Showing papers by "Indian Agricultural Statistics Research Institute published in 2018"
TL;DR: Exogenous auxin and genetic manipulation of auxin synthesis and signalling will be useful to mitigate spikelet sterility and stabilize the grain yield of rice under drought and heat stresses.
71 citations
TL;DR: Nine most important MTAs were selected for biofortification and were associated with three traits (GPC, GFeC and GYPP), which can be used in wheat improvement programs either using marker-assisted recurrent selection or pseudo-backcrossing method.
Abstract: The present study was conducted to study the genetic architecture of grain micronutrients (Zn, Fe and β-carotene contents), grain protein content and four yield traits in a spring wheat reference set comprising 246 genotypes. Phenotypic data on these traits recorded at two locations and the genotyping data for 17,937 SNP markers (obtained through outsourcing) were used for genome wide association study, which gave following results after Bonferroni correction using four methods: (1) single locus single trait analysis gave 136 marker-trait associations; (2) multi-locus mixed model gave 587 MTAs; (3) multi-trait mixed model gave 28 MTAs and (4) matrix-variate linear mixed model gave 33 MTAs. As many as 73 epistatic interactions were also detected. Keeping all the results in mind, nine most important MTAs were selected for biofortification. These markers were associated with three traits (GPC, GFeC and GYPP). These MTAs can be used in wheat improvement programs either using marker-assisted recurrent selection or pseudo-backcrossing method.
60 citations
TL;DR: The analysis suggests that a coordinated yet complex interplay between hormones, cellular tolerance, cell wall synthesis and ROS metabolism are required for drought induced root growth in wheat.
52 citations
TL;DR: De novo assembly-based transcriptomic signature of drought response induced by irrigation withdrawal in pearl millet is reported and role of purine and tryptophan metabolism in ABA accumulation mediating abiotic response in which MAPK acts as major intracellular signal sensing drought is revealed.
Abstract: Pearl millet, (Pennisetum glaucum L.), an efficient (C4) crop of arid/semi-arid regions is known for hardiness. Crop is valuable for bio-fortification combating malnutrition and diabetes, higher caloric value and wider climatic resilience. Limited studies are done in pot-based experiments for drought response at gene-expression level, but field-based experiment mimicking drought by withdrawal of irrigation is still warranted. We report de novo assembly-based transcriptomic signature of drought response induced by irrigation withdrawal in pearl millet. We found 19983 differentially expressed genes, 7595 transcription factors, gene regulatory network having 45 hub genes controlling drought response. We report 34652 putative markers (4192 simple sequence repeats, 12111 SNPs and 6249 InDels). Study reveals role of purine and tryptophan metabolism in ABA accumulation mediating abiotic response in which MAPK acts as major intracellular signal sensing drought. Results were validated by qPCR of 13 randomly selected genes. We report the first web-based genomic resource ( http://webtom.cabgrid.res.in/pmdtdb/ ) which can be used for candidate genes-based SNP discovery programs and trait-based association studies. Looking at climatic change, nutritional and pharmaceutical importance of this crop, present investigation has immense value in understanding drought response in field condition. This is important in germplasm management and improvement in endeavour of pearl millet productivity.
41 citations
TL;DR: In this article, the authors analyzed the effect of three medium-term tillage practices and four intensive crop rotations on selected soil organic carbon pools and microbial properties over a period of 6 years.
Abstract: SUMMARY: Conservation agriculture (CA) practices such as zero tillage (ZT) and permanent raised beds (PB) accelerate deposition of soil organic matter and augment associated biological properties of soil through enhanced inputs of organic carbon However, the potential benefit of CA under intensive cereal‐based systems for key soil health indicators (such as carbon pools and biological activities) is only partially known Therefore, we analysed the effect of three medium‐term tillage practices and four intensive crop rotations on selected soil organic carbon pools and microbial properties The tillage practices consist of ZT, PB and conventional tillage (CT) in main plots and four crop rotations (MWMb, maize–wheat–mungbean; MCS, maize–chickpea–Sesbania; MMuMb, maize–mustard–mungbean; MMS, maize–maize–Sesbania) in subplots The experimental design was split‐plot with three replications After 6 years, we observed a significant positive effect of CA practices on soil organic carbon (SOC) content, labile SOC fractions, soil microbial biomass carbon (MBC) and dehydrogenase activity (DHA) The total organic carbon (TOC) was greatly affected by medium‐term tillage and diversified cropping systems; it was larger for CA and MCS and MWMb systems The interaction effect between tillage and cropping systems for SOC content was not significant at all soil depths Significantly larger contributions (85–255%) of labile SOC pools to TOC at various soil depths were recorded in PB and ZT There was a significant positive effect of CA practices and diversified crop rotations on MBC and DHA at all the soil depths and sampling times, but the interaction effect between tillage and cropping systems was not significant Thus, our medium‐term (≥ 5‐years) study showed that the combination of CA (PB and ZT) practices and appropriate choice of rotations (MCS and MWMb) appears to be the most appropriate option for restoration and improvement of the soil health of light‐textured Inceptisols through the accumulation of soil organic matter (SOM) and improvement in soil biological properties HIGHLIGHTS: Effect of conservation agriculture (CA) on soil labile carbon inputs and biological properties Observed changes in SOC stock and C‐pools at different soil depths after 6 years Significant effects of tillage and crop rotations observed for labile‐C pools Adoption of ZT and PB enhanced SOC stock, C‐pools and microbial activity compared to CT
39 citations
TL;DR: 109 novel SNPs associated with important agro-morphological traits, reported for the first time in this study, could be precisely utilized in finger millet genetic improvement after validation.
