Institutional Publications

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    Functional genomics of abiotic stress tolerance in plants: A CRISPR approach
    (Frontiers Media S.A., 2015) Jain, Mukesh
    Various abiotic stresses, such as drought, salinity, heat, flooding, ion toxicity and radiation are the major constraints to agricultural production. The understanding of molecular basis of plant response to these environmental conditions has been a major focus of research in the past decades. Several genes/pathways and regulatory networks involved in stress responses have been worked out employing various approaches. Quite a few of these components have been used for engineering abiotic stress tolerance in model and crop plants via classical biotechnological and/or breeding approaches. Success to generate stress-tolerant plants has been achieved to some extent, which has resulted in increased crop yield (Mickelbart et al., 2015). However, novel strategies are desirable to overcome the limitations of classical methods, such as lack of precision and requirement of substantial time to increase the crop production in the current climate change and ever increasing population scenario. The recent availability of genome editing tools provides ample opportunity to introduce targeted modifications in the genome efficiently to study the functional aspects of various components of the genome in diverse plants and offers potential avenues for production of abiotic stress-tolerant crop plants.
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    Genome-wide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance
    (John Wiley & Sons, 2014) Jain, Mukesh; Moharana, Kanhu Charan; Shankar, Rama; Kumari, Romika; Garg, Rohini
    Next-generation sequencing technologies provide opportunities to understand the genetic basis of phenotypic differences, such as abiotic stress response, even in the closely related cultivars via identification of large number of DNA polymorphisms. We performed whole- genome resequencing of three rice cultivars with contrasting responses to drought and salinity stress (sensitive IR64, drought-tolerant Nagina 22 and salinity-tolerant Pokkali). More than 356 million 90-bp paired-end reads were generated, which provided about 85% coverage of the rice genome. Applying stringent parameters, we identified a total of 1 784 583 nonredundant single-nucleotide polymorphisms (SNPs) and 154 275 InDels between reference (Nipponbare) and the three resequenced cultivars. We detected 401 683 and 662 509 SNPs between IR64 and Pokkali, and IR64 and N22 cultivars, respectively. The distribution of DNA polymorphisms was found to be uneven across and within the rice chromosomes. One-fourth of the SNPs and InDels were detected in genic regions, and about 3.5% of the total SNPs resulted in nonsynonymous changes. Large-effect SNPs and InDels, which affect the integrity of the encoded protein, were also identified. Further, we identified DNA polymorphisms present in the differentially expressed genes within the known quantitative trait loci. Among these, a total of 548 SNPs in 232 genes, located in the conserved functional domains, were identified. The data presented in this study provide functional markers and promising target genes for salinity and drought tolerance and present a valuable resource for high-throughput genotyping and molecular breeding for abiotic stress traits in rice.