Complex relationship between DNA methylation and gene expression due to Lr28 in wheat-leaf rust pathosystem.

Differential DNA methylation due to Lr28 was examined in susceptible (S) wheat cv. HD2329 and its resistant (R) near isogenic line (NIL) (HD2329+Lr28) using two approaches: methylation sensitive amplified polymorphism (MSAP) and methylated DNA immunoprecipitation (MeDIP). S/R lines each had a large number of hypomethylated genes and relatively fewer hypermethylated genes at 96 hai (hours after inoculation) relative to 0 hbi (hours before inoculation), suggesting activation of many genes during the passage of time (96 hai), although identity of genes may differ in S and R lines. When R NIL was compared with S cultivar, there were many hypermethylated and fewer hypomethylated genes in R NIL relative to S cultivar, suggesting that many genes that are active in S cultivar are silenced in R NIL, both at 0 hbi and at 96 hai. Level of methylation was generally abundant in intergenic regions followed by that in promoters, transcription termination sites (TTSs) and exons/introns. Hypermethylation in promoter and gene body regions was not always associated with inhibition of gene expression and vice-versa, indicating that more than one regulatory mechanisms may control the expression of genes due to pathogen attack in presence and absence of Lr28. MSAP analysis also showed abundance of mCG methylation in S cultivar and that of mCCG methylation in R NIL (at 96 hai), suggesting differences in methylation context in NILs with and without Lr28. The results of the present study improved our understanding of the epigenetic control of leaf rust resistance in wheat.

No yield penalty under favorable conditions paving the way for successful adoption of flood tolerant rice.

Flooding is one of the major constraints for rice production in rainfed lowlands, especially in years and areas of high rainfall. Incorporating the Sub1 (Submergence1) gene into high yielding popular varieties has proven to be the most feasible approach to sustain rice production in submergence-prone areas. Introgression of this QTL into popular varieties has resulted in considerable improvement in yield after flooding. However, its impact under non-flooded conditions or years have not been thoroughly evaluated which is important for the farmers to accept and adopt any new version of their popular varieties. The present study was carried out to evaluate the effect of Sub1 on grain yield of rice in different genetic backgrounds, under non-submergence conditions, over years and locations. The study was carried out using head to head trials in farmer's fields, which enable the farmers to more accurately compare the performance of Sub1 varieties with their recurrent parents under own management. The data generated from different head to head trials revealed that the grain yield of Sub1 varieties was either statistically similar or higher than their non-Sub1 counterparts under non-submergence conditions. Thus, Sub1 rice varieties show no instance of yield penalty of the introgressed gene.

Identification and molecular characterization of begomovirus and associated satellite DNA molecules infecting Cyamopsis tetragonoloba.

Monopartite begomoviruses comprise DNA-A as the main genome and associated satellite DNAs. Viral DNA extracted from guar (Cyamopsis tetragonoloba) showing leaf curl symptoms exhibited positive amplification of coat protein (CP) gene of DNA-A component, suggesting the presence of begomovirus. Full length DNA-A was amplified by primer pair re-designed from CP gene nucleotide sequence. The associated alphasatellite and betasatellite DNA molecules were amplified and sequenced, confirming the presence of monopartite begomovirus. Sequence comparisons showed 89% identity with other begomoviruses. The Neighbor-Joining tree based on full length DNA-A nucleotide sequence showed that the guar infecting begomovirus clustered separately from other known begomoviruses. The betasatellite shared a high (96%) nucleotide identity to Cotton leaf curl Multan betasatellites. The alphasatellite showed 91% nucleotide identity to alphasatellite associated with begomovirus infecting Okra. Recombination analyses showed three recombinant fragments in DNA-A, two in betasatellite, and four in alphasatellite. The results suggest that the begomovirus identified in this study was a new recombinant virus. Its name was proposed as Cyamopsis tetragonoloba leaf curl virus (CyTLCuV).

AFLP-based genetic diversity and its comparison with diversity based on SSR, SAMPL, and phenotypic traits in bread wheat.

Data on AFLP (eight primer pairs) and 14 phenotypic traits, collected on 55 elite and exotic bread wheat genotypes, were utilized for estimations of genetic diversity. We earlier used these 55 genotypes for a similar study using SSRs and SAMPL. As many as 615 scorable AFLP bands visualized included 287 (46.6%) polymorphic bands. The phenotypic traits included yield and its component traits, as well as physiomorphological traits like flag leaf area. Dendrograms were prepared using cluster analysis based on Jaccard's similarity coefficients in case of AFLP and on squared Euclidean distances in case of phenotypic traits. PCA was conducted using AFLP data and a PCA plot was prepared, which was compared with clustering patterns in two dendrograms, one each for AFLP and phenotypic traits. The results were also compared with published results that included studies conducted elsewhere using entirely different wheat germplasm and our own SSR and SAMPL studies based on the same 55 genotypes used in the present study. It was shown that molecular markers are superior to phenotypic traits and that AFLP and SAMPL are superior to other molecular markers for estimation of genetic diversity. On the basis of AFLP analysis and keeping in view the yield performance and stability, a pair of genotypes (E3876 and E677) was recommended for hybridization in order to develop superior cultivars.