Abstract: Finger millet (Eleusine coracana L.) is an important dry-land cereal in Asia and Africa because of its ability to provide assured harvest under extreme dry conditions and excellent nutritional properties. However, the genetic improvement of the crop is lacking in the absence of suitable genomic resources for reliable genotype-phenotype associations. Keeping this in view, a diverse global finger millet germplasm collection of 113 accessions was evaluated for 14 agro-morphological characters in two environments viz. ICAR-Vivekananda Institute of Hill Agriculture, Almora (E1) and Crop Research Centre (CRC), GBPUA&T, Pantnagar (E2), India. Principal component analysis and cluster analysis of phenotypic data separated the Indian and exotic accessions into two separate groups. Previously generated SNPs through genotyping by sequencing (GBS) were used for association mapping to identify reliable marker(s) linked to grain yield and its component traits. The marker trait associations were determined using single locus single trait (SLST), multi-locus mixed model (MLMM) and multi-trait mixed model (MTMM) approaches. SLST led to the identification of 20 marker-trait associations (MTAs) (p value<0.01 and <0.001) for 5 traits. While advanced models, MLMM and MTMM resulted in additional 36 and 53 MTAs, respectively. Nine MTAs were common out of total 109 associations in all the three mapping approaches (SLST, MLMM and MTMM). Among these nine SNPs, five SNP sequences showed homology to candidate genes of Oryza sativa (Rice) and Setaria italica (Foxtail millet), which play an important role in flowering, maturity and grain yield. In addition, 67 and 14 epistatic interactions were identified for 10 and 7 traits at E1 and E2 locations, respectively. Hence, the 109 novel SNPs associated with important agro-morphological traits, reported for the first time in this study could be precisely utilized in finger millet genetic improvement after validation.
37 citations
TL;DR: The results indicate the potential of germination rates, crop duration, urea utilization and its effect on root growth in the development of novel phenotypic traits for screening genotypes and crop improvement for NUE, at least in rice.
Abstract: The biological improvement of fertilizer nitrogen use efficiency (NUE) is hampered by the poor characterization of the phenotype and genotype for crop N response and NUE. In an attempt to identify phenotypic traits for N-response and NUE in the earliest stages of plant growth, we analysed the N-responsive germination, respiration, urease activities and root/shoot growth of 21 Indica genotypes of rice (O. sativa var. Indica). We found that N delays germination from 0 to 12 hrs in a genotype-dependent and source-dependent manner, especially with urea and nitrate. We identified contrasting groups of fast germinating genotypes such as Aditya, Nidhi and Swarnadhan, which were also least delayed by N and slow germinating genotypes such as Panvel1, Triguna and Vikramarya, which were also most delayed by N. Oxygen uptake measurements in the seeds of contrasting genotypes revealed that they were affected by N source in accordance with germination rates, especially with urea. Germinating seeds were found to have endogenous urease activity, indicating the need to explore genotypic differences in the effective urea uptake and metabolism, which remain unexplored so far. Urea was found to significantly inhibit early root growth in all genotypes but not shoot growth. Field evaluation of 15 of the above genotypes clearly showed that germination rates, crop duration and yield are linked to NUE. Slow germinating genotypes had longer crop duration and higher yield even at lower N, indicating their higher N use efficiency, relative to fast germinating or short duration genotypes. Moreover, longer duration genotypes suffered lesser yield losses at reduced N levels as compared to short duration genotypes, which is also a measure of their NUE. Together, these results indicate the potential of germination rates, crop duration, urea utilization and its effect on root growth in the development of novel phenotypic traits for screening genotypes and crop improvement for N use efficiency, at least in rice.
32 citations
TL;DR: In this article, the salt responsive gene-based SSR markers were used for characterizing molecular diversity in a panel of wheat genotypes, including salt tolerant and susceptible lines, and the selected markers generated an average of 2.83 alleles/locus.
