Indian Agricultural Research Institute

This paper reports the genome sequence of domesticated tomato, a major crop plant, and a draft sequence for its closest wild relative; comparative genomics reveal very little divergence between the two genomes but some important differences with the potato genome, another important food crop in the genus Solanum. Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

Crop models are essential tools for assessing the threat of climate change to local and global food production. Present models used to predict wheat grain yield are highly uncertain when simulating how crops respond to temperature. Here we systematically tested 30 different wheat crop models of the Agricultural Model Intercomparison and Improvement Project against field experiments in which growing season mean temperatures ranged from 15 °C to 32 °C, including experiments with artificial heating. Many models simulated yields well, but were less accurate at higher temperatures. The model ensemble median was consistently more accurate in simulating the crop temperature response than any single model, regardless of the input information used. Extrapolating the model ensemble temperature response indicates that warming is already slowing yield gains at a majority of wheat-growing locations. Global wheat production is estimated to fall by 6% for each °C of further temperature increase and become more variable over space and time.

An ordered draft sequence of the 17-gigabase hexaploid bread wheat ( Triticum aestivum ) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.

One‐fifth of irrigated agriculture is adversely affected by soil salinity. Hence, developing salt‐tolerant crops is essential for sustaining food production. Progress in breeding for salt‐tolerant crops has been hampered by the lack of understanding of the molecular basis of salt tolerance and lack of availability of genes that confer salt tolerance. Genetic evidence suggests that perception of salt stress leads to a cytosolic calcium‐signal that activates the calcium sensor protein SOS3. SOS3 binds to and activates a ser/thr protein kinase SOS2. The activated SOS2 kinase regulates activities of SOS1, a plasma membrane Na + /H + antiporter, and NHX1, a tonoplast Na + /H + antiporter. This results in Na + efflux and vacuolar compartmentation. A putative osmosensory histidine kinase (AtHK1)‐MAPK cascade probably regulates osmotic homeostasis and ROS scavenging. Osmotic stress and ABA (abscisic acid)‐mediated regulation of LEA (late‐embryogenesis‐abundant)‐type proteins also play important roles in plant salt tolerance. Genetic engineering of ion transporters and their regulators, and of the CBF (C‐repeat‐binding factor) regulons, holds promise for future development of salt‐tolerant crops.

Knowledge about germplasm diversity and genetic relationships among breeding materials could be an invaluable aid in crop improvement strategies. A number of methods are currently available for analysis of genetic diversity in germplasm accessions, breeding lines, and populations. These methods have relied on pedigree data, morphological data, agronomic performance data, biochemical data, and more recently molecular (DNA‐based) data. For reasonably accurate and unbiased estimates of genetic diversity, adequate attention has to be devoted to (i) sampling strategies; (ii) utilization of various data sets on the basis of the understanding of their strengths and constraints; (iii) choice of genetic distance measure(s), clustering procedures, and other multivariate methods in analyses of data; and (iv) objective determination of genetic relationships. Judicious combination and utilization of statistical tools and techniques, such as bootstrapping, is vital for addressing complex issues related to data analysis and interpretation of results from different types of data sets, particularly through clustering procedures. This review focuses on application of statistical tools and techniques in analysis of genetic diversity at the intraspecific level in crop plants.

Abstract Some of the most exciting research in the last decade has been the discovery of a group of nutrients, which have protective effects against cell oxidation. These naturally occurring compounds impart bright colour to fruits and vegetables and act as antioxidants in the body by scavenging harmful free radicals, which are implicated in most degenerative diseases. Epidemiological studies have established a positive correlation between the intake of fruits and vegetables and prevention of diseases like atheroscelerosis, cancer, diabetes, arthritis and also ageing. So pronounced has been their effect on ageing that they have been called ‘fountains of youth’. Fruits and vegetables have thus had conferred on them the status of ‘functional foods’, capable of promoting good health and preventing or alleviating diseases. Phenolic flavonoids, lycopene, carotenoids and glucosinolates are among the most thoroughly studied antioxidants. The present review highlights the potential of fruits and vegetables rich in antioxidants, their health benefits and the effect of processing on the bioavailability of these nutrients. The paper also reviews some of the important methods used to determine the antioxidant activity.

