Showing papers by "Indian Agricultural Statistics Research Institute published in 2017"
TL;DR: This study made an attempt to develop a support vector machine (SVM) based computational approach for prediction of AMPs with improved accuracy, and achieved higher accuracy than several existing approaches, while compared using benchmark dataset.
Abstract: Antimicrobial peptides (AMPs) are important components of the innate immune system that have been found to be effective against disease causing pathogens. Identification of AMPs through wet-lab experiment is expensive. Therefore, development of efficient computational tool is essential to identify the best candidate AMP prior to the in vitro experimentation. In this study, we made an attempt to develop a support vector machine (SVM) based computational approach for prediction of AMPs with improved accuracy. Initially, compositional, physico-chemical and structural features of the peptides were generated that were subsequently used as input in SVM for prediction of AMPs. The proposed approach achieved higher accuracy than several existing approaches, while compared using benchmark dataset. Based on the proposed approach, an online prediction server iAMPpred has also been developed to help the scientific community in predicting AMPs, which is freely accessible at http://cabgrid.res.in:8080/amppred/. The proposed approach is believed to supplement the tools and techniques that have been developed in the past for prediction of AMPs.
313 citations
TL;DR: In this paper, the effect of chitosan coating on the storage life and quality of "Santa Rosa" plums was investigated, and it was shown that chitosa had a significant effect in maintaining fruit firmness, retarding weight loss, respiration and ethylene evolution rates.
119 citations
TL;DR: This study identified candidate miRNAs and mRNAs operating in important pathways under drought stress conditions, and these candidates will be useful in the development of drought-tolerant maize hybrids.
Abstract: MicroRNA-mediated gene regulation plays a crucial role in controlling drought tolerance In the present investigation, 13 drought-associated miRNA families consisting of 65 members and regulating 42 unique target mRNAs were identified from drought-associated microarray expression data in maize and were subjected to structural and functional characterization The largest number of members (14) was found in the zma-miR166 and zma-miR395 families, with several targets However, zma-miR160, zma-miR390, zma-miR393 and zma-miR2275 each showed a single target Twenty-three major drought-responsive cis-regulatory elements were found in the upstream regions of miRNAs Many drought-related transcription factors, such as GAMYB, HD-Zip III and NAC, were associated with the target mRNAs Furthermore, two contrasting subtropical maize genotypes (tolerant: HKI-1532 and sensitive: V-372) were used to understand the miRNA-assisted regulation of target mRNA under drought stress Approximately 35% and 31% of miRNAs were up-regulated in HKI-1532 and V-372, respectively The up-regulation of target mRNAs was as high as 142% in HKI-1532 but was only 238% in V-372 The expression patterns of miRNA-target mRNA pairs were classified into four different types: Type I- up-regulation, Type II- down-regulation, Type III- neutral regulation and Type IV- opposite regulation HKI-1532 displayed 46 Type I, 13 Type II and 23 Type III patterns, whereas V-372 had mostly Type IV interactions (151) A low level of negative regulations of miRNA associated with a higher level of mRNA activity in the tolerant genotype helped to maintain crucial biological functions such as ABA signaling, the auxin response pathway, the light-responsive pathway and endosperm expression under stress conditions, thereby leading to drought tolerance Our study identified candidate miRNAs and mRNAs operating in important pathways under drought stress conditions, and these candidates will be useful in the development of drought-tolerant maize hybrids
57 citations
TL;DR: In this article, a regression model was obtained using Ordinary Least Square technique which predicted a formula for the total glucosinolate content obtained by the prediction formula when compared with HPLC data.
Abstract: Glucosinolates are anti-nutritional factors present abundantly in the seed meal fraction of oilseed Brassica species. They are found in varying levels among different genotypes. Those genotypes containing less than 30 µmol/g are considered low/zero glucosinolate type and are preferred for edible purposes due to low pungency. Twenty two different genotypes were taken for the analysis of glucosinolates by spectrophotometry. A regression model was obtained using Ordinary Least Square technique which predicted a formula. Total glucosinolates (µmol/g) = 1.40 + 118.86 × A425, where A425 is the absorbance at 425 nm. The total glucosinolate content obtained by the prediction formula when compared with HPLC data showed a correlation coefficient of 0.942. This high correlation between the two data sets validated the developed methodology. This method also simplifies the estimation of total glucosinolates by excluding the use of HPLC or other sophisticated instruments.
48 citations
TL;DR: This investigation provided significant evidence of genes operating in the adaptive traits such as ethylene production and aerenchyma formation to cope-up the waterlogging stress.
