NIPGR Digital Knowledge Repository (NDKR)
Welcome To NIPGR Digital Knowledge Repository
Welcome to Digital Knowledge Repository of the National Institute of Plant Genome Research (NIPGR), New Delhi, India. Digital Knowledge Repository @ NIPGR aims to collect, preserve and disseminate different Institutional Publications (journal articles, conference proceedings articles, annual reports, etc.). You can search, browse and access publications of NIPGR from this collection.
Members of the Institute interested in submitting electronic material to it, should contact the Administrator of this Digital Library.
Quick Links :
Communities in DSpace
Select a community to browse its collections.
- This contains digital contents of different Institutional Publications
- Inhouse publications of NIPGR
- Supplementary Digital Files
Recent Submissions
An EMS mutant of rice cultivar Nagina 22 exhibits tolerance to diverse abiotic stresses
(Elsevier B.V., 2026) Das, Prajna Priyadarshini; Nagalakshmi, Sanivarapu; Yugandhar, Poli; Shrivastva, Mayank; Vamshi, P.; Rao, V. Papa; Tuti, Mangal Deep; Anantha, M. S.; Barbadikar, Kalyani M.; Neeraja, C. N.; Giri, Jitender; Sundaram, R. M.; Mangrauthia, Satendra Kumar
Rice frequently encounters diverse abiotic stresses under changing climatic conditions, including high temperature, osmotic stress, and nutrient deficiencies, which severely limit productivity. Nagina 22 (N22), an aus rice cultivar, is widely recognized as an important donor for drought and heat tolerance traits. However, its sensitivity to phosphorus deficiency poses a significant limitation, particularly under drought and high-temperature conditions, which further reduce the availability of inorganic phosphate (Pi). We hypothesized that mutagenesis of N22 would yield superior variants with enhanced agronomic performance and conserved stress-response mechanisms. One of the Ethyl methanesulfonate (EMS) mutants, NH733, outperformed N22 by maintaining higher photosynthetic efficiency, biomass, reproductive fertility, and grain yield, supported by a more efficient antioxidant machinery under high temperature and low-soil-phosphorus (P) conditions. RNA sequencing under diverse (osmotic stress, high temperature, and low-P) stresses revealed the potential roles of HSFA2D, PCF3, and GHD7 in broad-spectrum stress adaptation of NH733, thereby establishing this mutant line as a valuable genetic resource for breeding climate-resilient rice varieties. Functional validation of the genes and regulators identified in this study will further facilitate their exploitation in genome editing or genomic assisted breeding–driven crop improvement programs.
Establishment of a CRISPR-Cas9 library for indica rice and identification of OsOPR5 (LOC_Os06g11210) as a regulator of root architecture
(John Wiley & Sons, 2026) Chowdhury, Sankhadeep; Nayak, Suprava Priyadarsini; Pattanayak, Rajashree; Sardar, Shaswati; Majhi, Ashis; Yadav, Banita; Dasari, Abhilash; Mandlik, Rushil; Sonah, Humira; Deshmukh, Rupesh; Gupta, Ishaan; Bauer, Petra; Ram, Hasthi
Functional characterization of a large number of rice genes remains a major challenge despite the availability of genome sequences and large-scale transcriptomic datasets. CRISPR-Cas9 library is a powerful approach for high-throughput targeted mutagenesis; however, its application in indica rice cultivars remains limited due to low transformation and regeneration efficiencies. In this study, we developed a CRISPR-Cas9 library targeting 12,000 rice genes and evaluated its utility for functional genomics in the indica cultivar MTU-1010. Sanger sequencing and NGS analysis of the plasmid library revealed high sgRNA coverage and more than 80% accuracy. Transformation of the developed library into the indica cultivar MTU-1010 resulted in a high target editing efficiency, with 90% of analyzed transgenic plants carrying mutations at the intended target site. Functional analysis of one homozygous mutant identified a previously uncharacterized role for OsOPR5 (LOC_Os06g11210), a member of the 12-oxophytodienoate reductase family in root architecture. The opr5 mutants exhibited significant reductions in lateral root number, seminal and crown root number, and root length, demonstrating that OsOPR5 positively regulates root system architecture in rice. Notably, endogenous jasmonic acid (JA) and JA-isoleucine levels were not significantly altered in the mutant, suggesting potential functional specialization or redundancy among rice OPR family members for JA accumulation. The root system architecture is a key determinant of water and nutrient acquisition; our results suggest that OsOPR5 may play an important role in adaptation under adverse environmental conditions. Collectively, this study establishes an efficient genome-editing platform for indica rice and identifies OsOPR5 as a novel regulator of root development.