Abstract The anti-oxidant activity of extracts from 36 vegetables was evaluated by using a model system consisting of β-carotene and linoleic acid. The total phenolics of the extracts was determined spectrophotometrically according to the Folin–Ciocalteau procedure and ranged from 34 to 400 mg (100 g)−1 on a fresh weight basis. Mint, aonla, black carrots, chenopodium, fenugreek, kachnar and ginger had high phenolic contents. The anti-oxidant activity expressed as per percent inhibition of oxidation ranged from a high of 92% in turmeric extracts to a low of 12.8% in long melon. Other vegetables found to have high anti-oxidant activity (>70%) were kachnar, aonla, ginger, fenugreek, mint, beetroot, black carrots, Brussels sprouts, broccoli, lotus stem, yam, coriander and tomato. Anti-oxidant activity correlated significantly and positively with total phenolics (r2=0.6578, P < 0.05). The results indicate that vegetables containing high phenolics may provide a source of dietary anti-oxidants.

Educational institutes across the world have closed due to the COVID-19 pandemic jeopardizing the academic calendars. Most educational institutes have shifted to online learning platforms to keep the academic activities going. However, the questions about the preparedness, designing and effectiveness of e-learning is still not clearly understood, particularly for a developing country like India, where the technical constraints like suitability of devices and bandwidth availability poses a serious challenge. In this study, we focus on understanding Agricultural Student's perception and preference towards the online learning through an online survey of 307 students. We also explored the student's preferences for various attributes of online classes, which will be helpful to design effective online learning environment. The results indicated that majority of the respondents (70%) are ready to opt for online classes to manage the curriculum during this pandemic. Majority of the students preferred to use smart phone for online learning. Using content analysis, we found that students prefer recorded classes with quiz at the end of each class to improve the effectiveness of learning. The students opined that flexibility and convenience of online classes makes it attractive option, whereas broadband connectivity issues in rural areas makes it a challenge for students to make use of online learning initiatives. However, in agricultural education system where many courses are practical oriented, shifting completely to online mode may not be possible and need to device a hybrid mode, the insights from this article can be helpful in designing the curriculum for the new normal.

Lead (Pb) toxicity has been a subject of interest for environmental scientists due to its toxic effect on plants, animals, and humans. An increase in several Pb related industrial activities and use of Pb containing products such as agrochemicals, oil and paint, mining, etc. can lead to Pb contamination in the environment and thereby, can enter the food chain. Being one of the most toxic heavy metals, Pb ingestion via the food chain has proven to be a potential health hazard for plants and humans. The current review aims to summarize the research updates on Pb toxicity and its effects on plants, soil, and human health. Relevant literature from the past 20 years encompassing comprehensive details on Pb toxicity has been considered with key issues such as i) Pb bioavailability in soil, ii) Pb biomagnification, and iii) Pb- remediation, which has been addressed in detail through physical, chemical, and biological lenses. In the review, among different Pb-remediation approaches, we have highlighted certain advanced approaches such as microbial assisted phytoremediation which could possibly minimize the Pb load from the resources in a sustainable manner and would be a viable option to ensure a safe food production system.

This open access edited book is a collection of 21 chapters synthesized from nearly 100 lectures by >70 eminent international and Indian experts.

, are widely spread in nature and have severely contaminated food supplies of humans and animals, resulting in health hazards and even death. Therefore, there is great demand for aflatoxins research to develop suitable methods for their quantification, precise detection and control to ensure the safety of consumers' health. Here, the chemistry and biosynthesis process of the mycotoxins is discussed in brief along with their occurrence, and the health hazards to humans and livestock. This review focuses on resources, production, detection and control measures of aflatoxins to ensure food and feed safety. The review is informative for health-conscious consumers and research experts in the fields. Furthermore, providing knowledge on aflatoxins toxicity will help in ensure food safety and meet the future demands of the increasing population by decreasing the incidence of outbreaks due to aflatoxins.