Abstract: Waterlogging causes yield penalty in maize-growing countries of subtropical regions. Transcriptome analysis of the roots of a tolerant inbred HKI1105 using RNA sequencing revealed 21,364 differentially expressed genes (DEGs) under waterlogged stress condition. These 21,364 DEGs are known to regulate important pathways including energy-production, programmed cell death (PCD), aerenchyma formation, and ethylene responsiveness. High up-regulation of invertase (49-fold) and hexokinase (36-fold) in roots explained the ATP requirement in waterlogging condition. Also, high up-regulation of expansins (42-fold), plant aspartic protease A3 (19-fold), polygalacturonases (16-fold), respiratory burst oxidase homolog (12-fold), and hydrolases (11-fold) explained the PCD of root cortical cells followed by the formation of aerenchyma tissue during waterlogging stress. We hypothesized that the oxygen transfer in waterlogged roots is promoted by a cross-talk of fermentative, metabolic, and glycolytic pathways that generate ATPs for PCD and aerenchyma formation in root cortical cells. SNPs were mapped to the DEGs regulating aerenchyma formation (12), ethylene-responsive factors (11), and glycolysis (4) under stress. RNAseq derived SNPs can be used in selection approaches to breed tolerant hybrids. Overall, this investigation provided significant evidence of genes operating in the adaptive traits such as ethylene production and aerenchyma formation to cope-up the waterlogging stress.
47 citations
TL;DR: It can be concluded that consumption of three cups of tea infusion per day does not have any adverse effect on human health with respect to the referred micronutrients rather got beneficial effects to human.
Abstract: Tea (Camellia sinensis L.) is a perennial acidophilic crop, and known to be a nonalcoholic stimulating beverage that is most widely consumed after water. The aim of this review paper is to provide a detailed documentation of selected micronutrient contents, viz. boron (B), cobalt (Co), copper (Cu), iron (Fe), manganese (Mn), molybdenum (Mo), and zinc (Zn) in made tea and tea infusion. Available data from the literature were used to calculate human health aspect associated with the consumption of tea infusion. A wide range of micronutrients reported in both made tea and tea infusion could be the major sources of micronutrients for human. The content of B, Co, Cu, Fe, Mn, Mo, and Zn in made tea are ranged from 3.04 to 58.44 μg g−1, below detectable limit (BDL) to 122.4 μg g−1, BDL to 602 μg g−1, 0.275 to 13,040 μg g−1, 0.004 to 15,866 μg g−1, 0.04 to 570.80 μg g−1 and 0.01 to 1120 μg g−1, respectively. Only 3.2 μg L−1 to 7.25 mg L−1, 0.01 μg L−1 to 7 mg L−1, 3.80 μg L−1 to 6.13 mg L−1, 135.59 μg L−1...
45 citations
TL;DR: The proposed gene selection technique outperformed most of the existing techniques for selecting robust set of informative genes and revealed the underlying molecular mechanisms of Aluminum toxic stress response in soybean.
Abstract: Selection of informative genes is an important problem in gene expression studies. The small sample size and the large number of genes in gene expression data make the selection process complex. Further, the selected informative genes may act as a vital input for gene co-expression network analysis. Moreover, the identification of hub genes and module interactions in gene co-expression networks is yet to be fully explored. This paper presents a statistically sound gene selection technique based on support vector machine algorithm for selecting informative genes from high dimensional gene expression data. Also, an attempt has been made to develop a statistical approach for identification of hub genes in the gene co-expression network. Besides, a differential hub gene analysis approach has also been developed to group the identified hub genes into various groups based on their gene connectivity in a case vs. control study. Based on this proposed approach, an R package, i.e., dhga (https://cran.r-project.org/web/packages/dhga) has been developed. The comparative performance of the proposed gene selection technique as well as hub gene identification approach was evaluated on three different crop microarray datasets. The proposed gene selection technique outperformed most of the existing techniques for selecting robust set of informative genes. Based on the proposed hub gene identification approach, a few number of hub genes were identified as compared to the existing approach, which is in accordance with the principle of scale free property of real networks. In this study, some key genes along with their Arabidopsis orthologs has been reported, which can be used for Aluminum toxic stress response engineering in soybean. The functional analysis of various selected key genes revealed the underlying molecular mechanisms of Aluminum toxic stress response in soybean.
41 citations
TL;DR: Findings from this study will lay a foundation for marker assisted breeding for abiotic stress tolerant varieties of B. juncea by identifying molecular markers such as Simple Sequence Repeats and Single Nucleotide Polymorphism (SNPs).
Abstract: Abiotic stress is one of the major factors responsible for huge yield loss in crop plants. MicroRNAs play a key role in adaptive responses of plants under abiotic stress conditions through post-transcriptional gene regulations. In present study, 95 potential miRNAs were predicted in Brassica juncea using comparative genomics approach. It was noted that these miRNAs, target several transcription factors (TFs), transporter family proteins, signaling related genes, and protease encoding genes. Nineteen distinct miRNA-target regulatory networks were observed with significant involvement in regulation of transcription, response to stimulus, hormone and auxin mediated signaling pathway related gene ontology (GO) term. The sucrose-starch metabolism and pentose-gluconate interconversion pathways were found significantly enriched for these target genes. Molecular markers such as Simple Sequence Repeats (SSR) and Single Nucleotide Polymorphism (SNPs) were identified on miRNAs (miR-SSRs and miR-SNPs) and their target genes in B. juncea. Notably, one of the miR-SNP (C/T) was found at the 5th position on mature region of miR2926. This C/T transition led to the distorted and unstable hairpin structure of miR2926, consequently complete loss of target function. Hence, findings from this study will lay a foundation for marker assisted breeding for abiotic stress tolerant varieties of B. juncea.