Abstract: Salinity severely limits wheat production in many parts of the world. Development of salt tolerant varieties represents the most practical option for enhancing wheat production from these areas. Application of marker assisted selection may assist in fast tracking development of salt tolerant wheat varieties. However, SSR markers available in the public domain are not specifically targeted to functional regions of wheat genome, therefore large numbers of these need to be analysed for identification of markers associated with traits of interest. With the availability of a fully annotated wheat genome assembly, it is possible to develop SSR markers specifically targeted to genic regions. We performed extensive analysis to identify candidate gene based SSRs and assessed their utility in characterizing molecular diversity in a panel of wheat genotypes. Our analysis revealed, 161 SSR motifs in 94 salt tolerance candidate genes of wheat. These SSR motifs were nearly equally distributed on the three wheat sub-genomes; 29.8% in A, 35.7% in B and 34.4% in D sub-genome. The maximum number of SSR motifs was present in exons (31.1%) followed by promoters (29.8%), 5’UTRs (21.1%), introns (14.3%) and 3’UTRs (3.7%). Out of the 65 candidate gene based SSR markers selected for validation, 30 were found polymorphic based on initial screening and employed for characterizing genetic diversity in a panel of wheat genotypes including salt tolerant and susceptible lines. These markers generated an average of 2.83 alleles/locus. Phylogenetic analysis revealed four clusters. Salt susceptible genotypes were mainly represented in clusters I and III, whereas high and moderate salt tolerant genotypes were distributed in the remaining two clusters. Population structure analysis revealed two sub-populations, sub-population 1 contained the majority of salt tolerant whereas sub-population 2 contained majority of susceptible genotypes. Moreover, we observed reasonably higher transferability of SSR markers to related wheat species. We have developed salt responsive gene based SSRs in wheat for the first time. These were highly useful in unravelling functional diversity among wheat genotypes with varying responses to salt stress. The identified gene based SSR markers will be valuable genomic resources for genetic/association mapping of salinity tolerance in wheat.
31 citations
TL;DR: The results suggested that lac-based coating of plum fruits was most effective to extend the storage life of ‘Santa Rosa’ plums over other coatings and uncoated fruits under low temperature storage conditions.
Abstract: Plum is a perishable fruit with a very short shelf life of 3–4 days. Several studies have suggested the possible use of edible coatings on maintaining quality and prolonging storage life of fresh horticultural produce. Hence, different edible coatings, namely, lac-based (2:3), Semperfresh™ (1:3) and Niprofresh® (1:5) were selected to observe their efficacy on quality retention of ‘Santa Rosa’ plums. The effects of these coatings on the physical, physiological and biochemical attributes were studied under cold storage conditions (2 ± 1 °C and 85–90% relative humidity). Our results revealed that all the coatings, especially the lac-based significantly reduced the weight loss and maintained higher firmness throughout the storage period. These surface coatings modified the respiration and ethylene rates of the plums and slowed down their metabolism as shown by the retention of texture of the tissue and delayed colour development. At the end of 35 days of cold storage, lac-based coating helped to retain nearly 55% higher fruit firmness and 21% higher antioxidant activity in fruits as compared to uncoated ones. However, the changes in total anthocyanin content were found to be suppressed by 13% in lac-based coated fruits. Overall, the results suggested that lac-based coating of plum fruits was most effective to extend the storage life of ‘Santa Rosa’ plums over other coatings and uncoated fruits under low temperature storage conditions.
28 citations
TL;DR: Clothianidin leaching was minimized in soil of Manipur compared to Delhi after incorporation of FYM, and mobility can be reduced by organic amendment application as the volume of water increased upto 160 mL, mobility increased and residues moved to lower depth.
Abstract: Clothianidin is a widely used insecticide under Indian subtropical condition. The objective of this study was to generate residue data which aims to understand leaching potential of clothianidin [(E)-1-(2-chloro-1,3-thiazol-5-ylmethyl)-3-methyl-2- nitroguanidine] through packed soil column. The maximum amount of clothianidin was recovered at 0–5 cm soil depth in both Manipur (67.15%) and Delhi soil (52.0%) under continuous flow condition. Manipur and Delhi soil concentrated maximum residue with or without farm yard manure (FYM) in 0–20 cm soil depth. The effect of varying the amount of water enhanced the distribution of residues in the first 0–5 cm layer. Among the tested soils, residue was detected in the leachate from Delhi soil (0.04 µg/mL). Clothianidin leaching was minimized in soil of Manipur compared to Delhi after incorporation of FYM. As the volume of water increased upto 160 mL, mobility increased and residues moved to lower depth. Clothianidin did not leach out of the 25 cm long soil columns even after percolating water equivalent to 415.42 mm rainfall. Clothianidin is mobile in soil system and mobility can be reduced by organic amendment application.
25 citations
TL;DR: This study is the first report of determining heterotic combinations utilizing cytoplasmic male sterile and doubled haploid inbred lines for antioxidant compounds in snowball cauliflower to help develop F1 hybrids with better combining ability and better per se performance.
