Development and evaluation of a high-throughput,low-cost genotyping platform based on oligonucleotide microarrays in rice

Background  

We report the development of a microarray platform for rapid and cost-effective genetic mapping, and its evaluation using rice as a model. In contrast to methods employing whole-genome tiling microarrays for genotyping, our method is based on low-cost spotted microarray production, focusing only on known polymorphic features.     

A Seasonal Assessment of the Impact of Coal Fly Ash Disposal on the River Yamuna,Delhi. I. Chemistry

The impact of fly ash on the chemistry of the River Yamuna was studied. By-products from a 200 MW capacity I.P. thermal power station on the west bank of the River Yamuna, Delhi are largely from coal combustion (fly ash) and are disposed of as a slurry to off-site ash ponds. Many elements associated with fly ash are soluble and become available to the biota. A two-year survey was made of the seasonal variations in limnochemical features in the non-impacted and the impacted segments of the river receiving fly ash effluent and the ash treatment ponds. Conductivity, TDS, DO, hardness, sulphate and nitrate increased significantly in the receiving waters over background values. The reverse was noticed for free CO₂, alkalinity and phosphate. Changes in some other parameters were insignificant. Fly ash effluents from the ash ponds significantly increased the concentration of some elements, viz., Al, Sb, Bi, Cd, Cr, Co, Li, Mn, Mo, K, Si, and Zn in river water. Generally, the highest concentration of most parameters were recorded in the ash ponds. This investigation was helpful in assessing the effect of wet ash disposal on the river limnology and understanding the solubility of various elements in the ash ponds.     

PHYSIOLOGICAL AND BIOCHEMICAL CHANGES IN CATHARANTHUS ROSEUS L. IN RESPONSE TO BORON NUTRITION

Catharanthus roseus L., a medicinally important plant was grown till maturity at varying levels of boron (0.033, 0.066, 0.33 and 3.3 mg B L^?1) supply. Optimum yield was observed in plants receiving 0.33 mg B L^?1. Plants receiving deficient boron showed growth reduction and visual symptoms such as chlorosis and cupping of young emerging leaves and apical tip necrosis. The number and size of the flowers, pods and seeds formed and the pollen viability of the boron deficient plants was markedly reduced. The threshold values for deficiency and toxicity were 57 and 79 μg B g^?1 dry weight for vegetative growth and 60.4 and 68.9 μg B g^?1 dry weight for reproductive growth, respectively, and is reported for the first time in periwinkle. An increase was observed in reducing and non-reducing sugars and in activity of acid phosphatase and ribonuclease in boron stressed plants.     

Physiological and biochemical effects of boron toxicity in mustard during the seedling stage

A study was conducted to determine the physiological and biochemical effects of boron in seedlings of mustard (Brassica juncea L. var Varuna). For this seeds were sown in petridishes with varying concentrations of boron (0, 0.33, 3.3, 33, 330 mM) in seed germinator. Seed germination and vigor index was found to be decreased and percentage phytotoxicity was increased in seeds with increase in the concentration of boron in germinating solution. There was accumulation of sugars and decreased starch concentration in cotyledons and embryonic axes of growing seedling with increasing boron stress. For the estimation of oxidative damage in cotyledons and embryonic axes of mustard seedlings, hydrogen peroxide (H₂O₂), thiobarbituric acid reactive substances (TBARS), phenols and activities of antioxidative enzymes- polyphenoloxydase (PPO), superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) were determined. Boron toxicity caused accumulation of H₂O₂, TBARS and phenols and affected the antioxidative enzyme activity in growing seedling components.     

Growth and centelloside production in hydroponically established medicinal plant-Centella asiatica (L.)

Conditions to cultivate medicinally important herb Centella asiatica in hydroponic system are reported here for the first time. Growth kinetics of hydroponically grown plants was monitored over a period of 70 days. The maximum growth and dry matter accumulation (156.3% increment over the initial inoculum weight) in the cultured plants occurred around 42nd day. High Performance Liquid Chromatography (HPLC) analysis of the bioactive centellosides in the crude triterpenoids extract of the harvested leaves showed the presence of 11 mg, 1.7 mg, 36.6 mg and 6.3 mg of madecassoside, asiaticoside, madecassic acid and asiatic acid on per gram dry weight basis, respectively. The results of this study suggest that the cultivation of C. asiatica in hydroponic systems can be an effective platform for the production of clean and good quality C. asiatica herb for the pharmaceutical companies.     