39 citations
TL;DR: A new contamination index named as Tea Research Association Heavy Metal Contamination Index (TRAHMCI) for tea growing soils was formulated based on individual contamination factor using statistical technique and applied to the present dataset which provided a more holistic understanding of overall tea growing soil behavior.
38 citations
TL;DR: The interactions of CDPK genes in various pathways play crucial role in imparting drought tolerance through different ABA and MAPK signaling cascades and could be targeted in development of drought tolerant genotypes in maize, rice, and sorghum through appropriate breeding approaches.
Abstract: Calcium dependent protein kinases (CDPKs) play significant role in regulation of plant growth and development in response to various stresses including drought. A set of 32 CDPK genes identified in maize were further used for searching of orthologs in the model plant Arabidopsis (72) and major food crops such as rice (78) and sorghum (91). We comprehensively studied the phylogenetic relationship, annotations, gene duplications, gene structure, divergence time, 3-D protein structures and tissue-specific drought induced expression of CDPK genes in all four species. Variation in intron frequency in the studied species was one of the reasons for the functional diversity of CDPK genes to various stress responses. Protein kinase and protein kinase C phosphorylation site domains were the most conserved motifs identified in all species. Four groups were identified from the sequence-based phylogenetic analysis, in which maize CDPKs were clustered in group III. Expression data showed that the CDPK genes were highly expressed in leaf of maize, rice, and sorghum whereas in Arabidopsis the maximum expression was observed in root. The expression assay showed 5, 6, 11, and 9 were the commonly and differentially expressed drought-related orthologous genes in maize, Arabidopsis, rice, and sorghum, respectively. 3-D protein structure were predicted for the nine genes (Arabidopsis: 2, maize: 2, rice: 3, and sorghum: 2) showing differential expression in at least three species. The predicted 3-D structures were further evaluated and validated by Ramachandran plot, ANOLEA, ProSA, and Verify-3D. The superimposed 3-D structure of drought-related orthologous proteins retained similar folding pattern owing to their conserved nature. Functional annotation revealed the involvement of CDPK genes in various pathways such as osmotic homeostasis, cell protection, and root growth. The interactions of CDPK genes in various pathways play crucial role in imparting drought tolerance through different ABA and MAPK signaling cascades. These selected candidate genes could be targeted in development of drought tolerant genotypes in maize, rice, and sorghum through appropriate breeding approaches. Our comparative experiments of CDPK genes could also be extended in the drought stress breeding programmes of the related species.
38 citations
TL;DR: The interaction of genes involved in crucial biological functions during stress was identified and the results will be useful in targeting important gene interactions to understand drought tolerance in greater detail.
Abstract: A genomewide transcriptome assay of two subtropical genotypes of maize was used to observe the expression of genes at seedling stage of drought stress. The number of genes expressed differentially was greater in HKI1532 (a drought tolerant genotype) than in PC3 (a drought sensitive genotype), indicating primary differences at the transcriptional level in stress tolerance. The global coexpression networks of the two genotypes differed significantly with respect to the number of modules and the coexpression pattern within the modules. A total of 174 drought-responsive genes were selected from HKI1532, and their coexpression network revealed key correlations between different adaptive pathways, each cluster of the network representing a specific biological function. Transcription factors related to ABA-dependent stomatal closure, signalling, and phosphoprotein cascades work in concert to compensate for reduced photosynthesis. Under stress, water balance was maintained by coexpression of the genes involved in osmotic adjustments and transporter proteins. Metabolism was maintained by the coexpression of genes involved in cell wall modification and protein and lipid metabolism. The interaction of genes involved in crucial biological functions during stress was identified and the results will be useful in targeting important gene interactions to understand drought tolerance in greater detail.
TL;DR: The improved performance of FS‐HB is attributed to the important features used for developing the classifier thereby reducing the complexity of the algorithm and the use of ensemble methodology, which added to the classical bias variance trade‐off and performed better than standalone classifiers.
Abstract: Hybrid models based on feature selection and machine learning techniques have significantly enhanced the accuracy of standalone models This paper presents a feature selection-based hybrid-bagging algorithm (FS-HB) for improved credit risk evaluation The 2 feature selection methods chi-square and principal component analysis were used for ranking and selecting the important features from the datasets The classifiers were built on 5 training and test data partitions of the input data set The performance of the hybrid algorithm was compared with that of the standalone classifiers: feature selection-based classifiers and bagging The hybrid FS-HB algorithm performed best for qualitative dataset with less features and tree-based unstable base classifier Its performance on numeric data was also better than other standalone classifiers, whereas comparable to bagging with only selected features Its performance was found better on 70:30 data partition and the type II error, which is very significant in risk evaluation was also reduced significantly The improved performance of FS-HB is attributed to the important features used for developing the classifier thereby reducing the complexity of the algorithm and the use of ensemble methodology, which added to the classical bias variance trade-off and performed better than standalone classifiers
TL;DR: In this paper, the half-life of tricyclazole in Delhi field capacity soil amended with Blue Green Algae (BGA), was 150.5 compared to 167.1% in unamended soil, indicating that BGA amendment enhanced the rate of dissipation of in both the selected soils.