Abstract: The Brassica vegetable crops are rich source of important antioxidant compounds having anticancer and health promoting properties. Development of F1 hybrids with better nutritional traits is one of the main breeding objectives in different vegetable crops. Our study is the first report of determining heterotic combinations utilizing cytoplasmic male sterile (CMS) and doubled haploid (DH) inbred lines for antioxidant compounds in snowball cauliflower. Twenty genetically diverse Ogura CMS lines of cauliflower and six DH male fertile inbred lines were crossed to develop 120 F1 hybrids in line × tester mating design. The resulting 120 test cross progenies along with 26 parents and 4 standard checks were evaluated in 10 × 15 alpha lattice design with three replications during next cropping season. The CMS lines Ogu33-1A, Ogu122-5A and Ogu119-1A were good general combiner and CMS line Ogu118-6A was poor general combiner for majority of traits. Most of the heterotic hybrids were associated with high positive SCA effects. The proportions of σ2A/D and $$\upsigma^{2}_{\text{gca}} /\upsigma^{2}_{\text{sca}}$$
ratios were less than unity in all the cases indicating preponderance of non-additive gene action in the genetic control of all the traits. Highest number of heterotic hybrids with SCA effects in desired positive direction was recorded for ascorbic acid content and phenolic content followed by total carotenoid content. The F1 hybrids with better combining ability and better per se performance could be useful in accumulation of favourable allele for higher concentration of important anti-oxidant compounds.
TL;DR: The information generated on structural and functional characteristics, expression, and interaction of the drought-related TF families will be useful to decipher the drought tolerance mechanisms and to breed drought-tolerant genotypes in maize.
Abstract: Drought is one of the major threats to the maize yield especially in subtropical production systems. Understanding the genes and regulatory mechanisms of drought tolerance is important to sustain the yield. Transcription factors (TFs) play a major role in gene regulation under drought stress. In the present study, a set of 15 major TF families comprising 1,436 genes was structurally and functionally characterized. The functional annotation indicated that the genes were involved in ABA signaling, ROS scavenging, photosynthesis, stomatal regulation, and sucrose metabolism. Duplication was identified as the primary force in divergence and expansion of TF families. Phylogenetic relationship was developed for individual TF and combined TF families. Phylogenetic analysis clustered the genes into specific and mixed groups. Gene structure analysis revealed that more number of genes were intron-rich as compared to intron-less. Drought-responsive cis-regulatory elements such as ABREA, ABREB, DRE1, and DRECRTCOREAT have been identified. Expression and interaction analyses identified leaf-specific bZIP TF, GRMZM2G140355, as a potential contributor toward drought tolerance in maize. Protein-protein interaction network of 269 drought-responsive genes belonging to different TFs has been provided. The information generated on structural and functional characteristics, expression, and interaction of the drought-related TF families will be useful to decipher the drought tolerance mechanisms and to breed drought-tolerant genotypes in maize.
TL;DR: An integrated pipeline of software/servers has been used for the identification and functional annotation of 124 unique HPs of T. aestivum and functional analysis has revealed the role of few HPs in abiotic stress, which were further verified by phylogenetic analysis.
Abstract: Cereal grain bread wheat (T. aestivum) is an important source of food and belongs to Poaceae family. Hypothetical proteins (HPs), i.e., proteins with unknown functions, share a substantial portion of wheat proteomes and play important roles in growth and physiology of plant system. Several functional annotations studies utilizing the protein sequences for characterization of role of individual protein in physiology of plant systems were being reported in recent past. In this study, an integrated pipeline of software/servers has been used for the identification and functional annotation of 124 unique HPs of T. aestivum considering available data in NCBI till date. All HPs were broadly annotated, out of which functions of 77 HPs were successfully assigned with high confidence level. Precisely functional annotation of remaining 47 HPs is also characterized with low confidence. Several latest versions of protein family databases, pathways information, genomics context methods and in silico tools were utilized to identify and assign function for individual HPs. Annotation result of several HPs mainly belongs to cellular protein, metabolic enzymes, binding proteins, transmembrane proteins, transcription factors and photosystem regulator proteins. Subsequently, functional analysis has revealed the role of few HPs in abiotic stress, which were further verified by phylogenetic analysis. The functionally associated proteins with each of above-mentioned abiotic stress-related proteins were identified through protein-protein interaction network analysis. The outcome of this study may be helpful for formulating general set pipeline/protocols for a better understanding of the role of HPs in physiological development of various plant systems.
TL;DR: The HA-GGE biplot analysis recognised the best test environments, restructured the ecological zones for lentil-rust testing, and identified stable sources of resistance for lentils rust disease, under multi-location and multi-year trials.