Summary Geminiviruses form the second largest family of plant viruses, the Geminiviridae , represented by four genera: Mastrevirus, Curtovirus, Topocuvirus and Begomovirus . During the last two decades these viruses have emerged as devastating pathogens, particularly in the tropics and subtropics, causing huge economic losses and threatening crop production. Epidemics caused by re‐emerging and newly emerging geminiviruses are becoming frequent even in regions that were earlier free from these viruses. Compared to mastreviruses and curtoviruses, begomoviruses have emerged as more serious problems in a variety of crops, for example, cassava, cotton, grain legumes and vegetables. Major contributory factors for the emergence and spread of new geminivirus diseases are the evolution of variants of the viruses, the appearance of the whitefly ‘B’ biotype and the increase in the vector population. Variability in geminiviruses has arisen through mutations, recombination and pseudorecombination. Genomic recombination in geminiviruses, not only between the variants of the same virus but also between species and even between genera, has resulted in rapid diversification. From the disease point of view, most virulent variants have developed through recombination of viral genomes such as those associated with cassava mosaic, cotton leaf curl, and tomato leaf curl diseases. Heterologous recombinants containing parts of the host genome and/or sequences from satellite‐like molecules associated with monopartite begomoviruses provide unlimited evolutionary opportunities. Human activity has also played an important role in the emergence of serious geminivirus diseases across the globe, like the changes in cropping systems, the introduction of new crops, the movement of infected planting materials and the introduction of host susceptibility genes through the exchange of germplasm.

Potential consequences of climate change on crop production can be studied using mechanistic crop simulation models. While a broad variety of maize simulation models exist, it is not known whether different models diverge on grain yield responses to changes in climatic factors, or whether they agree in their general trends related to phenology, growth, and yield. With the goal of analyzing the sensitivity of simulated yields to changes in temperature and atmospheric carbon dioxide concentrations [CO2 ], we present the largest maize crop model intercomparison to date, including 23 different models. These models were evaluated for four locations representing a wide range of maize production conditions in the world: Lusignan (France), Ames (USA), Rio Verde (Brazil) and Morogoro (Tanzania). While individual models differed considerably in absolute yield simulation at the four sites, an ensemble of a minimum number of models was able to simulate absolute yields accurately at the four sites even with low data for calibration, thus suggesting that using an ensemble of models has merit. Temperature increase had strong negative influence on modeled yield response of roughly -0.5 Mg ha(-1) per °C. Doubling [CO2 ] from 360 to 720 μmol mol(-1) increased grain yield by 7.5% on average across models and the sites. That would therefore make temperature the main factor altering maize yields at the end of this century. Furthermore, there was a large uncertainty in the yield response to [CO2 ] among models. Model responses to temperature and [CO2 ] did not differ whether models were simulated with low calibration information or, simulated with high level of calibration information.

BACKGROUND: MADS-box transcription factors, besides being involved in floral organ specification, have also been implicated in several aspects of plant growth and development. In recent years, there have been reports on genomic localization, protein motif structure, phylogenetic relationships, gene structure and expression of the entire MADS-box family in the model plant system, Arabidopsis. Though there have been some studies in rice as well, an analysis of the complete MADS-box family along with a comprehensive expression profiling was still awaited after the completion of rice genome sequencing. Furthermore, owing to the role of MADS-box family in flower development, an analysis involving structure, expression and functional aspects of MADS-box genes in rice and Arabidopsis was required to understand the role of this gene family in reproductive development. RESULTS: A genome-wide molecular characterization and microarray-based expression profiling of the genes encoding MADS-box transcription factor family in rice is presented. Using a thorough annotation exercise, 75 MADS-box genes have been identified in rice and categorized into MIKCc, MIKC*, Malpha, Mbeta and Mgamma groups based on phylogeny. Chromosomal localization of these genes reveals that 16 MADS-box genes, mostly MIKCc-type, are located within the duplicated segments of the rice genome, whereas most of the M-type genes, 20 in all, seem to have resulted from tandem duplications. Nine members belonging to the Mbeta group, which was considered absent in monocots, have also been identified. The expression profiles of all the MADS-box genes have been analyzed under 11 temporal stages of panicle and seed development, three abiotic stress conditions, along with three stages of vegetative development. Transcripts for 31 genes accumulate preferentially in the reproductive phase, of which, 12 genes are specifically expressed in seeds, and six genes show expression specific to panicle development. Differential expression of seven genes under stress conditions is also evident. An attempt has been made to gain insight into plausible functions of rice MADS-box genes by collating the expression data of functionally validated genes in rice and Arabidopsis. CONCLUSION: Only a limited number of MADS genes have been functionally validated in rice. A comprehensive annotation and transcriptome profiling undertaken in this investigation adds to our understanding of the involvement of MADS-box family genes during reproductive development and stress in rice and also provides the basis for selection of candidate genes for functional validation studies.

