Our microsatellite results cluster all Indian cultivars, including putatively remnant Andean landrace populations, with the Chilean landraces, and none with the "old Andigenum" landraces. Some of these Indian landraces, however, lack the cpDNA typical of Chilean landraces and advanced cultivars, indicating they likely are hybrids of Andean landraces with Chilean clones or more advanced cultivars. These results lead us to reexamine the hypothesis that early introductions of potato to Europe were solely from the Andes.

Small but mighty RNA-mediated interference in plants

RNA silencing is a conserved phenomenon of regulation of gene expression by small RNAs derived from cleavage of double-stranded RNA (dsRNA). The present review deals with three overlapping modes of small RNA-mediated silencing particularly in plants. In case of post-transcriptional gene silencing (PTGS), Dicer, an endonuclease, cleaves dsRNA to produce approximately 21nt-long small interfering RNAs (siRNAs), which guide RISC, another nuclease complex, to destroy specific target mRNAs based on sequence complementarity with the siRNA. Another class of siRNAs of 25nt-long is also produced from dsRNA by Dicer, different from that generates 21nt-long siRNA. These longer siRNAs are probably involved in systemic silencing during PTGS and guide methylation of both DNA and histone, and induce heterochromatinization and consequent transcriptional repression of the targeted gene. Both siRNA-mediated PTGS and epigenetic modification of the genome are considered as defense mechanisms to protect against invading viruses, transposons or aberrantly expressing transgenes. Regulation of expression of endogenous genes is mediated by another class of 21nt-long small RNAs called microRNAs (miRNA). Genes encoding the miRNAs are present either in the intergenic regions, introns or coding regions of the plant genome. Cleavage of a stem-loop precursor transcript called pre-miRNA, by another class of Dicer generates miRNAs, which in association with nuclease complex similar to RISC, if not identical, either degrade target mRNA or cause translational repression. The applications of RNA silencing in functional genomics and crop improvement are discussed.

Characterization of genetic diversity of some serovars of Bacillus thuringiensis by RAPD

RAPD based fingerprinting of 21 serovars of Bacillus thuringiensis (Bt) representing different serotypes was performed using 19 random decamer primers. A total of 172 polymorphic fragments, ranging in size from 161-2789 bp, were amplified from 13 of the 19 primers. Pairwise genetic similarity analysis revealed very low similarity values, ranging from 3-68%, among the serovars of Bt, indicating high genetic divergence. Nineteen serovars of Bt fell in two major clusters and remaining two formed solitary clusters in the dendogram. Clustering of Bt strains established genetic relatedness between serovars and serotypes. It has been suggested that RAPD analysis can be used for genotypic characterization of Bt to complement flagellar serotyping.

Online identification of viruses

A computerized animal virus information system is developed in the Sequence Retrieval System (SRS) format. This database is available on the Word Wide Web (WWW) at the site http://bioinfo.ernet.in/www/avis/avis++ +.html. The database has been used to generate large number of identification matrices for each family. The software is developed in C. Unix shell scripts and Hypertext Marked-up Language (HTML) to assign the family to an unknown virus deterministically and to identify the virus probabilistically. It has been shown that such web based virus identification approach provides results with high confidence in those cases where identification matrix uses large number of independent characters. Protein sequence data for animal viruses have been analyzed and oligopeptides specific to each virus family and also specific to each virus species are identified for several viruses. These peptides thus could be used to identify the virus and to assign the virus family with high confidence showing the usefulness of sequence data in virus identification.

Computer-aided virus identification on the World Wide Web

An attempt has been made to devise computer software that will aid virologists to identify unknown virus isolates using the World Wide Web. Computerized information from the Animal Virus Information System was used to obtain data on various characters of a virus species. Sequence data banks are used to obtain the molecular data. A probabilistic method of virus identification based on Willcox's implementation of Bayes' theorem is implemented. The program provides hints to the users to carry out additional tests required to obtain higher confidence in identification of virus species. Signature peptides of the virus can also be used to confirm identification. The software is implemented on a UNIX machine and is written in C, UNIX shell scripts and HTML to run on the World Wide Web. This is the first species identification software that allows the user to carry out identification online through Internet.

Respiratory responses and blood sugar level of the crab, Barytelphusa cunicularis (Westwood), exposed to mercury, copper and zinc

Barytelphusa cunicularis (Westwood), a freshwater crab was exposed to mercuric chloride, copper sulphate and zinc sulphate from 0 to 12 hr and the oxygen consumption of the animal was measured in order to study the stress caused by these heavy metals. Normal oxygen consumption was affected by the three heavy metals. Similarly, crabs exposed to sublethal concentrations of the same pollutants for 24, 48, 72 and 96 hr showed an elevation in the blood sugar level with a maximum increase at 48 hr. The results indicate a switch towards glycolysis in order to overcome the anaerobic stress caused by the heavy metals.

Susceptibility studies on Culex tritaeniorhynchus Giles, 1901, to insecticides in the state of Goa

Tests conducted on the adults of C. tritaeniorhynchus in Goa during 1988-89 against organochlorine, organophosphate and carbamate insecticides showed that the LC50 values against DDT and dieldrin after 1 h of exposure were 2.2 and 1.2 per cent respectively. The LT50 values against malathion (5%), fenitrothion (1%) and propoxur (0.1%) were 19, 22 and 35 min respectively. Thus, taking into consideration the base-line data available for C. quinquefasciatus, the species can be considered susceptible to dieldrin, malathion, fenitrothion and propoxur. However, the results with DDT were equivocal and require verification.

Isolation of Japanese encephalitis virus from Culex pseudovishnui Colless, 1957 (Diptera: Culicidae) in Goa

A strain of Japanese encephalitis virus was isolated from a pool of 54 female C. pseudovishnui Colless, 1957. The mosquitoes were collected in August 1988 during the period of epidemic of JE. This is the first report of isolation of JE virus from mosquitoes in Goa in the western coastal belt of peninsular India. In view of this isolation, C. pseudovishnui acquires greater importance, even though its density and relative prevalence during the current study was found to be far lower than C. tritaeniorhynchus.

Breeding habitats of mosquitoes in Goa

Studies carried out in Goa from 1986 to 1987 revealed immature stages of 43 species of mosquitoes. Breeding habitats were divided into three categories, viz., (i) Ground water habitats consisting of ground pools and tanks, rocky pools, paddy fields and stream beds, yielding 30 species; (ii) Plant habitats consisting of tree holes and fallen coconut shells and leaf sheaths yielding 20 species; and (iii) Domestic/peridomestic habitats consisting of cement tanks, glass, earthen, metallic containers and tyres yielding 11 species. Five species viz., Anopheles subpictus, Aedes albopictus, Armigeres subalbatus, Culex quinquefasciatus and Cx. pallidothorax were found in all three types of habitats. Cx. tritaeniorhynchus preferred to breed in ground pools and paddy fields but was found in domestic cement tanks and ground tanks in adverse season. Majority of the anophelines and culicines were found in ground water habitats. Five out of 11 species of Aedes were found in tree holes. Aedes aegypti and Toxorhynchites splendens were found only in discarded tyres. Three species of the genus Uranotaenia, viz., U. bicolor, U. stricklandi and U. campestris were recorded from stream beds and plant containers.