Browsing by Author "Singh, Nagendra Pratap"

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The chickpea WIP2 gene underlying a major QTL contributes to lateral root development
(Oxford University Press, 2024) Dwivedi, Vikas; Pal, Lalita; Singh, Shilpi; Singh, Nagendra Pratap; Parida, Swarup K.; Chattopadhyay, Debasis
Lateral root is a major component of root system architecture and lateral root count (LRC) positively contributes to yield under drought in chickpea. To understand the genetic regulation of LRC, a biparental mapping population derived from two chickpea accessions having contrasting LRC was genotyped by sequencing and phenotyped to map four major quantitative trait loci (QTLs) contributing to 13 to 32% of the LRC trait variation. A SNP tightly linked to the locus contributing to highest trait variation was located on the coding region of a gene (CaWIP2) orthologous to WIP2 gene of Arabidopsis thaliana. A polymorphic simple sequence repeat (SSR) in the CaWIP2 promoter showed differentiation between low vs. high LRC parents and mapping individuals suggesting its utility for marker-assisted selection. CaWIP2 promoter showed strong activities in chickpea apical root meristem and lateral root primordia. Expression of CaWIP2 under its native promoter in Arabidopsis wip2wip4wip5 mutant rescued its root-less phenotype to produce more lateral root than the wild type plants and led to formation of amyloplasts in the columella. CaWIP2 expression also induced expression of genes that regulate lateral root emergence. Our study identified a gene-based marker for LRC which will be useful to develop drought tolerant high-yielding chickpea.
Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations
(BioMed Central Ltd, 2023) Francis, Aleena; Ghosh, Srayan; Tyagi, Kriti; Prakasam, V.; Rani, Mamta; Singh, Nagendra Pratap; Pradhan, Amrita; Sundaram, R. M.; Priyanka, C.; Laha, G. S.; Kannan, C.; Prasad, M. S.; Chattopadhyay, Debasis; Jha, Gopaljee
Background: Rhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into the AGs and the evolution of pathogenicity-associated genes remain poorly understood. Results: We report a recent whole-genome duplication and sequential segmental duplications in AG1-IA strains of R. solani. Transposable element (TE) clusters have caused loss of synteny in the duplicated blocks and introduced differential structural alterations in the functional domains of several pathogenicity-associated paralogous gene pairs. We demonstrate that the TE-mediated structural variations in a glycosyl hydrolase domain and a GMC oxidoreductase domain in two paralogous pairs affect the pathogenicity of R. solani. Furthermore, to investigate the association of TEs with the natural selection and evolution of pathogenicity, we sequenced the genomes of forty-two rice field isolates of R. solani AG1-IA. The genomic regions with high population mutation rates and with the lowest nucleotide diversity are enriched with TEs. Genetic diversity analysis predicted the genes that are most likely under diversifying and purifying selections. We present evidence that a smaller variant of a glucosamine phosphate N-acetyltransferase (GNAT) protein, predicted to be under purifying selection, and an LPMP_AA9 domain-containing protein, predicted to be under diversifying selection, are important for the successful pathogenesis of R. solani in rice as well as tomato. Conclusions: Our study has unravelled whole-genome duplication, TE-mediated neofunctionalization of genes and evolution of pathogenicity traits in R. solani AG1-IA. The pathogenicity-associated genes identified during the study can serve as novel targets for disease control.
The ricebean genome provides insight into Vigna genome evolution and facilitates genetic enhancement
(John Wiley & Sons, 2023) Francis, Aleena; Singh, Nagendra Pratap; Singh, Mohar; Sharma, Paras; Gayacharan; Kumar, Durgesh; Basu, Udita; Bajaj, Deepak; Varshney, Nidhi; Joshi, Dinesh Chandra; Semwal, Dinesh Prasad; Tyagi, Vandana; Wankhede, Dhammaprakash; Bharadwaj, Rakesh; Singh, Amit Kumar; Parida, Swarup K.; Chattopadhyay, Debasis
Ricebean [Vigna umbellata (Thunb.) Ohwi and Ohashi] (2n = 2x = 22) is a warm-season dietary pulse legume crop and was originated in the Indo-China region. It is known to provide food security to the small and marginal farmers of South and South-East Asia. Ricebean is well known for its high nutritional quality and resistance to bacterial leaf spot, Mungbean yellow mosaic virus and bruchid, which are devastating for the other Vigna family crops (Dhaliwal et al., 2022). We report a reference grade de novo genome assembly, which is anchored to the genetic linkage groups and covered almost the whole estimated genome length of ricebean and so far, the largest among the sequenced Vigna species.
