Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis

Roots are the primary site of interaction between plants and microorganisms. To meet food demands in changing climates, improved yields and stress resistance are increasingly important, stimulating efforts to identify factors that affect plant productivity. The role of bacterial endophytes that reside inside plants remains largely unexplored, because analysis of their specific functions is impeded by difficulties in cultivating most prokaryotes. Here, we present the first metagenomic approach to analyze an endophytic bacterial community resident inside roots of rice, one of the most important staple foods. Metagenome sequences were obtained from endophyte cells extracted from roots of field-grown plants. Putative functions were deduced from protein domains or similarity analyses of protein-encoding gene fragments, and allowed insights into the capacities of endophyte cells. This allowed us to predict traits and metabolic processes important for the endophytic lifestyle, suggesting that the endorhizosphere is an exclusive microhabitat requiring numerous adaptations. Prominent features included flagella, plant-polymer-degrading enzymes, protein secretion systems, iron acquisition and storage, quorum sensing, and detoxification of reactive oxygen species. Surprisingly, endophytes might be involved in the entire nitrogen cycle, as protein domains involved in N(2)-fixation, denitrification, and nitrification were detected and selected genes expressed. Our data suggest a high potential of the endophyte community for plant-growth promotion, improvement of plant stress resistance, biocontrol against pathogens, and bioremediation, regardless of their culturability.     

A comparative study on lipid peroxidation, activities of antioxidant enzymes and viability of cattle and buffalo bull spermatozoa during storage at refrigeration temperature

A comparative study was conducted to monitor the activities of some antioxidant enzymes, lipid peroxidation and viability of cattle and buffalo bull spermatozoa during storage of semen at refrigeration temperature over a period of 72 h. Semen samples, collected from six cross bred cattle bulls (group I) and six Murrah buffalo bulls (group II), were diluted in egg-yolk-citrate and the spermatozoa were separated from seminal plasma by centrifugation at 4 degrees C in a refrigerated centrifuge. The malondialdehyde (MDA) production in group I increased from 1.17+/-0.29 at 0 h to 7.50+/-0.52 nmol/10(8)spermatozoa after 72 h of storage while in group II it increased from 1.99+/-0.26 to 8.70+/-0.10 nmol/10(8)spermatozoa in the same period. However, buffalo bull spermatozoa had a significantly higher (p<0.05) lipid peroxidation at 0 h as well as at 12, 24 and 48 h (p<0.01) periods. The activities of antioxidant enzymes viz. SOD, GPx and G6PD in both the groups showed a similar pattern of change i.e. the activities declined successively in spermatozoa and increased in the seminal plasma. However, the activities of these three enzymes remained significantly higher in the cattle bull spermatozoa than that in buffalo bull spermatozoa. Amount of MDA produced in spermatozoa of both the groups was negatively correlated while SOD, GPx and G6PD activities in spermatozoa were positively correlated to the motility and viability of spermatozoa. Sperm motility as well as viability was significantly less (p<0.05) in group II than that in group I. SOD, GPx and G6PD activities in spermatozoa of both the groups were negatively correlated to lipid peroxidation of spermatozoa cell membrane. The results showed that the less activities of antioxidant enzymes in buffalo bull spermatozoa was due to higher lipid peroxidation that indicated that they were more prone to oxidative stress as compared to cattle bull spermatozoa when stored at refrigeration temperature.     

Effects of Migration on Genetic Variability and Parent–Offspring Correlation Coefficients in Anthropometric and Physiometric Phenotypes Among Three Groups of Population in Punjab, India

In the present study, we examined the migration effects on genetic variabilities and heritabilities patterns between three groups of population like parental population in Punjab, migrant from Pakistan, and migrant from other states of India in Punjab using anthropometric and physiometric traits. A total of 500 adult individuals from 300 families were studied. Statistical comparisons were carried out through mean coefficients, Student’s t test, heritability, and regression analysis. The results suggest a significant migration effect on almost all traits. Correlation coefficient for first-degree relatives, the slope factors, and heritabilities for almost all variables have been found significant among the three groups of populations. However, the discrimination is more prominent among migrant from other states of India because of more genetic heterogeneity.     