Abstract: Lentil rust incited by the fungus Uromyces viciae-fabae is a major impedance to lentil (Lens culinaris Medik.) production globally. Host-plant resistance is the most reliable, efficient and viable strategy among the various approaches to control this disease. In this study, 26 lentil genotypes comprising advanced breeding lines and released varieties along with a susceptible check were evaluated consecutively for rust resistance under natural incidence for two years and at five test locations in India. A heritability-adjusted genotype main effect plus genotype × environment interaction (HA-GGE) biplot program was used to analyse disease-severity data. The results revealed that, among the interactive factors, the GE interaction had the greatest impact (27.81%), whereas environment and genotype showed lower effects of 17.2% and 20.98%, respectively. The high GE variation made possible the evaluation of the genotypes at different test locations. The HA-GGE biplot method identified two sites (Gurdaspur and Pantnagar) as the ideal test environments in this study, with high efficiency for selection of durable and rust-resistant genotypes, whereas two other sites (Kanpur and Faizabad) were the least desirable test environments. In addition, the HA-GGE biplot analysis identified three distinct mega-environments for rust severity in India. Furthermore, the analysis identified three genotypes, DPL 62, PL 165 and PL 157, as best performing and durable for rust resistance in this study. The HA-GGE biplot analysis recognised the best test environments, restructured the ecological zones for lentil-rust testing, and identified stable sources of resistance for lentil rust disease, under multi-location and multi-year trials.
TL;DR: The existence of higher heterogeneity and genetic variability in S. sclerotiorum isolates collection is observed and indicates the presence of clonal and sexual progenies of the pathogen in the mustard growing regions of India surveyed in this study.
Abstract: White mold or stem rot disease are ubiquitously distributed throughout the world and the causal organism of this disease Sclerotinia sclerotiorum (Lib.) de Bary, is known to infect over 400 plant species. Sclerotinia stem rot is one of the most devastating fungal diseases and poses a serious threat to the worldwide cultivation of oilseed Brassica including India. S. sclerotiorum pathogen usually infects the stem but in severe cases leaves and pods also affected at different developmental stages that deteriorate not only the oil quality but also causing the seed and oil yield losses up to 90% depending on the severity of the disease infestation. This study investigated the morphological and molecular characterization of pathogenic S. sclerotiorum (Lib) de Bary geographical isolates from oilseed Brassica including Brassica juncea (Indian mustard). The aim of this study was to compare isolates of S. sclerotiorum originated from different agro-climatic conditions and to analyse similarity or differences between them as well as to examine the virulence of this pathogen specifically in Brassica for the first time. The collection of S. sclerotiorum isolates from symptomatic Brassica plants was done and analyzed for morphological features, and molecular characterization. The virulence evaluation test of 65 isolates on four Brassica cultivars has shown 5 of them were highly virulent, 46 were virulent and 14 were moderately virulent. Phylogenetic analysis encompassing all the morphological features, SSR polymorphism, and ITS sequencing has shown the existence of high genetic diversity among the isolates that categorized all the isolates in three evolutionary lineages in the derived dendrogram. Further, genetic variability analysis based on sequences variation in ITS region of all the isolates has shown the existence of either insertions or deletions of the nucleotides in the ITS region has led to the interspecies variability and observed the variation were in a clade-specific manner. Together this analysis observed the existence of higher heterogeneity and genetic variability in S. sclerotiorum isolates collection and indicates the presence of clonal and sexual progenies of the pathogen in the mustard growing regions of India surveyed in this study. With a higher level of genetic variability and diversity among the S. sclerotiorum population needs robust screening approaches to identify the donor parent and utilize them in resistance breeding program for effectively counter the menace of stem rot disease in Brassica.
TL;DR: In this article, the authors report genome-wide methylation profiles of pigeonpea sterile and fertile inbred lines and their fertile F1 hybrid at single base resolution, and identify differentially methylated regions (DMRs) in the fertile and sterile parent.
Abstract: DNA methylation is an important heritable landmark conferring epigenetic changes in hybrids and has fascinated biologists and plant-breeders over the years. Although epigenetic changes have been documented in rice and maize hybrids, such investigations have not been reported in pigeonpea. Here, we report genome-wide methylation profiles of pigeonpea sterile and fertile inbred lines and their fertile F1 hybrid at single base resolution. We found that pigeonpea genome is relatively enriched in CG methylation. Identification of differentially methylated regions (DMRs) in the sterile and fertile parent revealed remarkable differences between their methylation patterns. Investigation of methylation status of parental DMRs in hybrid revealed non-additive methylation patterns resulting from trans-chromosomal methylation and trans-chromosomal demethylation events. Furthermore, we discovered several DMRs negatively associated with gene expression in the hybrid and fertile parent. Interestingly, many of those DMRs belonged to transposable elements and genes encoding pentatricopeptide repeats associated proteins, which may mediate a role in modulating the genes impacting pollen fertility. Overall, our findings provide an understanding of two parental epigenomes interacting to give rise to an altered methylome in pigeonpea hybrids, from genome-wide point of view.
TL;DR: The present study believed to provide significant information of potential ligand inhibitors against VP-3 to design and develop the next generation malaria therapeutics through computational approach.