TL;DR: This study reports 174 known and conserved differentially expressed miRs of 27 miR families of maize plant and provides an insight into the composite regulatory mechanism of miRs in maize in response to Pi deficiency.
Abstract: Globally important cereal crop maize provides important nutritions and starch in dietary foods. Low phosphate (LPi) availability in the soil frequently limits the maize quality and yield across the world. Small non-coding RNAs (Snc-RNAs) play crucial roles in growth and adaptation of plants to the environment. Snc-RNAs like microRNAs (miRs) and trans-acting small interfering RNAs (Tasi-Rs) play important functions in posttranscriptional regulation of gene expression, which controls plant development, reproduction, and biotic/abiotic stress responses. In order to identify the miR and Tasi-R alterations in leaf and root of maize in response to sufficient phosphate and LPi at 3LS and 4LS, the snc-RNA population libraries for 0th, 1st, 2nd, 4th, and 8th day were constructed. These libraries were used for genome-wide alignment and RNA-fold analysis for possible prediction of potential miRs and Tasi-Rs. This study reported 174 known and conserved differentially expressed miRs of 27 miR families of maize plant. In addition, leaf and root specific potential novel miRs representing 155 new families were also discovered. Differentially expressed conserved as well as novel miR functions in root and leaf during early stage of Pi starvation were extensively discussed. Leaf and root specific miRs as well as common miRs with their target genes, participating in different biological, cellular, and metabolic processes were explored. Further, four miR390-directed Tasi-Rs which belong to TAS3 gene family along with other orthologs of Tasi-Rs were also identified. Finally, the study provides an insight into the composite regulatory mechanism of miRs in maize in response to Pi deficiency.
TL;DR: Jasmonate mediated signalling pathway, which is known to play crucial role during defense response against necrotrophs, could be strengthened in Brassica plants to combat the disease.
Abstract: The productivity of Oilseed Brassica, one of the economically important crops of India, is seriously affected by the disease, Alternaria blight. The disease is mainly caused by two major necrotrophic fungi, Alternaria brassicae and Alternaria brassicicola which are responsible for significant yield losses. Till date, no resistant source is available against Alternaria blight, hence plant breeding methods can not be used to develop disease resistant varieties. Jasmonate mediated signalling pathway, which is known to play crucial role during defense response against necrotrophs, could be strengthened in Brassica plants to combat the disease. Since scanty information is available in Brassica-Alternaria pathosystems at molecular level therefore, in the present study efforts have been made to model jasmonic acid pathway in Arabidopsis thaliana to simulate the dynamic behaviour of molecular species in the model. Besides, the developed model was also analyzed topologically for investigation of the hubs node. COI1 is identified as one of the promising candidate genes in response to Alternaria and other linked components of plant defense mechanisms against the pathogens. The findings from present study are therefore informative for understanding the molecular basis of pathophysiology and rational management of Alternaria blight for securing food and nutritional security.
TL;DR: Results of this study revealed that the consumption of 600 mL tea infusion produced from 24 g of made tea per day may be beneficial to human in terms of these micronutrients content.
Abstract: The current study aims to assess the infusion pattern of three important micronutrients namely copper (Cu), iron (Fe), and zinc (Zn) contents from black tea samples produced in Assam (India) and Thohoyandou (South Africa). Average daily intakes and hazardous quotient were reported for these micronutrients. Total content for Cu, Fe, and Zn varied from 2.25 to 48.82 mg kg−1, 14.75 to 148.18 mg kg−1, and 28.48 to 106.68 mg kg−1, respectively. The average contents of each of the three micronutrients were higher in tea leaves samples collected from South Africa than those from India while the contents in tea infusions in Indian samples were higher than in South African tea samples. Results of this study revealed that the consumption of 600 mL tea infusion produced from 24 g of made tea per day may be beneficial to human in terms of these micronutrients content. Application of nonparametric tests revealed that most of the data sets do not satisfy the normality assumptions. Hence, the use of both parametric and nonparametric statistical analysis that subsequently revealed significant differences in elemental contents among Indian and South African tea.
TL;DR: In this paper, the carbon sequestration potential (CSP) of existing agroforestry systems (AFS) for simulation period of 30 years in twenty six districts from ten selected states of India.
Abstract: India launched National Agroforestry Policy on 10th February, 2014 which has the potential to substantially reduce poverty in rural India and revive wood based industry, besides integrating food production with environmental services. The policy is not only crucial to India’s ambitious goal of achieving 33 per cent forest and tree cover but also to mitigate GHG emissions from agriculture sector. Dynamic CO2FIX-v3.1 model has been used to estimate the carbon sequestration potential (CSP) of existing agroforestry systems (AFS) for simulation period of 30 years in twenty six districts from ten selected states of India. The observed number of trees on farmers’ field in these districts varied from 1.81 to 204 per hectare with an average value of 19.44 trees per hectare. The biomass in the tree component varied from 0.58 to 48.50 Mg DM ha−1, whereas, the total biomass (tree and crop) ranged from 4.96 to 58.96 Mg DM ha−1. The soil organic carbon ranged from 4.28 to 24.13 Mg C ha−1. The average estimated carbon sequestration potential of the AFS, representing varying edapho-climatic conditions, on farmers field at country level was 0.21 Mg C ha−1yr−1. At national level, existing AFS are estimated to mitigate 109.34 million tons CO2 annually, which may offsets one-third (33 %) of the total GHG emissions from agriculture sector.