Last‐century changes of alpine grassland water‐use efficiency: a reconstruction through carbon isotope analysis of a time‐series of Capra ibex horns

The ecophysiological response of an alpine grassland to recent climate change and increasing atmospheric CO₂ concentration was investigated with a new strategy to go back in time: using a time‐series of Capra ibex horns as archives of the alpine grasslands' carbon isotope discrimination (¹³Δ). From the collection of the Natural History Museum of Bern, horns of 24 males from the population of the Augstmatthorn–Brienzer Rothorn mountains, Switzerland, were sampled covering the period from 1938 to 2006. Samples were taken from the beginning of each year‐ring of the horns, representing the beginning of the horn growth period, the spring. The horns' carbon ¹³C content (Δ¹³C) declined together with that of atmospheric CO₂ over the 69‐year period, but ¹³Δ increased slightly (+0.4‰), though significantly (P<0.05), over the observation period. Estimated intercellular CO₂ concentration increased (+56 μmol mol^?1) less than the atmospheric CO₂ concentration (+81 μmol mol^?1), so that intrinsic water‐use efficiency increased by 17.8% during the 69‐year period. However, the atmospheric evaporative demand at the site increased by approximately 0.1 kPa between 1955 and 2006, thus counteracting the improvement of intrinsic water‐use efficiency. As a result, instantaneous water‐use efficiency did not change. The observed changes in intrinsic water‐use efficiency were in the same range as those of trees (as reported by others), indicating that leaf‐level control of water‐use efficiency of grassland and forests followed the same principles. This is the first reconstruction of the water‐use efficiency response of a natural grassland ecosystem to last century CO₂ and climatic changes. The results indicate that the alpine grassland community has responded to climate change by improving the physiological control of carbon gain to water loss, following the increases in atmospheric CO₂ and evaporative demand. But, effective leaf‐level water‐use efficiency has remained unchanged.     

Machine learning techniques in disease forecasting: a case study on rice blast prediction

Background  

Diverse modeling approaches viz. neural networks and multiple regression have been followed to date for disease prediction in plant populations. However, due to their inability to predict value of unknown data points and longer training times, there is need for exploiting new prediction softwares for better understanding of plant-pathogen-environment relationships. Further, there is no online tool available which can help the plant researchers or farmers in timely application of control measures. This paper introduces a new prediction approach based on support vector machines for developing weather-based prediction models of plant diseases.     

A translocation tester set in pearl millet

Summary Sixteen translocation stocks developed in pearl millet, Pennisetum typhoides (Burm.) S.&H. (2 n = 14) were inter-crossed and the meiotic configurations of f₁'s analysed. A translocation tester set comprising five translocation stocks, each involving two non-homologous chromosomes has been developed.     

The Oryza Map Alignment Project: The Golden Path to Unlocking the Genetic Potential of Wild Rice Species

The wild species of the genus Oryza offer enormous potential to make a significant impact on agricultural productivity of the cultivated rice species Oryza sativa and Oryza glaberrima. To unlock the genetic potential of wild rice we have initiated a project entitled the ‘Oryza Map Alignment Project’ (OMAP) with the ultimate goal of constructing and aligning BAC/STC based physical maps of 11 wild and one cultivated rice species to the International Rice Genome Sequencing Project’s finished reference genome – O. sativa ssp. japonica c. v. Nipponbare. The 11 wild rice species comprise nine different genome types and include six diploid genomes (AA, BB, CC, EE, FF and GG) and four tetrapliod genomes (BBCC, CCDD, HHKK and HHJJ) with broad geographical distribution and ecological adaptation. In this paper we describe our strategy to construct robust physical maps of all 12 rice species with an emphasis on the AA diploid O. nivara – thought to be the progenitor of modern cultivated rice.