TL;DR: The panel exhibits considerable variation for SB resistance and also provides a good scope of marker-assisted selection using the identified SNP markers linked to resistant QTLs.
Abstract: Spot blotch (SB) caused by Bipolaris sorokiniana, is one of the most important diseases of wheat in the eastern part of south Asia causing considerable yield loss to the wheat crop. There is an urgent need to identify genetic loci closely associated with resistance to this pathogen for developing resistant cultivars. Hence, genomic regions responsible for SB resistance were searched using a wheat association mapping initiative (WAMI) panel involving 287 spring wheat genotypes of different origin. Genome-wide association mapping (GWAM) was performed using single nucleotide polymorphism (SNP) markers from a custom 90 K wheat SNP array. A mixed linear model (MLM) was used for assessing the association of SNP markers with spot blotch resistance in three consecutive years. Three traits were measured: incubation period, lesion number and area under the disease progress curve (AUDPC). Significant SNP markers were found linked to five, six and four quantitative trait loci (QTLs) for incubation period, lesion number and AUDPC respectively. They were detected on 11 different chromosomes: 1A, 1B, 1D, 4A, 5A, 5B, 6A, 6B, 6D, 7A, 7B with marker R2 range of 0.083 to 0.11. The greatest number of significant SNP-markers was found for lesion number and AUDPC on chromosome 6B and 5B, respectively, representing a better coverage of B-genome by SNPs. On the other hand, the most significant and largest SNP markers for incubation period were detected on 6A and 4A chromosomes indicating that this trait is associated with the A-genome of wheat. Although, QTLs for spot blotch resistance have been reported in wheat on these same chromosomes, the association of incubation period and lesion number with SB resistance has not been reported in previous studies. The panel exhibits considerable variation for SB resistance and also provides a good scope of marker-assisted selection using the identified SNP markers linked to resistant QTLs.
TL;DR: In this paper, the authors focused on the trends of national and regional rainfall anomalies (wetness/dryness) along with their interrelationship using time series data of past 158 years.
Abstract: Rainfall anomaly during crop-growing season can have large impact on the agricultural output of a country, especially like India, where two-thirds of the crop land is rain-fed. In such situation, decreased agricultural production not only challenges food security of the country but directly and immediately hits the livelihood of its farming community. In a vast country like India, rainfall or its anomalies hardly follow a specific pattern, rather it is having high variability in spatial domain. This study focused on the trends of national and regional rainfall anomalies (wetness/dryness) along with their interrelationship using time series data of past 158 years. The significant reducing wetness trend (p < 0.05) over north mountainous India was prominent with an increasing trend over southern peninsular India (p < 0.10). However, long-term annual wetness was increasing over entire peninsular India. The results of change point tests indicate that major abrupt changes occurred between early to mid-twentieth century having regional variations. The regional interrelationship was studied using principal component, hierarchical clustering, and pair-wise difference test, which clearly indicated a significantly different pattern in rainfall anomalies for north east India (p = 0.022), north central India (p = 0.022), and north mountainous India (p = 0.011) from that of the all India. Result of this study affirmed high spatial variability in rainfall anomaly and most importantly established the unalike pattern in trends of regional rainfall vis-a-vis national level, ushering towards paradigm shift in rainfall forecast from country scale to regional scale for pragmatic planning.
TL;DR: The results reemphasize the utility of satellite borne hyperspectral data to extract endmembers and delineate the potential of random forest as expert classifier to assess land cover with higher classification accuracy that outperformed the SVM by 19% and SAM by 27% in overall accuracy.
Abstract: The study was carried out for Indian capital city Delhi using Hyperion sensor onboard EO-1 satellite of NASA. After MODTRAN-4 based atmospheric correction, MNF, PPI and n-D visualizer were applied and endmembers of 11 LCLU classes were derived which were employed in classification of LULC. To incur better classification accuracy, a comparative study was also carried out to evaluate the potential of three classifier algorithms namely Random Forest (RF), Support Vector Machines (SVM) and Spectral Angle Mapper (SAM). The results of this study reemphasize the utility of satellite borne hyperspectral data to extract endmembers and also to delineate the potential of random forest as expert classifier to assess land cover with higher classification accuracy that outperformed the SVM by 19% and SAM by 27% in overall accuracy. This research work contributes positively to the issue of land cover classification through exploration of hyperspectral endmembers. The comparison of classification algorithms’ performance is valuable for decision makers to choose better classifier for more accurate information extraction.
02 Jan 2018
TL;DR: Significant association of NCPGR206 and H2L102 with the MSI trait and SSR markers GA9, TR31 and TA113 exhibited significant association with SCMR trait are discovered, which may help improve knowledge about the genetic architecture of HS tolerance in chickpea.