Influence of organic amendments on dissipation kinetics of two different pesticides in soil: a case study

A study was undertaken to investigate the remedial effect of some soil amendments (farmyard manure (FYM), press mud compost (PMC), cereal straw (CS) at 5 t ha^?1 and fresh cow dung slurry (FCD) @ 0.5 t ha^?1) on dissipation kinetics of imidacloprid and sulfosulfuron under laboratory conditions. Incorporation of CS or FCD was found to be most effective in degrading both the pesticides at faster rates. Dissipation of both the pesticides could be well accounted by two component (1 + 1) first order kinetics. The computed values of parameters revealed that use of organic amendments increased the dissipated fraction of imidacloprid and sulfosulfuron. Incorporation of CS or FCD in soil maintained relatively higher dissipation rate constants for both faster and slower dissipation processes of pesticides in comparison to control. Hence, eco-friendly practices of CS or FCD incorporation as soil amendment in soil can play a vital role in preventing soil and water pollution.     

Cryptic species composition and genetic diversity within Bemisia tabaci complex in soybean in India revealed by mtCOI DNA sequence

Bemisia tabaci is a cryptic species complex, causing significant loss on many agriculturally important crops worldwide. Knowledge on species composition and diversity within B. tabaci complex is critical for evolving sustainable pest management strategies. Here we investigate the whitefly species complex in soybean in major soybean growing states of India. The mitochondrial cytochrome oxidase gene subunit-1(mt COI) based phylogenetic relationships established using Bayesian methods indicated the existence of three cryptic species namely AsiaⅠ, AsiaⅡ1, and AsiaⅡ7. All the haplotypes detected in the study could be assigned to these three cryptic species following the species demarcation criteria of 3.5% divergence threshold. Of these, AsiaⅡ1 was found to be predominant with wide spread distribution across the surveyed regions from cool temperate zones to hot and humid tropical plains. On the contrary, cryptic species AsiaⅡ7 showed localized distribution. The AsiaⅡ1 exhibited the highest haplotype diversity and AsiaⅠ showed high level of nucleotide diversity. There was a significantly high genetic differentiation among these three cryptic species. The MEAM 1, a dreadful invasive species was not detected in the specimens tested in the current study. The diversity and distribution of three cryptic species is discussed in the light of current knowledge on distribution of whitefly species in India and yellow mosaic disease observed during sampling survey.     

Cytogenetical and molecular investigations on somatic hybrids of Sinapis alba and Brassica juncea and their backcross progeny

Somatic hybrids of Sinapis alba+Brassica juncea (Sal Sal AABB) were synthesized by protoplast electrofusion. They were true genomic allopolyploids since they possessed 60 chromosomes, i.e. the sum of S. alba (2n= 24) and B. juncea (2n= 36) chromosomes. Chromosome pairing was predominantly bivalent with the occasional occurrence of multivalents in the pollen mother cells at diakinesis and metaphase I. Hybrids were completely pollen-sterile, but produced seeds on back-crossing with B. juncea and B. campestris. A total of 37 BC₁ plants were raised from two somatic hybrids (JS-1 and JS-2) and 24 of these were analysed cytologically. The 22 plants originating from the pollinations of somatic hybrids with B. juncea showed a chromosome configuration of 18II+12I and had 42–86% pollen fertility. Two plants from the backcrosses of the somatic hybrid with B. campestris formed 10II +20I, and had 0–4% fertile pollen. Total DNA analysis by probing with pTA71 carrying a full-length 18S–25S rDNA fragment of the wheat nuclear genome revealed that the two somatic hybrids possessed all the characteristic bands of both the species, confirming their hybridity. Probing with the mitochondrial coxI and atp9 genes indicated mitochondrial genome recombination in the hybrids. Hybridization with chloroplast-specific psbD indicated that both the somatic hybrids possessed the cp genome of S. alba origin.     

Indole-3-acetic Acid-producing bacteria are associated with cranberry stem gall

ABSTRACT Cranberry stem gall is characterized by tumors that girdle stems, thereby killing all distal leaves, flowers, and fruit. Among bacteria isolated from galls, all 11 isolates that were identified as members of the family Enterobacteriaceae caused galls on 50 to 100% of micropropagated cranberry plants that were inoculated. Four of fifteen isolates identified as Pseudomonas spp. caused galls on 10 to 83% of plants inoculated. Twelve of fifteen isolates identified as either Agrobacterium spp. or Rhizobium spp. caused galls on 10 to 50% of plants inoculated, but the galls were smaller than those caused by members of the family Enterobacteriaceae or Pseudomonas spp. There was a positive correlation between the ability of bacteria to produce IAA in vitro and cause galls. In 2002 and 2003, bacteria were isolated from plant and soil samples collected from beds where stem gall had been observed in the past 2 years and beds where stem gall had never been observed. IAA-producing bacteria were common in all samples, although trends were different across years. The results of this study support the hypothesis that IAA-producing bacteria cause cranberry stem gall and suggest that rather than one bacterial species being the cause, multiple strains of bacteria that produce IAA may be responsible for gall formation.