Use of SAMPL for a study of DNA polymorphism, genetic diversity and possible gene tagging in bread wheat.

Selective Amplification of Microsatellite Polymorphic Loci (SAMPL) technology was used in bread wheat for the first time for a study of genetic diversity, genotype identification and gene tagging. The diversity studies involved 55 wheat genotypes and two SAMPL primer pairs (SAMPL-6 and SAMPL-7, each with a M-CAG primer), which together gave 43 polymorphic bands out of a total of 87 SAMPL bands. The average polymorphic information content (PIC) of SAMPL primers was 0.221 and that of SAMPL markers was 0.264. The marker index of SAMPL markers was 9.61. The genetic similarity (GS) coefficients for 1,485 pairs of genotypes ranged from 0.35 to 0.96 with an average of 0.65. A dendrogram was prepared on the basis of a similarity matrix using the UPGMA algorithm, which corresponded well with the results of principal component analysis (PCA). From a total of 55 genotypes, 54 could be distinguished using the SAMPL banding patterns of both primers. For gene tagging, 568 bands from a total of 1,185 SAMPL bands detected polymorphism between each of the three pairs of parents differing for grain protein content (GPC), pre-harvest sprouting tolerance (PHST) and grain weight (GW). An association of six bands with GPC, of seven bands with PHST and four bands with GW was observed using bulked segregant analysis (BSA).

Polymorphism at rDNA loci in barley and its relation with climatic variables.

The variation in length of the intergenic spacer (IGS) region of the ribosomal DNA repeat unit was examined in 63 accessions of wild barley, Hordeum spontaneum, and seven accessions of cultivated barley, Hordeum vulgare. The accessions of wild barley were collected from ecologically diverse climatic and edaphic microsites in Israel, and the barley cultivars were those grown in India. Sixteen spacer-length variants (slvs) observed in the present study presumably belonged to two known rDNA loci ( Rrn1 and Rrn2). Each accession had one or more variants, which together represented the rDNA phenotype. The rDNA phenotypes of wild barley accessions were widely diverse and differed substantially from those of cultivated barley. The slv phenotypes and the corresponding alleles were shown to be largely correlated with different climatic, edaphic and ecogeographical microsites and niches (the "Evolution Canyon" at Lower Nahal Oren, Mount Carmel; and Tabigha, Eastern Upper Galilee Mountains), so that a particular rDNA phenotype of an accession could be used to predict the climate and soil to which the accession belonged. This sharp microsite ecogeographic variation in ribosomal DNA appears adaptive in nature, and is presumably driven by climatic and edaphic natural selection.

Organising activities of engrailed, hedgehog, wingless and decapentaplegic in the genital discs of Drosophila melanogaster.

The genes engrailed (en), hedgehog (hh), wingless (wg) and decapentaplegic (dpp) have been shown to play vital organising roles in the development and differentiation of thoracic imaginal discs. We have analysed the roles of these genes in organising the development and differentiation of the genital discs, which are bilaterally symmetrical and possess different primordia, namely, the male and female genital primordia and an anal primordium. Our results suggest that the organising activity of en in genital discs programs the normal development and differentiation of the genital disc by regulating the expression of hh. Hh in turn induces wg and dpp, the genes whose products act as secondary signalling molecules. Moreover, the complementary patterns of wg and dpp expression are essential for the bilateral symmetry and are maintained by mutual repression.

1(2)gl gene regulates late expression of segment polarity genes in Drosophila.

To analyse the possible roles of Drosophila tumour suppressor genes, 1(2)gl and 1(2)gd, in differentiation programmes of imaginal cells, we investigated their interactions with two segment polarity genes, viz., cubitus interruptus Dominant (ci-D) and engrailed (en), by examining their patterns of expression in tumourous imaginal discs of 1(2)gl4 or 1(2)gd1 homozygous larvae. While the 1(2)gd1 mutation did not have much effect, the areas of expression of ci-D and en in the tumourous discs of 1(2)gl homozygous larvae were significantly increased and the anterior-posterior compartment boundary was no longer identifiable. To examine if the loss of en expression compartment boundary in 1(2)gl tumourous discs was due to overproliferation of the posterior compartment cells or due to a deregulated expression of en in the anterior compartment cells, 1(2)gl4 homozygous cell clones were generated in 1(2)gl4 enlacZ/++ background. A distinct X-gal staining in 1(2)gl homozygous clones in the anterior compartment in wing imaginal discs or in adult wings confirmed deregulated ectopic expression of en in 1(2)gl mutant anterior compartment cells. We suggest that 1(2)gl is involved in regulating post embryonic expression of segment polarity genes.