TL;DR: In this paper, the empirical predictor for small area counts (NSEP) under an area level generalized linear mixed model (NSGLMM) is proposed, where the fixed effect parameters of a GLMM are spatially invariant and do not account for the presence of spatial nonstationarity in the population of interest.
Abstract: There is a growing need for current and reliable counts at small area level. The empirical predictor under a generalised linear mixed model (GLMM) is often used for small area estimation (SAE) of such counts. However, the fixed effect parameters of a GLMM are spatially invariant and do not account for the presence of spatial nonstationarity in the population of interest. A geographically weighted regression extension of the GLMM is developed, extending this model to allow for spatial nonstationarity, and SAE based on this spatially nonstationary model (NSGLMM) is described. The empirical predictor for small area counts (NSEP) under an area level NSGLMM is proposed. Analytic and bootstrap approaches to estimating the mean squared error of the NSEP are also developed, and a parametric approach to testing for spatial nonstationarity is described. The approach is illustrated by applying it to a study of poverty mapping using socio-economic survey data from India.
TL;DR: First transcriptomic studies of chickpea or even any legume crop using two herbicide susceptible and tolerant genotypes exposed to imidazoline and the role of cytochrome P450, xyloglucan endotransglucosylase/hydrolase, glutamate dehydrogenase, methyl crotonoyl carboxylase and of thaumatin-like genes in herbicide resistance are revealed.
Abstract: Background Chickpea (Cicer arietinum L) contributes 75% of total pulse production Being cheaper than animal protein, makes it important in dietary requirement of developing countries Weed not only competes with chickpea resulting into drastic yield reduction but also creates problem of harbouring fungi, bacterial diseases and insect pests Chemical approach having new herbicide discovery has constraint of limited lead molecule options, statutory regulations and environmental clearance Through genetic approach, transgenic herbicide tolerant crop has given successful result but led to serious concern over ecological safety thus non-transgenic approach like marker assisted selection is desirable Since large variability in tolerance limit of herbicide already exists in chickpea varieties, thus the genes offering herbicide tolerance can be introgressed in variety improvement programme Transcriptome studies can discover such associated key genes with herbicide tolerance in chickpea Results This is first transcriptomic studies of chickpea or even any legume crop using two herbicide susceptible and tolerant genotypes exposed to imidazoline (Imazethapyr) Approximately 90 million paired-end reads generated from four samples were processed and assembled into 30803 contigs using reference based assembly We report 5759 differentially expressed genes (DEGs), of which 3037 were regulated by 980 miRNAs, 1528 transcription factors associated with 897 DEGs, 47 Hub proteins, 3540 putative Simple Sequence Repeat-Functional Domain Marker (SSR-FDM), 13778 genic Single Nucleotide Polymorphism (SNP) putative markers and 1174 Indels Randomly selected 20 DEGs were validated using qPCR Pathway analysis suggested that xenobiotic degradation related gene, glutathione S-transferase (GST) were only up-regulated in presence of herbicide Down-regulation of DNA replication genes and up-regulation of abscisic acid pathway genes were observed Study further reveals the role of cytochrome P450, xyloglucan endotransglucosylase/hydrolase, glutamate dehydrogenase, methyl crotonoyl carboxylase and of thaumatin-like genes in herbicide resistance Conclusion Reported DEGs can be used as genomic resource for future discovery of candidate genes associated with herbicide tolerance Reported markers can be used for future association studies in order to develop marker assisted selection (MAS) for refinement In endeavour of chickpea variety development programme, these findings can be of immense use in improving productivity of chickpea germplasm
TL;DR: In this paper, empirical models were developed by taking 30-year long-term (1985-2014) air and soil temperature data for prediction of soil temperatures at three depths (5, 15, 30 cm) in morning (0636 Indian standard time) and afternoon (1336 Indian Standard Time) for alluvial soils in lower Indo-Gangetic plain.
Abstract: Abstract Soil temperature is an important factor in biogeochemical processes. On-site monitoring of soil temperature is limited in spatiotemporal scale as compared to air temperature data inventories due to various management difficulties. Therefore, empirical models were developed by taking 30-year long-term (1985-2014) air and soil temperature data for prediction of soil temperatures at three depths (5, 15, 30 cm) in morning (0636 Indian standard time) and afternoon (1336 Indian standard time) for alluvial soils in lower Indo-Gangetic plain. At 5 cm depth, power and exponential regression models were best fitted for daily data in morning and afternoon, respectively, but it was reverse at 15 cm. However, at 30 cm, exponential models were best fitted for both the times. Regression analysis revealed that in morning for all three depths and in afternoon for 30 cm depth, soil temperatures (daily, weekly, and monthly) could be predicted more efficiently with the help of corresponding mean air temperature than that of maximum and minimum. However, in afternoon, prediction of soil temperature at 5 and 15 cm depths were more precised for all the time intervals when maximum air temperature was used, except for weekly soil temperature at 15 cm, where the use of mean air temperature gave better prediction.
