Kapil K. Tiwari

Bio: Kapil K. Tiwari is an academic researcher from Sardarkrushinagar Dantiwada Agricultural University. The author has contributed to research in topics: Microsatellite & Genetic diversity. The author has an hindex of 6, co-authored 11 publications receiving 285 citations.

Genome-wide association mapping of salinity tolerance in rice (Oryza sativa)

Abstract: Salinity tolerance in rice is highly desirable to sustain production in areas rendered saline due tovarious reasons. It is a complex quantitative trait having different components, which can be dissected effectively by genome-wide association study (GWAS). Here, we implemented GWAS to identify loci controlling salinity tolerance in rice. A custom-designed array based on 6,000 single nucleotide polymorphisms (SNPs) in as many stress-responsive genes, distributed at an average physical interval of <100 kb on 12 rice chromosomes, was used to genotype 220 rice accessions using Infinium highthroughput assay. Genetic association was analysed with 12 different traits recorded on these accessions under field conditions at reproductive stage. We identified 20 SNPs (loci) significantly associated with Na + /K + ratio, and 44 SNPs with other traits observed under stress condition. The loci identified for various salinity indices through GWAS explained 5–18% of the phenotypic variance. The region harbouring Saltol, a major quantitative trait loci (QTLs) on chromosome 1 in rice, which is known to control salinity tolerance at seedling stage, was detected as a major association with Na + / K + ratio measured at reproductive stage in our study. In addition to Saltol, we also found GWAS peaks representing new QTLs on chromosomes 4, 6 and 7. The current association mapping panel contained mostly indica accessions that can serve as source of novel salt tolerance genes and alleles. The gene-based SNP array used in this study was found cost-effective and efficient in unveiling genomic regions/candidate genes regulating salinity stress tolerance in rice.

Identification of a diverse mini‐core panel of Indian rice germplasm based on genotyping using microsatellite markers

Abstract: Identification of a small core germplasm set representing the available genetic diversity is essential for its proper evaluation and subsequent utilization in rice improvement programmes. For constituting a small diverse mini-core panel of Indian rice germplasm, a representative set of 6912 accessions drawn based on their geographic origin from the whole rice germplasm collection available in the National Gene Bank was genotyped using 36 microsatellite markers. Automated fragment analysis of amplicons yielded a total of 435 alleles, with an average 12.4 and range of 3–29 alleles per locus. Polymorphism information content (PIC) ranged from 0.08 (RGNMS190) to 0.86 (RM552) with an average of 0.528. Based on genotyping data, a mini-core consisting of 98 genotypes was identified. Ninety-four per cent of the alleles present in the core set were present in the mini-core. The identified small but diverse panel will be useful for further intensive trait-specific evaluation and utilization in allele mining.

A set of SCAR markers in cluster bean ( Cyamopsis tetragonoloba L. Taub) genotypes

Abstract: Cluster bean, one of the most important cash legume crop has played an increasingly important role in wide range of industries. Owing to the significance of molecular marker studies in numerous applications including in genetic improvement of crops, there is an obvious need to undertake such studies in cluster bean. In the present work, 35 genotypes of cluster bean were collected from different states of India and analyzed using RAPD and ISSR markers. Further SCAR marker system was introduced in order to increase the reproducibility of the polymorphism and specificity. For this polymorphic (RP-3, 1000 bp; RP-19, 1250 bp and 1100 bp) and geographical specific bands (RP-9, 650 bp) from RAPD as well as genotype specific band (IS-8, 550 bp) from genotype RGC-1031 (Rajasthan) from ISSR were selected and converted into SCAR markers. The study revealed first set of sequence-based SCAR markers in cluster bean which found more specific information using RAPD and ISSR profiles. One genotype specific SCAR-20 for RGC-1031 (tolerant genotype against Macrophomina phaseolina), could be used to prove identity of the genotype for improvement as well for its genetic purity assessment. Another SCAR-8 was selected due to its specificity for cluster bean genotypes from Rajasthan which might be important for population admixture studies.