Abstract: Understanding genetic diversity and population structure is prerequisite to broaden the cultivated base of any crop. In the current investigation, we report discovery of a total of 319 alleles by assaying 81 SSRs on 71 chickpea genotypes. The cluster analysis based on Jaccard coefficient and unweighted neighbor joining algorithm categorized all genotypes into two major clusters. Cultivars grown within the same agro-climatic zones were clustered together, whereas the remaining genotypes particularly advanced breeding lines and accessions assigned to another cluster. Population structure analysis separated the entire collection into two subpopulations (K = 2) and the clustering pattern remained in close agreement with those of distance-based methods. Importantly, we also discovered marker trait association for membrane stability index (MSI) and leaf chlorophyll content measured as SPAD chlorophyll meter reading (SCMR), the two important physiological parameters indicative of heat stress (HS) tolerance in chickpea. Association analysis using both general linear and mixed linear models of the mean phenotypic data of traits recorded in 2016 and 2017 uncovered significant association of NCPGR206 and H2L102 with the MSI trait. Likewise, SSR markers GA9, TR31 and TA113 exhibited significant association with SCMR trait. The genomic regions putatively linked with two traits may be investigated in greater detail to further improve knowledge about the genetic architecture of HS tolerance in chickpea.
TL;DR: Variation in polyphenolic compounds, antioxidant activity, sugars and organic acid in 16 pummelo genotypes in India is determined.
TL;DR: Calcium fortification through vacuum impregnation technique for a widely acceptable potato based snack can be helpful in changing the perception of consumers for potato based snacks from the category of ‘Junk food to Healthy food’.
Abstract: Processed potato products such as potato chips are widely consumed among vulnerable (children and teenager), therefore can be used as an ideal carrier for targeted nutrient’s delivery i.e. macronutrient calcium. The present study was carried out to standardize the process for development of calcium fortified potato chips through vacuum impregnation technique and to explore the acceptability of developed product through storage study of 3 months period at ambient storage conditions (~ 250 °C, 51% RH) in LDPE (low density polyethylene) packaging. Fortification of potato chips was done at 15 mm Hg vacuum pressure with GRAS fortificant of calcium (calcium chloride, E509) using different combinations of blanching time, vacuum time, and restoration time as per Box–Behnken design of response surface methodology. optimization was done on the basis of fortified calcium content as well as hardness of the end product. Results showed optimized process conditions (calcium chloride at 1.05% level, blanching for 1.69 min, vacuum exposure for 14.99 min, and rest time of 15.80 min) can fortify potato chips at 700 mg/100 g of calcium level with acceptable sensory attributes. The standardized product was also evaluated for its structural attributes through surface electron microscopy, flavor (umami) compounds along with shelf life. The developed fortified product has 4.5 and 7.1 times higher calcium content than its control and commercial counterparts respectively. Storage studies parameters (FFA value, PV value, sensory attributes and non enzymatic browning) showed that the fortified potato chips were acceptable up to 60 days of storage at ambient condition. Thus, calcium fortification through vacuum impregnation technique for a widely acceptable potato based snacks can be helpful in changing the perception of consumers for potato based snacks from the category of ‘Junk food to Healthy food’.
TL;DR: An application of small area estimation (SAE) approach is described to improve the precision of estimates of poverty incidence at district level in the State of Bihar in India by linking data from the Household Consumer Expenditure Survey 2011–12 of NSSO and the Population Census 2011.
Abstract: Poverty affects many people, but the ramifications and impacts affect all aspects of society. Information about the incidence of poverty is therefore an important parameter of the population for policy analysis and decision making. In order to provide specific, targeted solutions when addressing poverty disadvantage small area statistics are needed. Surveys are typically designed and planned to produce reliable estimates of population characteristics of interest mainly at higher geographic area such as national and state level. Sample sizes are usually not large enough to provide reliable estimates for disaggregated analysis. In many instances estimates are required for areas of the population for which the survey providing the data was unplanned. Then, for areas with small sample sizes, direct survey estimation of population characteristics based only on the data available from the particular area tends to be unreliable. This paper describes an application of small area estimation (SAE) approach to improve the precision of estimates of poverty incidence at district level in the State of Bihar in India by linking data from the Household Consumer Expenditure Survey 2011–12 of NSSO and the Population Census 2011. The results show that the district level estimates generated by SAE method are more precise and representative. In contrast, the direct survey estimates based on survey data alone are less stable.
TL;DR: The developed computational method is expected to supplement the currently available approaches for prediction of HSPs, to the extent of their families and sub-types, and achieve higher accuracy as compared to most of the existing approaches.