TL;DR: Owing to the presence of nutritionally important, health-promoting bioactive compounds, especially isoflavones, soybean has acquired the status of a functional food and understanding the miRNA-based genetic regulation of is oflavone pathway would assist in selection and manipulation to get high-performing soybean genotypes with better isof lavone yield.
Abstract: Owing to the presence of nutritionally important, health-promoting bioactive compounds, especially isoflavones, soybean has acquired the status of a functional food. miRNAs are tiny riboregulator of gene expression by either decreasing and/or increasing the expression of their corresponding target genes. Despite several works on identification and functional characterization of plant miRNAs, the role of miRNAs in the regulation of isoflavones metabolism is still a virgin field. In the present study, we identified a total of 31 new miRNAs along with their 245 putative target genes from soybean seed-specific ESTs using computational approach. The Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that miRNA putatively regulates metabolism and genetic information processing. Out of that, a total of 5 miRNAs (Gma-miRNA12, Gma-miRNA24, Gma-miRNA26, Gma-miRNA28 and Gma-miRNA29) were predicted and validated for their probable role during isoflavone biosynthesis. We also validated their five target genes using RA-PCR, which is as good as 5’RLM-RACE. Temporal regulation (35DAF, 45DAF, 55DAF and 65DAF) of miRNAs and their targets showed differential expression schema. Differential expression of Gma-miR26 and Gma-miRNA28 along with their corresponding target genes (Glyma.10G197900 and Glyma.09G127200) showed a direct relationship with the total isoflavone content. Therefore, understanding the miRNA-based genetic regulation of isoflavone pathway would assist in selection and manipulation to get high-performing soybean genotypes with better isoflavone yield.
TL;DR: Analysis of variance showed that the effect of genotype (G) and environment (E) for disease incidence was highly significant, and the sources of resistance to fusarium wilt have great potential for use in lentil-breeding programs.
Abstract: Fusarium wilt (caused by Fusarium oxysporum f. sp. lentis) is the most crucial limiting variable for decreasing yield levels of lentils (Lens culinaris Medik.) around the world. A set of 20 diverse lentil genotypes comprising breeding lines and released varieties was evaluated, along with susceptible controls, for resistance to fusarium wilt through natural incidence for two continuous years (2010–11 and 2011–12) in six diverse lentil-growing environments in India. Analysis of variance showed that the effect of genotype (G) and environment (E) for disease incidence was highly significant. Among the three sources of variation, the biggest contribution in disease occurrence was accounted for by environment (54.68%), followed by G × E interaction (17.32%). The high G × E variation necessitated assessment of the genotypes at different locations (environments). GGE biplot analysis of the studied genotypes revealed that genotype PL 101 and released cultivar L 4076 had low levels of disease incidence. The sources of resistance to fusarium wilt have great potential for use in lentil-breeding programs. Another biplot of relationships among environments demonstrated that, among the test locations, Sehore and Faizabad, were the most effective for differentiation of genotypes. On the basis of discriminating ability and representativeness, the Sehore location appeared an ideal testing site for natural incidence of F. oxysporum f. sp. lentis.
TL;DR: In this article, the effect of different amount of human hair to tannery sludge, roadside pond sediment, municipal solid waste and cow dung was investigated during 70-day composting cycle.
Abstract: In general, farmers from developing countries often use several feeding mixtures based on materials available in their vicinity resulting in a final poor-quality compost product. Human hair as a composting feed could impact on the nutrient status in prepared compost. In this study, the effect of different amount of human hair to tannery sludge, roadside pond sediment, municipal solid waste and cow dung was investigated during 70-day composting cycle. Human hair addition increased N, P and K from 1.36 to 22.85, 53.06 to 189.80 and 4.13 to 39.26%, respectively, over control. Total metal and arsenic contaminations were significantly higher than in control but lower than the Indian permissible limit. Highest amount of human hair in composting feed indicated that the germination index for tea seed (Camellia sinensis L.) was less than 80% reflecting the possible remaining phytotoxic substances. Redundancy analysis revealed that there was a significance influence of the physico-chemical variables on bacterial community.
TL;DR: A series of Chalcone - like compounds described that preferentially inhibit HIF-1 dimer, which can interact with amino acids within the active site of the protein, are useful in the design of small molecule therapeutics or the treatment of different abnormalities associated with impaired Hif-1α.