Genetic diversity analysis and molecular characterization of grain amaranth genotypes using inter simple sequence repeat (ISSR) markers

Abstract: Grain amaranth (Amaranthus spp.) has been cultivated since ancient times in some countries in the world and it is one of the oldest food crops. At present, the crop has gained more importance in the plains of India, especially in parts of Gujarat and Maharashtra. Grain amaranth exhibits an incredible extent of morphological diversity and an extensive adaptability to diverse eco-geographical conditions. Hence, the aim of the recent research was to evaluate the genetic diversity of 19 genotypes from four diverse species of Amaranthus from India using ISSR markers. The set of 11 polymorphic ISSR primers produced a total of 114 amplicons, among which 98 amplicons were polymorphic. The mean number of polymorphic amplicons per primer was 8.91. Overall, the size of PCR-amplified DNA fragments ranged from 200 to 3702 bp. The average percent polymorphism was 87.15%, and the average PIC value was 0.853, which indicates good selection of primers in the present study for the assessment of genetic diversity. The unique amplicon (marker)-producing primers were also found which can be used for identification of genotypes. The dendrogram grouped 19 grain amaranth genotypes into two major clusters. The groups formed on the principle component analysis (PCA) plot resembles with the results of the dendrogram although some genotypes have been diverted on the PCA plot. The technique may be used to obtain reasonably precise information on the genetic relationship among grain amaranth genotypes. Such information may be useful for selecting the diverse parents and monitoring the genetic diversity periodically in the breeder’s working collection of grain amaranth.

Impact of Climate Change on Crops Adaptation and Strategies to Tackle Its Outcome: A Review.

Abstract: Agriculture and climate change are internally correlated with each other in various aspects, as climate change is the main cause of biotic and abiotic stresses, which have adverse effects on the agriculture of a region. The land and its agriculture are being affected by climate changes in different ways, e.g., variations in annual rainfall, average temperature, heat waves, modifications in weeds, pests or microbes, global change of atmospheric CO2 or ozone level, and fluctuations in sea level. The threat of varying global climate has greatly driven the attention of scientists, as these variations are imparting negative impact on global crop production and compromising food security worldwide. According to some predicted reports, agriculture is considered the most endangered activity adversely affected by climate changes. To date, food security and ecosystem resilience are the most concerning subjects worldwide. Climate-smart agriculture is the only way to lower the negative impact of climate variations on crop adaptation, before it might affect global crop production drastically. In this review paper, we summarize the causes of climate change, stresses produced due to climate change, impacts on crops, modern breeding technologies, and biotechnological strategies to cope with climate change, in order to develop climate resilient crops. Revolutions in genetic engineering techniques can also aid in overcoming food security issues against extreme environmental conditions, by producing transgenic plants.