Multiple specific chromosomal alterations in a rat ascitic histiocytoma 'AK-5'.

In the rat ascitic histiocytoma, AK-5, chromosome numbers vary between 33 and 41 with a peak at 40 chromosomes. None of the metaphase spreads showed double minute chromosomes. The karyotype of this tumor was characterized by hypodiploid chromosome constitution. Giemsa banding analysis revealed 12 clonal marker chromosomes (M1-M12). Tentative identification of these markers were: M1 = ins(1q); M2 = t(5;?); M3 = t(8;10); M4 = t(8;?); M5 = t(10;X); M6 - t(15;?); M7 = t(5;6); M8 = del(13p); M9-M12 = unidentified. M3 being a large near metacentric chromosome serves as a characteristic marker for this tumor. All marker chromosomes except M2 and M4 were present in single copy per cell. In some metaphases M2 was present in 2 copies while M4 was present in 2 or 3 copies per cell. The total cell cycle duration of AK-5 cells was 15.5 h and the different phases, G1, S, G2 + M were estimated as 1.2, 12.2, and 2 h, respectively.

The hyperactive X chromosome is not early replicating in mitotically active somatic cells of Drosophila nasuta males.

The temporal order of replication of the X chromosome(s) in mitotically dividing male and female cells in early embryos and in brain ganglia of Drosophila nasuta larvae was examined using [3H]thymidine pulse labelling and autoradiography. Both the X chromosomes in female cells and the single X chromosome in male cells replicated in complete synchrony with the autosome set in the nucleus. Thus, unlike the well-known early completion of replication by the hemizygous X chromosome in polytene nuclei in the salivary glands of male Drosophila larvae, the single X chromosome in mitotically dividing cells does not replicate earlier than the autosomes. We conclude that transcriptional hyperactivity of the single X chromosome required for dosage compensation in somatic cells of male Drosophila is not dependent upon its early replication.

Factors influencing predation of the waterbugs Sphaerodema annulatum (Fab). and S. rusticum (Fab.) on the disease transmitting snail Lymnaea (Radix) luteola (Lamarck).

Variations in the rate of predation of the waterbugs Sphaerodema annulatum and S. rusticum on the snails Lymnaea (Radix) luteola have been noted in respect to the morphs of the waterbugs, size of the prey individuals, densities of prey and predators, temperature and surface area of the waterbody concerned and the seasons. Consumption rate was highest (7.2 and 2.2 individuals per day per individual of S. annulatum and S. rusticum, respectively) in prereproductive ages of the waterbugs. This was followed by a gradual decline with the increase in age of the predators. The consumption rate was gradually higher with the increase of temperature from 20 degrees C to 35 degrees C. The bugs failed to survive beyond 35 days at 35 degrees C. Though the bugs prey upon the snails of all sizes preference for 6.5 x 4.5 mm to 8 x 5 mm individuals by S. annulatum and for 5 x 3 mm to 6.5 x 4.5 mm individuals by S. rusticum is established. The waterbugs, irrespective of species, consumed the snail individuals belonged to 3 x 2 - 4 x 3 mm size group maximum when supplied separately. The rate of predation gradually declined with the rise of predator's density irrespective of waterbug species. Predation rate increased with increasing prey density. This was level off when the prey snails were 1100 and 700 in number for S. annulatum and S. rusticum respectively. An adult S. annulatum and S. rusticum consumed 5.04, 3.7, 1.43 and 3.36, 2.49, 1.04 snails per day respectively in summer, monsoon and winter.

A study of heterochromatin in Drosophila nasuta by the 5-bromodeoxyuridine-Giemsa staining technique.

Larval brain ganglia of Drosophila nasuta were cultured in vitro in the presence of 5-bromodeoxyuridine for 1 or 5 h at 24 degrees C and the air-dried chromosome preparations stained by the Hoechst 33258-Giemsa technique to reveal bromodeoxyuridine induced sister chromatid differentiation. In 1 h as well as 5 h preparations, 10-15% of well spread metaphase plates show a sister chromatid differentiation in only C-band heterochromatin regions of different chromosomes. We infer that this sister chromatid differentiation in all heterochromatic regions is seen after bromodeoxyuridine incorporation for only one replication cycle and is related to the presence of asymmetric A-T rich satellite sequences in all the C-band regions of D. nasuta karyotype.