Browsing by Author "Singh, Nagendra K."

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CRISPR-Cas9 directed genome engineering for enhancing salt stress tolerance in rice
(Elsevier B.V., 2019) Farhat, Sufia; Jain, Neha; Singh, Nisha; Sreevathsa, Rohini; Dash, Prasanta K.; Rai, Rhitu; Yadav, Sandeep; Kumar, Pramod; Sarkar, Ananda K.; Jain, Ajay; Singh, Nagendra K.; Rai, Vandna
Crop productivity in rice is harshly limited due to high concentration of salt in the soil. To understand the intricacies of the mechanism it is important to unravel the key pathways operating inside the plant cell. Emerging state-of-the art technologies have provided the tools to discover the key components inside the plant cell for salt tolerance. Among the molecular entities, transcription factors and/or other important components of sensing and signaling cascades have been the attractive targets and the role of NHX and SOS1 transporters amply described. Not only marker assisted programs but also transgenic approaches by using reverse genetic strategies (knockout or knockdown) or overexpression have been extensively used to engineer rice crop. CRISPR/Cas is an attractive paradigm and provides the feasibility for manipulating several genes simultaneously. Here, in this review we highlight some of the molecular entities that could be potentially targeted for generating rice amenable to sustain growth under high salinity conditions by employing CRISPR/Cas. We also try to address key questions for rice salt stress tolerance other than what is already known.
Molecular genetics and breeding of grain legume crops for the semi-arid tropics
(Springer, 2007) Varshney, Rajeev K.; Hoisington, David A.; Upadhyaya, Hari D.; Gaur, Pooran M.; Nigam, Shyam N.; Saxena, Kulbhushan; Vadez, Vincent; Sethy, Niroj K.; Bhatia, Sabhyata; Aruna, Rupakula; Gowda, M. V. Channabyre; Singh, Nagendra K.
Grain legumes are important crops for providing key components in the diets of resource-poor people of the semi-arid tropic (SAT) regions of the world. Although there are several grain legume crops grown in SAT, the present chapter deals with three important legumes i.e. groundnut or peanut (Arachis hypogaea), chickpea (Cicer arietinum) and pigeonpea (Cajanus cajan). Production of these legume crops are challenged by serious abiotic stresses e.g. drought, salinity as well as several fungal, viral and nematode diseases. To tackle these constraints through molecular breeding, some efforts have been initiated to develop genomic resources e.g. molecular markers, molecular genetic maps, expressed sequence tags (ESTs), macro-/micro- arrays, bacterial artificial chromosomes (BACs), etc. These genomic resources together with recently developed genetic and genomics strategies e.g. functional molecular markers, linkage-disequilibrium (LD) based association mapping, functional and comparative genomics offer the possibility of accelerating molecular breeding for abiotic and biotic stress tolerances in the legume crops. However, low level of polymorphism present in the cultivated genepools of these legume crops, imprecise phenotyping of the germplasm and the higher costs of development and application of genomic tools are critical factors in utilizing genomics in breeding of these legume crops.
Single nucleotide polymorphism in sugar pathway and disease resistance genes in sugarcane
(Springer, 2016) Parida, Swarup K.; Kalia, Sanjay; Pandit, Awadhesh; Nayak, Preetam; Singh, Ram Kushal; Gaikwad, Kishor; Srivastava, Prem Shankar; Singh, Nagendra K.; Mohapatra, Trilochan
Single nucleotide polymorphism in sugar pathway and disease resistance genes showing genetic association with sugar content and red rot resistance would be useful in marker-assisted genetic improvement of sugarcane. Validation and genotyping of potential sequence variants in candidate genes are necessary to understand their functional significance and trait association potential. We discovered, characterized, validated and genotyped SNPs and InDels in sugar pathway and disease resistance genes of Saccharum complex and sugarcane varieties using amplicon sequencing and CAPS assays. The SNPs were abundant in the non-coding 3'UTRs than 5'UTRs and coding sequences depicting a strong bias toward C to T transition substitutions than transversions. Sequencing of cloned amplicons validated 61.6 and 45.2 % SNPs detected in silico in 21 sugar pathway and 16 disease resistance genes, respectively. Sixteen SNPs in four sugar pathway genes and 10 SNPs in nine disease resistance genes were validated through cost-effective CAPS assay. Functional and adaptive significance of SNP and protein haplotypes identified in sugar pathway and disease resistance genes was assessed by correlating their allelic variation with missense amino acid substitutions in the functional domains, alteration in protein structure models and possible modulation of catalytic enzyme activity in contrasting high and low sugar and moderately red rot resistant and highly susceptible sugarcane genotypes. A strong genetic association of five SNPs in the sugar pathway and disease resistance genes, and an InDel marker in the promoter sequence of sucrose synthase-2 gene, with sugar content and red rot resistance, was evident. The functionally relevant SNPs and InDels, detected and validated in sugar pathway and disease resistance genes, and genic CAPS markers designed, would be of immense use in marker-assisted genetic improvement of sugarcane for sugar content and disease resistance.
The tomato sequencing project, the first cornerstone of the international Solanaceae project (SOL)
(Wiley-Blackwell, 2005) Mueller, Lukas A.; Tanksley, Steven D.; Giovannoni, Jim J.; Eck, Joyce van; Stack, Stephen; Choi, Doil; Kim, Byung Dong; Chen, Mingsheng; Cheng, Zhukuan; Li, Chuanyou; Ling, Hongqing; Xue, Yongbiao; Seymour, Graham; Bishop, Gerard; Bryan, Glenn; Sharma, Rameshwar; Khurana, Jitendra; Tyagi, Akhilesh K.; Chattopadhyay, Debasis; Singh, Nagendra K.; Stiekema, Willem; Lindhout, P.; Jesse, Taco; Lankhorst, Rene Klein; Bouzayen, Mondher; Shibata, Daisuke; Tabata, Satoshi; Granell, Antonio; Botella, Miguel A.; Giuliano, Giovanni; Frusciante, Luigi; Causse, Mathilde; Zamir, Dani
The genome of tomato (Solanum lycopersicum) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, The Netherlands, France, Japan, Spain, Italy and the United States) as part of a larger initiative called the ‘International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation’. The goal of this grassroots initiative, launched in November 2003, is to establish a network of information, resources and scientists to ultimately tackle two of the most significant questions in plant biology and agriculture: (1) How can a common set of genes/proteins give rise to a wide range of morphologically and ecologically distinct organisms that occupy our planet? (2) How can a deeper understanding of the genetic basis of plant diversity be harnessed to better meet the needs of society in an environmentally friendly and sustainable manner? The Solanaceae and closely related species such as coffee, which are included in the scope of the SOL project, are ideally suited to address both of these questions. The first step of the SOL project is to use an ordered BAC approach to generate a high quality sequence for the euchromatic portions of the tomato as a reference for the Solanaceae. Due to the high level of macro and micro-synteny in the Solanaceae the BAC-by-BAC tomato sequence will form the framework for shotgun sequencing of other species. The starting point for sequencing the genome is BACs anchored to the genetic map by overgo hybridization and AFLP technology. The overgos are derived from approximately 1500 markers from the tomato high density F2-2000 genetic map (http://sgn.cornell.edu/). These seed BACs will be used as anchors from which to radiate the tiling path using BAC end sequence data. Annotation will be performed according to SOL project guidelines. All the information generated under the SOL umbrella will be made available in a comprehensive website. The information will be interlinked with the ultimate goal that the comparative biology of the Solanaceae — and beyond — achieves a context that will facilitate a systems biology approach.