Plant abiotic stress challenges from the changing environment

Abstract: The challenges of abiotic stress on plant growth and development are evident among the emerging ecological impacts of climate change (Bellard et al., 2012), and the constraints to crop production exacerbated with the increasing human population competing for environmental resources (Wallace et al., 2003). Climate change is predicted to affect agricultural production the most, primarily at low latitudes populated by developing countries, with adverse effects of increasing carbon dioxide and high temperature, challenging researchers toward devising adaptation strategies (Rosenzweig et al., 2014). These constraints to global food supply and a balanced environment encourage research and development of climate smart crops, resilient to climate change (Wheeler and Von Braun, 2013). The field of plant abiotic stress encompasses all studies on abiotic factors or stressors from the environment that can impose stress on a variety of species (Sulmon et al., 2015). These stressors include extreme levels of light (high and low), radiation (UV-B and UV-A), temperature [high and low (chilling, freezing)], water (drought, flooding, and submergence), chemical factors (heavy metals and pH), salinity due to excessive Na+, deficient or in excess of essential nutrients, gaseous pollutants (ozone, sulfur dioxide), mechanical factors, and other less frequently occurring stressors. Since combinations of these stresses such as heat and drought frequently occur under field conditions, and can cause unique effects that cannot be predicted from individual stressors (Suzuki et al., 2014), a multiplicity of physiological interactions can be expected, needing individual novel solutions. Plants are rooted in the environment they grow in, and have to adapt to the changing conditions brought about by the multitude of environmental factors, with extreme levels eliciting abiotic stress. A grand challenge in abiotic stress biology is to decipher how plants perceive the different stressors, how the early signals are transduced within the plant, what is the diversity of response pathways elicited by them, and how are they genetically determined (Yoshida et al., 2014). Beyond model plants and reference genotypes, the challenge is to identify how signaling pathways have evolved within a species to program a suite of responses differing in signals and regulatory networks, and constitute genotypes that are adapted to specific stressful environments. Many studies have begun to deal with the comparison of a few genotypes, such as tolerant and sensitive within a species, for the analysis of differential responses to a defined stress. Since these responses can be due to differences in sets of genes, an understanding of the diversity in signaling pathways can come only by making a systems level study of the differences between genotypes. Such comparative studies offer a challenge for the integration of diverse functional genomics datasets of gene expression, metabolomics, and stress physiological responses to make comparisons in the network of responses across genotypes. A compatible environment for one plant genotype may not be for another, and all external factors abiotic or biotic, can raise a challenge or stress to the plant depending on the plants genetic constitution and adaptive response. The specific genotype × environment interaction combinations offer multitude of effects in response to the environment (Des Marais et al., 2013). Molecular genetic analysis of specific genes conferring stress tolerance from tolerant crop accessions have resulted in the map-based isolation of genes for submergence tolerance (Xu et al., 2006) and salt tolerance (Ren et al., 2005) in rice, among many others. The challenge ahead is in the analysis of natural variation in populations using genome wide association studies (GWAS) to dissect quantitative traits from field screens of diverse genotypes and map specific naturally occurring “stress tolerant loci.” This has been successful for salt tolerance (Kumar et al., 2015) in rice, and also led to the identification from maize of the first drought tolerance gene (Mao et al., 2015). The variation within the maize drought tolerance gene is particularly interesting because the drought sensitive allele contains a transposon insert in the promoter that is involved in epigenetic regulation of the gene that differs in distribution between temperate and tropical maize. Transposons as agents of regulation of genes in abiotic stress are being identified in maize as “controlling elements” involved in the regulation of around 20% of the abiotic stress responsive genes (Makarevitch et al., 2015), indicating evolution and selection of novel stress protective alleles active in natural populations. Similarly in rice, insertions of the mPing transposon with insertion preference in the 5′ regions of genes were shown to up-regulate the downstream genes and render them stress responsive (Naito et al., 2009). The intriguing challenge ahead is to now see how far McClintock's controlling elements (McClintock, 1984), that are induced to move under stress can help plants survive abiotic stresses by creating and regulating networks of genes for stress protection. The new challenges will come from genome-wide analyses of stress tolerant genotypes from multiple plant species that will probably reveal novel tolerance and selective mechanisms in natural populations. The supporting technologies from next-generation sequencing to GWAS are available in many plant species, and much research is concentrated in this area for stress tolerance. This is therefore an area for future discoveries that will reveal the evolution of diverse mechanisms for stress tolerance that could be valuable for the design of crop improvement strategies including for climate change challenges. A fruitful strategy for the identification of stress tolerance genes has been by reverse genetics analyses of candidate genes identified through gene expression studies and other bioinformatics methods. The biological role of such candidate genes has been most often tested by the analysis of overexpression, knockout/knockdown genotypes in model, and crop plants (Todaka et al., 2015). Overexpression studies with transcription factors and other regulatory genes have been popular in transgenic crops, with the objective of improving their stress tolerance and productivity (Mickelbart et al., 2015), and often enabling applications across plant species. The potential redundancy of stress tolerance genes remains a challenge, since overexpression studies might not represent the natural function of genes in the plant. Nevertheless, all studies testing the potential phenotype of genes for alterations in stress response provide useful information on the gene function as well as the applications. Gene expression analysis of plants in response to abiotic stresses reveals a large fraction of the genome can be perturbed, reflecting the plasticity in stress response and protection. The complexity of a plants' response to abiotic stress factors, in interaction with its genetic constitution, provides a multitude of morpho-physiological, biochemical, gene expression, and other molecular responses that can best be described by networks of response pathways leading to expression of tolerance and adaptation to the environment. The role of genetics and evolution propounded by Darwinism seemed to prevail over the opposing views of Lamarckism, proposing life forms could acquire information from their environment and pass it on in their genes. Now, two centuries later the evidence from epigenetics is showing us in surprising detail, with the sophistication of genomics technologies, how the epigenome carries information that is not encoded in the DNA to offspring, and can even provide a mechanism for acclimation and adaptation to stress (Avramova, 2015). The role of the environment, and subsequently stresses that might permanently plague plants, probably have a significant epigenetic influence on the behavior of plants and their progeny, and provide new challenges to re-visit plant–environment interactions. Abiotic stresses will remain a challenge to the natural environment and agriculture. The early evolution of land plants took place under dry conditions with extremes of temperature and harsh sunlight, while crop domestication occurred later in more favorable environments. Subsequently, the selection of plants for productivity traits did not always result in crops that are productive under random stress factors, although the natural variation of crops are genetic reservoirs for abiotic stress adaptation. Presently, with the competing uses of land and the growing world population we are challenged to produce more in less area with dwindling resources of water, confronted with climate change increases in temperature and carbon dioxide, and the unpredictable local microclimate adversely affecting crop productivity. The challenges before us in plant biology and crop improvement are to integrate the systems level information on abiotic stress response pathways, identify stress protective networks, and engineer environmentally stable crops that yield more, with less water and dwindling natural resources, to feed the growing world population.