Root-specific expression of chickpea cytokinin oxidase/dehydrogenase 6 leads to enhanced root growth, drought tolerance and yield without compromising nodulation
(John Wiley & Sons, 2020) Khandal, Hitaishi; Gupta, Santosh Kumar; Dwivedi, Vikas; Mandal, Drishti; Sharma, Nilesh Kumar; Vishwakarma, Niraj Kumar; Pal, Lalita; Choudhary, Megha; Francis, Aleena; Malakar, Paheli; Singh, Nagendra Pratap; Sharma, Kapil; Sinharoy, Senjuti; Singh, Narendra Pratap; Sharma, Rameshwar; Chattopadhyay, Debasis
Cytokinin group of phytohormones regulate root elongation and branching during post‐embryonic development. Cytokinin degrading enzymes cytokinin oxidases/dehydrogenases (CKXs) have been deployed to investigate biological activities of cytokinin and to engineer root growth. We expressed chickpea cytokinin oxidase 6 (CaCKX6) under the control of a chickpea root‐specific promoter of CaWRKY31 in Arabidopsis thaliana and chickpea having determinate and indeterminate growth patterns, respectively, to study the effect of cytokinin depletion on root growth and drought tolerance. Root‐specific expression of CaCKX6 led to a significant increase in lateral root number and root biomass in Arabidopsis and chickpea without any penalty to vegetative and reproductive growth of shoot. Transgenic chickpea lines showed increased CKX activity in root. Soil‐grown advanced chickpea transgenic lines exhibited higher root‐to‐shoot biomass ratio and enhanced long‐term drought tolerance. These chickpea lines were not compromised in root nodulation and nitrogen fixation. The seed yield in some lines was up to 25% higher with no penalty in protein content. Transgenic chickpea seeds possessed higher levels of zinc, iron, potassium and copper. Our results demonstrated the potential of cytokinin level manipulation in increasing lateral root number and root biomass for agronomic trait improvement in an edible legume crop with indeterminate growth habit.
Transcriptome-wide association mapping provides insights into the genetic basis and candidate genes governing flowering, maturity and seed weight in rice bean (Vigna umbellata)
(BioMed Central Ltd, 2024) Sahu, Tanmaya Kumar; Verma, Sachin Kumar; Gayacharan; Singh, Nagendra Pratap; Joshi, Dinesh Chandra; Wankhede, D. P.; Singh, Mohar; Bhardwaj, Rakesh; Singh, Badal; Parida, Swarup K.; Chattopadhyay, Debasis; Singh, Gyanendra Pratap; Singh, Amit Kumar
Background: Rice bean (Vigna umbellata), an underrated legume, adapts to diverse climatic conditions with the potential to support food and nutritional security worldwide. It is used as a vegetable, minor food crop and a fodder crop, being a rich source of proteins, minerals, and essential fatty acids. However, little effort has been made to decipher the genetic and molecular basis of various useful traits in this crop. Therefore, we considered three economically important traits i.e., flowering, maturity and seed weight of rice bean and identified the associated candidate genes employing an associative transcriptomics approach on 100 diverse genotypes out of 1800 evaluated rice bean accessions from the Indian National Genebank. Results: The transcriptomics-based genotyping of one-hundred diverse rice bean cultivars followed by pre-processing of genotypic data resulted in 49,271 filtered markers. The STRUCTURE, PCA and Neighbor-Joining clustering of 100 genotypes revealed three putative sub-populations. The marker-trait association analysis involving various genome-wide association study (GWAS) models revealed significant association of 82 markers on 48 transcripts for flowering, 26 markers on 22 transcripts for maturity and 22 markers on 21 transcripts for seed weight. The transcript annotation provided information on the putative candidate genes for the considered traits. The candidate genes identified for flowering include HSC80, P-II PsbX, phospholipid-transporting-ATPase-9, pectin-acetylesterase-8 and E3-ubiquitin-protein-ligase-RHG1A. Further, the WRKY1 and DEAD-box-RH27 were found to be associated with seed weight. Furthermore, the associations of PIF3 and pentatricopeptide-repeat-containing-gene with maturity and seed weight, and aldo–keto-reductase with flowering and maturity were revealed. Conclusion: This study offers insights into the genetic basis of key agronomic traits in rice bean, including flowering, maturity, and seed weight. The identified markers and associated candidate genes provide valuable resources for future exploration and targeted breeding, aiming to enhance the agronomic performance of rice bean cultivars. Notably, this research represents the first transcriptome-wide association study in pulse crop, uncovering the candidate genes for agronomically useful traits.
Uncovering DNA methylation landscapes to decipher evolutionary footprints of phenotypic diversity in chickpea
(Oxford University Press, 2024) Daware, Anurag; Mohanty, Jitendra K.; Narnoliya, Laxmi; Singh, Akansha; Rathore, Deepanshi; Thakro, Virevol; Francis, Aleena; Singh, Nagendra Pratap; Francis, Philip; Tripathi, Shailesh; Chattopadhyay, Debasis; Parida, Swarup K.
Genetic diversity and environmental factors are long believed to be the dominant contributor to phenotypic diversity in crop plants. However, it has been recently established that, besides genetic variation, epigenetic variation, especially variation in DNA methylation, plays a significant role in determining phenotypic diversity in crop plants. Therefore, assessing DNA methylation diversity in crop plants becomes vital, especially in the case of crops like chickpea, which has a narrow genetic base. Thus, in the present study, we employed whole-genome bisulfite sequencing to assess DNA methylation diversity in wild and cultivated (desi and kabuli) chickpea. This revealed extensive DNA methylation diversity in both wild and cultivated chickpea. Interestingly, the methylation diversity was found to be significantly higher than genetic diversity, suggesting its potential role in providing vital phenotypic diversity for the evolution and domestication of the Cicer gene pool. The phylogeny based on DNA methylation variation also indicates a potential complementary role of DNA methylation variation in addition to DNA sequence variation in shaping chickpea evolution. Besides, the study also identified diverse epi-alleles of many previously known genes of agronomic importance. The Cicer MethVarMap database developed in this study enables researchers to readily visualize methylation variation within the genes and genomic regions of their interest (http://223.31.159.7/cicer/public/). Therefore, epigenetic variation like DNA methylation variation can potentially explain the paradox of high phenotypic diversity despite the narrow genetic base in chickpea and can potentially be employed for crop improvement.