Abstract: Hypoxia inducible factor-1(HIF-1) is a bHLH-family transcription factor that control genes involved in glucolysis, angiogenesis, migration, as well as invasion factors that are important for tumor progression and metastasis. HIF-1, a hetero dimer of HIF-1α and HIF-1β, binds to the hypoxia responsive genes, such as vascular endothelial growth factor (VEGF). It is one the molecular target for angiogenesis. A series of Chalcone - like compounds described that preferentially inhibit HIF-1 dimer, which can interact with amino acids within the active site of the protein. It is of interest model the HIF-1 dimer protein and protein was subjected to molecular dynamics simulations using NAMD 2.9 software with CHARMM27 force field in water and the protein structure was minimized with 25000 steps for 500 ps and simulation with 1000000 steps for 2ns. 2500 compounds were screened from Zinc database through structure based virtual screening with references to Chalcone natural drug compound. The screened compounds were docked into the active site of the protein using AutoDock Vina in PyRx Virtual screening tool. The docking result showed the compounds Zinc04280532, Zinc04280533, Zinc04280469, Zinc04280534, Zinc16405915, Zinc04277060, Zinc04280538, Zinc04582923, Zinc05280554 and Zinc05943723 have high binding affinities then query compound. The lead hit compounds were also testing for toxicity and bioavailability using Osiris and Molinspiration online server. The active site amino acids such as TYR-21, ASN-34, VAL-35, MET-18, LYS-17, SER-36, ARG- 46 and ARG-14 are key role in the inhibitors activity. This is useful in the design of small molecule therapeutics or the treatment of different abnormalities associated with impaired HIF-1α.
TL;DR: World’s first web-based genomic resources for genetic improvement and germplasm management of mango are reported, based on 3-tier architecture, developed using PHP, MySQL and Javascript.
Abstract: Mango is one of the most important fruits of tropical ecological region of the world, well known for its nutritive value, aroma and taste. Its world production is >45MT worth >200 billion US dollars. Genomic resources are required for improvement in productivity and management of mango germplasm. There is no web-based genomic resources available for mango. Hence rapid and cost-effective high throughput putative marker discovery is required to develop such resources. RAD-based marker discovery can cater this urgent need till whole genome sequence of mango becomes available. Using a panel of 84 mango varieties, a total of 28.6 Gb data was generated by ddRAD-Seq approach on Illumina HiSeq 2000 platform. A total of 1.25 million SNPs were discovered. Phylogenetic tree using 749 common SNPs across these varieties revealed three major lineages which was compared with geographical locations. A web genomic resources MiSNPDb, available at http://webtom.cabgrid.res.in/mangosnps/ is based on 3-tier architecture, developed using PHP, MySQL and Javascript. This web genomic resources can be of immense use in the development of high density linkage map, QTL discovery, varietal differentiation, traceability, genome finishing and SNP chip development for future GWAS in genomic selection program. We report here world's first web-based genomic resources for genetic improvement and germplasm management of mango.
TL;DR: A database of highest number of SSRs (476,169) from complex, hexaploid wheat genome along with previously reported 268 SSR markers associated with 11 traits are reported.
Abstract: Wheat fulfills 20% of global caloric requirement. World needs 60% more wheat for 9 billion population by 2050 but climate change with increasing temperature is projected to affect wheat productivity adversely. Trait improvement and management of wheat germplasm requires genomic resource. Simple Sequence Repeats (SSRs) being highly polymorphic and ubiquitously distributed in the genome, can be a marker of choice but there is no structured marker database with options to generate primer pairs for genotyping on desired chromosome/physical location. Previously associated markers with different wheat trait are also not available in any database. Limitations of in vitro SSR discovery can be overcome by genome-wide in silico mining of SSR. Triticum aestivum SSR database (TaSSRDb) is an integrated online database with three-tier architecture, developed using PHP and MySQL and accessible at http://webtom.cabgrid.res.in/wheatssr/. For genotyping, Primer3 standalone code computes primers on user request. Chromosome-wise SSR calling for all the three sub genomes along with choice of motif types is provided in addition to the primer generation for desired marker. We report here a database of highest number of SSRs (476,169) from complex, hexaploid wheat genome (~17 GB) along with previously reported 268 SSR markers associated with 11 traits. Highest (116.93 SSRs/Mb) and lowest (74.57 SSRs/Mb) SSR densities were found on 2D and 3A chromosome, respectively. To obtain homozygous locus, e-PCR was done. Such 30 loci were randomly selected for PCR validation in panel of 18 wheat Advance Varietal Trial (AVT) lines. TaSSRDb can be a valuable genomic resource tool for linkage mapping, gene/QTL (Quantitative trait locus) discovery, diversity analysis, traceability and variety identification. Varietal specific profiling and differentiation can supplement DUS (Distinctiveness, Uniformity, and Stability) testing, EDV (Essentially Derived Variety)/IV (Initial Variety) disputes, seed purity and hybrid wheat testing. All these are required in germplasm management as well as also in the endeavor of wheat productivity.
TL;DR: Draft assembly of Athelia rolfsii genome is reported, revealing 16830 genes which are involved in fungicide resistance, virulence and pathogenicity along with putative effector and lethal genes for better understanding of the host-parasite interaction.