Smart Engineering of Genetic Resources for Enhanced Salinity Tolerance in Crop Plants

Abstract: Salinity is a consistent factor of crop productivity loss in the world and in particular arid and semi-arid areas where the soil salinity and saline water are major problems. Plants employ various mechanisms to cope with salinity stress and activate an array of stress-responsive genes to counteract the salinity-induced osmotic and ionic stresses. Genetic improvement for salinity tolerance is challenging, and thus progress attained over the several decades has been far less than anticipated. The generation of an explosion of knowledge and technology related to genetics and genomics over the last few decades is promising in providing powerful tools for future development of salinity-tolerant cultivars. Despite a major progress in defining the underlying mechanisms of salinity tolerance, there are still major challenges to be overcome in translating and integrating the resultant information at the molecular level into plant-breeding practices. Various approaches have been suggested to improve the eff...

Rice Improvement Through Genome-Based Functional Analysis and Molecular Breeding in India.

Abstract: Rice is one of the main pillars of food security in India. Its improvement for higher yield in sustainable agriculture system is also vital to provide energy and nutritional needs of growing world population, expected to reach more than 9 billion by 2050. The high quality genome sequence of rice has provided a rich resource to mine information about diversity of genes and alleles which can contribute to improvement of useful agronomic traits. Defining the function of each gene and regulatory element of rice remains a challenge for the rice community in the coming years. Subsequent to participation in IRGSP, India has continued to contribute in the areas of diversity analysis, transcriptomics, functional genomics, marker development, QTL mapping and molecular breeding, through national and multi-national research programs. These efforts have helped generate resources for rice improvement, some of which have already been deployed to mitigate loss due to environmental stress and pathogens. With renewed efforts, Indian researchers are making new strides, along with the international scientific community, in both basic research and realization of its translational impact.