BACKGROUND: The MYB gene family comprises one of the richest groups of transcription factors in plants. Plant MYB proteins are characterized by a highly conserved MYB DNA-binding domain. MYB proteins are classified into four major groups namely, 1R-MYB, 2R-MYB, 3R-MYB and 4R-MYB based on the number and position of MYB repeats. MYB transcription factors are involved in plant development, secondary metabolism, hormone signal transduction, disease resistance and abiotic stress tolerance. A comparative analysis of MYB family genes in rice and Arabidopsis will help reveal the evolution and function of MYB genes in plants. RESULTS: A genome-wide analysis identified at least 155 and 197 MYB genes in rice and Arabidopsis, respectively. Gene structure analysis revealed that MYB family genes possess relatively more number of introns in the middle as compared with C- and N-terminal regions of the predicted genes. Intronless MYB-genes are highly conserved both in rice and Arabidopsis. MYB genes encoding R2R3 repeat MYB proteins retained conserved gene structure with three exons and two introns, whereas genes encoding R1R2R3 repeat containing proteins consist of six exons and five introns. The splicing pattern is similar among R1R2R3 MYB genes in Arabidopsis. In contrast, variation in splicing pattern was observed among R1R2R3 MYB members of rice. Consensus motif analysis of 1kb upstream region (5' to translation initiation codon) of MYB gene ORFs led to the identification of conserved and over-represented cis-motifs in both rice and Arabidopsis. Real-time quantitative RT-PCR analysis showed that several members of MYBs are up-regulated by various abiotic stresses both in rice and Arabidopsis. CONCLUSION: A comprehensive genome-wide analysis of chromosomal distribution, tandem repeats and phylogenetic relationship of MYB family genes in rice and Arabidopsis suggested their evolution via duplication. Genome-wide comparative analysis of MYB genes and their expression analysis identified several MYBs with potential role in development and stress response of plants.

Agricultural crop residue burning contribute towards the emission of greenhouse gases (CO2, N2O, CH4), air pollutants (CO, NH3, NOx, SO2, NMHC, volatile organic compounds), particulates matter and smoke thereby posing threat to human health. In the present study a state-wise inventory of crop residue burnt in India and the air pollutants emitted was prepared using the Inter-Governmental Panel on Climate Change (IPCC) national inventory preparation guidelines for the year 2008–09. Total amount of residue generated in 2008–09 was 620 Mt out of which ~15.9% residue was burnt on farm. Rice straw contributed 40% of the total residue burnt followed by wheat straw (22%) and sugarcane trash (20%). Burning of crop residues emitted 8.57 Mt of CO, 141.15 Mt of CO2, 0.037 Mt of SOx, 0.23 Mt of NOx, 0.12 Mt of NH3 and 1.46 Mt NMVOC, 0.65 Mt of NMHC, 1.21 Mt of particulate matter for the year 2008–09. The variability of 21.46% in annual emission of air pollutants was observed from 1995 to 2009.