Abstract: Groundnut (Arachis hypogaea L.) is an important oil seed crop having major biotic constraint in production due to stem rot disease caused by fungus, Athelia rolfsii causing 25–80% loss in productivity. As chemical and biological combating strategies of this fungus are not very effective, thus genome sequencing can reveal virulence and pathogenicity related genes for better understanding of the host-parasite interaction. We report draft assembly of Athelia rolfsii genome of ~73 Mb having 8919 contigs. Annotation analysis revealed 16830 genes which are involved in fungicide resistance, virulence and pathogenicity along with putative effector and lethal genes. Secretome analysis revealed CAZY genes representing 1085 enzymatic genes, glycoside hydrolases, carbohydrate esterases, carbohydrate-binding modules, auxillary activities, glycosyl transferases and polysaccharide lyases. Repeat analysis revealed 11171 SSRs, LTR, GYPSY and COPIA elements. Comparative analysis with other existing ascomycotina genome predicted conserved domain family of WD40, CYP450, Pkinase and ABC transporter revealing insight of evolution of pathogenicity and virulence. This study would help in understanding pathogenicity and virulence at molecular level and development of new combating strategies. Such approach is imperative in endeavour of genome based solution in stem rot disease management leading to better productivity of groundnut crop in tropical region of world.
TL;DR: The present study culminated in greater understanding of the heat-response of tolerant genotype and has provided good candidate genes for the marker development and screening of wheat germplasm for thermotolerance.
Abstract: Global warming is a major threat for agriculture and food security, and in many cases the negative impacts are already apparent. Wheat is one of the most important staple food crops and is highly sensitive to the heat stress (HS) during reproductive and grain-filling stages. Here, whole transcriptome analysis of thermotolerant wheat cv. HD2985 was carried out at the post-anthesis stage under control (22 ± 3 °C) and HS-treated (42 °C, 2 h) conditions using Illumina Hiseq and Roche GS-FLX 454 platforms. We assembled ~24 million (control) and ~23 million (HS-treated) high-quality trimmed reads using different assemblers with optimal parameters. De novo assembly yielded 52,567 (control) and 59,658 (HS-treated) unigenes. We observed 785 transcripts to be upregulated and 431 transcripts to be downregulated under HS; 78 transcripts showed >10-fold upregulation such as HSPs, metabolic pathway-related genes, etc. Maximum number of upregulated genes was observed to be associated with processes such as HS-response, protein-folding, oxidation-reduction and photosynthesis. We identified 2008 and 2483 simple sequence repeats (SSRs) markers from control and HS-treated samples; 243 SSRs were observed to be overlying on stress-associated genes. Polymorphic study validated four SSRs to be heat-responsive in nature. Expression analysis of identified differentially expressed transcripts (DETs) showed very high fold increase in the expression of catalytic chaperones (HSP26, HSP17, and Rca) in contrasting wheat cvs. HD2985 and HD2329 under HS. We observed positive correlation between RNA-seq and qRT-PCR expression data. The present study culminated in greater understanding of the heat-response of tolerant genotype and has provided good candidate genes for the marker development and screening of wheat germplasm for thermotolerance.
08 Mar 2017-Journal of Environmental Science and Health Part B-pesticides Food Contaminants and Agricultural Wastes
TL;DR: The kinetics of imazethapyr release from the developed formulations was studied in water and it revealed that the developed formulas behaved as slow release formulations as compared to commercial formulation.
Abstract: Controlled release formulations of imazethapyr herbicide have been developed employing guar gum-g-cl-polyacrylate/bentonite clay hydrogel composite (GG-HG) and guar gum-g-cl-PNIPAm nano hydrogel (G...
TL;DR: The studied bio-inoculants were effective in the open as well as in the shade and can be utilized to overcome the adverse effect of shade to some extent in agroforestry systems.
Abstract: Beneficial effects of bio-inoculants on growth and yield of plants grown in sunlight have been reported world over but information on their effect under shade is meagre. Therefore, to assess the effect of shade on bio-inoculants, viz. rhizobial (RB) and phosphate-solubilizing bacteria (PSB), and arbuscular mycorrhizal fungi (AMF), which are associated with intercrops in agroforestry systems, a study was carried out on important rainy (Glycine max, Phaseolus mungo, and Vigna radiata) and winter season pulses (Cicer arietinum, Lens culinaris, and Pisum sativum) under 25% (shade) and 100% (no shade) full sun light. The results showed that plant height was higher under the shade in G. max, P. mungo, L. culinaris, and P. sativum, and lower in V. radiata and C. arietinum. Dry weight and yield plant−1 were lower under the shade than the corresponding values in the open for all pulses. In general, bio-inoculants increased plant height, dry weight, and yield plant−1 in all pulses, barring a few exceptions. The efficiencies of bio-inoculants in terms of percent increase of yield over respective control were more or less comparable under shade and no shade for most pulses. The shade reduced rhizobial nodulation and AMF colonization in all crops with a few exceptions. Application of bio-inoculants increased the nodulation and the colonization in most of the treatments. Maximum yield plant−1 was recorded in dual and/or triple inoculations under both shade and no shade suggesting that the bio-inoculants used in our study worked synergistically with each other. Thus, the studied bio-inoculants were effective in the open as well as in the shade and can be utilized to overcome the adverse effect of shade to some extent in agroforestry systems.