Abstract: Heat shock proteins (HSPs) play a pivotal role in cell growth and variability. Since conventional approaches are expensive and voluminous protein sequence information are available in the post-genomic era, development of an automated and accurate computational tool is highly desirable for prediction of HSPs, their families and sub-types. Thus, we propose a computational approach for reliable prediction of all these components in a single framework and with higher accuracy as well. The proposed approach achieved an overall accuracy of ~84% in predicting HSPs, ~97% in predicting six different families of HSPs and ~94% in predicting four types of DnaJ proteins, with bench mark datasets. The developed approach also achieved higher accuracy as compared to most of the existing approaches. For easy prediction of HSPs by experimental scientists, a user friendly web server ir-HSP is freely accessible at http://cabgrid.res.in:8080/ir-hsp. The ir-HSP was further evaluated for proteome-wide identification of HSPs by using proteome datasets of eight different species, and ~50% of the predicted HSPs in each species were found to be annotated with InterPro HSP families/domains. Thus, the developed computational method is expected to supplement the currently available approaches for HSP prediction to the extent of families and sub-types. Key words: Molecular chaperones, Heat shock, Protein folding, Machine learning, Di-peptide composition, DnaJ proteins
Journal Article•
TL;DR: In this paper, a hybrid model has been proposed which consists of linear and non-linear models to forecast yield of mango and banana of Karnataka, and the hybrid model with the combination of ARIMA and Support Vector Regression model performed better in both model building as well as in model validation as compared to other models.
Abstract: Horticulture sector plays a prominent role in economic growth for most of the developing countries. India is the largest producer of fruits and vegetables in the world next only to China. Among the horticultural crops, fruit crops are cultivated in majority of the area. Fruit crops play a significant role in the economic development, nutritional security, employment generation, and overall growth of a country. Among fruit crops, mango and banana are largest producing fruits of India. Generally, Karnataka is called as the horticultural state of India. In Karnataka, mango and banana are highest producing fruit crops. With these prospective, yield of mango and banana of Karnataka have been chosen as study variables. Forecasting is a primary aspect of developing economy so that proper planning can be undertaken for sustainable growth of the country. In this study, classes of linear and nonlinear, parametric and non-parametric statistical models have been employed to forecast yield of mango and banana of Karnataka. The major drawback of linear models is the presumed linear form of the model. In most of the cases, the time series are not purely linear or nonlinear as they contain both linear and nonlinear components. To overcome this problem a hybrid model has been proposed which consists of linear and nonlinear models. The hybrid model with the combination of Autoregressive Integrated Moving Average (ARIMA) and Support Vector Regression model performed better in both model building as well as in model validation as compared to other models.
TL;DR: An approach, which is first of its kind for the computational identification of nif proteins encoded by the six categories of nIf genes, was proposed and achieved >92% accuracy, while evaluated with blind (independent) test datasets.
Abstract: As inorganic nitrogen compounds are essential for basic building blocks of life (e.g., nucleotides and amino acids), the role of biological nitrogen-fixation (BNF) is indispensible. All nitrogen fixing microbes rely on the same nitrogenase enzyme for nitrogen reduction, which is in fact an enzyme complex consists of as many as 20 genes. However, the occurrence of six genes viz., nifB, nifD, nifE, nifH, nifK and nifN has been proposed to be essential for a functional nitrogenase enzyme. Therefore, identification of these genes is important to understand the mechanism of BNF as well as to explore the possibilities for improving BNF from agricultural sustainability point of view. Further, though the computational tools are available for the annotation and phylogenetic analysis of nifH gene sequences alone, to the best of our knowledge no tool is available for the computational prediction of the above mentioned six categories of nitrogen-fixation (nif) genes or proteins. Thus, we proposed an approach, which is first of its kind for the computational identification of nif proteins encoded by the six categories of nif genes. Sequence-derived features were employed to map the input sequences into vectors of numeric observations that were subsequently fed to the support vector machine as input. Two types of classifier were constructed: (i) a binary classifier for classification of nif and non-nitrogen-fixation (non-nif) proteins, and (ii) a multi-class classifier for classification of six categories of nif proteins. Higher accuracies were observed for the combination of composition-transition-distribution (CTD) feature set and radial kernel, as compared to the other feature-kernel combinations. The overall accuracies were observed >90% in both binary and multi-class classifications. The developed approach further achieved >92% accuracy, while evaluated with blind (independent) test datasets. The developed approach also produced higher accuracy in identifying nif proteins, while evaluated using proteome-wide datasets of several species. Furthermore, we established a prediction server nifPred (http://webapp.cabgrid.res.in/nifPred) to assist the scientific community for proteome-wide identification of six categories of nif proteins. Besides, the source code of nifPred is also available at https://github.com/PrabinaMeher/nifPred. The developed web server is expected to supplement the transcriptional profiling and comparative genomics studies for the identification
TL;DR: The empirical results show that when data are spatially non-stationary the proposed small area predictor outperforms other area level estimators in common use and that the proposed mean squared error estimator tracks the actualmean squared error reasonably well, with confidence intervals based on it achieving close to nominal coverage.
TL;DR: An attempt has been made in cluster bean for the first time to computationally identify lncRNAs based on a proposed index and study their targeted genes for their role in various biological processes like stress mechanisms, DNA damage repair, cell wall synthesis.