Soil degradation in India is estimated to be occurring on 147 million hectares (Mha) of land, including 94 Mha from water erosion, 16 Mha from acidification, 14 Mha from flooding, 9 Mha from wind erosion, 6 Mha from salinity, and 7 Mha from a combination of factors. This is extremely serious because India supports 18% of the world’s human population and 15% of the world’s livestock population, but has only 2.4% of the world’s land area. Despite its low proportional land area, India ranks second worldwide in farm output. Agriculture, forestry, and fisheries account for 17% of the gross domestic product and employs about 50% of the total workforce of the country. Causes of soil degradation are both natural and human-induced. Natural causes include earthquakes, tsunamis, droughts, avalanches, landslides, volcanic eruptions, floods, tornadoes, and wildfires. Human-induced soil degradation results from land clearing and deforestation, inappropriate agricultural practices, improper management of industrial effluents and wastes, over-grazing, careless management of forests, surface mining, urban sprawl, and commercial/industrial development. Inappropriate agricultural practices include excessive tillage and use of heavy machinery, excessive and unbalanced use of inorganic fertilizers, poor irrigation and water management techniques, pesticide overuse, inadequate crop residue and/or organic carbon inputs, and poor crop cycle planning. Some underlying social causes of soil degradation in India are land shortage, decline in per capita land availability, economic pressure on land, land tenancy, poverty, and population increase. In this review of land degradation in India, we summarize (1) the main causes of soil degradation in different agro-climatic regions; (2) research results documenting both soil degradation and soil health improvement in various agricultural systems; and (3) potential solutions to improve soil health in different regions using a variety of conservation agricultural approaches.

Industrially produced N-fertilizer is essential to the production of cereals that supports current and projected human populations. We constructed a top-down global N budget for maize, rice, and wheat for a 50-year period (1961 to 2010). Cereals harvested a total of 1551 Tg of N, of which 48% was supplied through fertilizer-N and 4% came from net soil depletion. An estimated 48% (737 Tg) of crop N, equal to 29, 38, and 25 kg ha(-1) yr(-1) for maize, rice, and wheat, respectively, is contributed by sources other than fertilizer- or soil-N. Non-symbiotic N2 fixation appears to be the major source of this N, which is 370 Tg or 24% of total N in the crop, corresponding to 13, 22, and 13 kg ha(-1) yr(-1) for maize, rice, and wheat, respectively. Manure (217 Tg or 14%) and atmospheric deposition (96 Tg or 6%) are the other sources of N. Crop residues and seed contribute marginally. Our scaling-down approach to estimate the contribution of non-symbiotic N2 fixation is robust because it focuses on global quantities of N in sources and sinks that are easier to estimate, in contrast to estimating N losses per se, because losses are highly soil-, climate-, and crop-specific.

Antibiotic is one of the most significant discoveries and have brought a revolution in the field of medicine for human therapy. In addition to the medical uses, antibiotics have broad applications in agriculture and animal husbandry. In developing nations, antibiotics use have helped to increase the life expectancy by lowering the deaths due to bacterial infections, but the risks associated with antibiotics pollution is largely affecting people. Since antibiotics are released partially degraded and undegraded into environment creating antibiotic pollution, and its bioremediation is a challenging task. In the present review, we have discussed the primary antibiotic sources like hospitals, dairy, and agriculture causing antibiotic pollution and their innovative detection methods. The strong commitment towards the resistance prevention and participation, nations through strict policies and their implementations now come to fight against the antibiotic resistance under WHO. The review also deciphers the bacterial evolution based strategies to overcome the effects of antibiotics, so the antibiotic degradation and elimination from the environment and its health benefits. The present review focuses on the environmental sources of antibiotics, it's possible degradation mechanisms, health effects, and bacterial antibiotics resistance mechanisms.

Abstract Wheat grain protein concentration is an important determinant of wheat quality for human nutrition that is often overlooked in efforts to improve crop production. We tested and applied a 32‐multi‐model ensemble to simulate global wheat yield and quality in a changing climate. Potential benefits of elevated atmospheric CO 2 concentration by 2050 on global wheat grain and protein yield are likely to be negated by impacts from rising temperature and changes in rainfall, but with considerable disparities between regions. Grain and protein yields are expected to be lower and more variable in most low‐rainfall regions, with nitrogen availability limiting growth stimulus from elevated CO 2 . Introducing genotypes adapted to warmer temperatures (and also considering changes in CO 2 and rainfall) could boost global wheat yield by 7% and protein yield by 2%, but grain protein concentration would be reduced by −1.1 percentage points, representing a relative change of −8.6%. Climate change adaptations that benefit grain yield are not always positive for grain quality, putting additional pressure on global wheat production.