Genome-wide association study delineating genomic regions contributing to heat stress tolerance at vegetative stage in mung bean [Vigna radiata (L.) R. Wilczek]
(Springer Nature Publishing AG, 2026) Jha, Uday Chand; Shafi, Sadiah; Mohanty, Jitendra Kumar; Nayyar, Harsh; Yadava, Yashwant Kumar; Ciampitti, Ignacio Antonio; Parida, Swarup Kumar; Siddique, Kadambot Hamza Mohamed; Prasad, Pagadala Venkata Vara
Intensifying climate change and increasing heat stress pose a growing challenge to global food crop production, including mung bean [Vigna radiata (L.) R. Wilczek]. Mung bean is a vital protein-rich pulse crop with essential vitamins and micronutrients. However, rising heat stress increasingly constrains its production worldwide. Despite extensive studies on physiological and biochemical responses, genomic resources for heat tolerance in mung bean remain limited. This study employed a genome-wide association study (GWAS) using 5,758 high-quality SNPs to identify genomic regions and candidate genes associated with heat stress tolerance at the vegetative stage. A globally diverse panel of 396 genotypes was evaluated under optimal (34/25 °C) and heat stress (42/30 °C) conditions, assessing six major morpho-physiological traits including leaf chlorophyll index measured by SPAD, photosystem II maximum quantum efficiency (Fv/Fm), membrane damage, plant height, days to flowering and plant biomass. Marker-trait association (MTA) analysis identified nine significant MTAs under optimal conditions and 12 under heat stress. Under heat stress, two MTAs for days to flowering were detected on chromosome (Chr) 3 (S3_8626095) and Chr5 (S5_26149549). These SNPs explained 2.3% to 4.3% of the phenotypic variance explained (PVE). Eleven putative candidate genes were identified, including LOC106757788 encoding phytochrome A-like proteins, LOC106770897 encoding leucine-rich repeat extension-like proteins (maintaining structural integrity under heat stress), and LOC106761867 encoding calcium ATPases (maintaining low cytoplasmic calcium and preventing cytotoxicity). These findings identify key genomic regions and pathways associated with heat stress tolerance, offering valuable resources for marker-assisted breeding of heat-resilient mung bean cultivars. Further validation of candidate genes will enable designing of improved climate resilient varieties. This article supports United Nations’ Sustainable Development Goal: SDG-2 (Zero Hunger) by advancing molecular and cytogenetic research for the genetic improvement of mung bean.
In vitro evaluation of effectiveness of antifungal agents against Macrophomina phaseolina
(Springer Nature Publishing AG, 2026) Acharya, Krishna Ramakrishnan; Chilakala, Aswin Reddy; Senthil-Kumar, Muthappa
Antifungal agents provide both preventive and curative effects by protecting plant surfaces and eliminating existing infections within plant tissues. Evaluating their impact against phytopathogenic fungi is critical for sustainable agriculture. Macrophomina phaseolina is a highly destructive soil-borne pathogen with a broad host range, causing charcoal rot and related diseases that result in severe yield losses in crops such as soybean, sorghum, maize, and legumes. Several methods are employed to assess the in vitro antifungal efficacy of various substances, including broth microdilution, disk diffusion, gradient screening, and agar-based screening. However, these conventional techniques are generally slower, more labor-intensive, and limited by reproducibility issues. The adoption of microplate reader-based antifungal efficacy testing has enhanced efficiency and scalability, enabling high-throughput evaluation of multiple antifungal agents across a range of concentrations while providing a streamlined platform for preliminary screening. This chapter presents a convenient and cost-effective protocol for assessing the activity of antifungal agents against fungi that produce microsclerotia, with emphasis on standardization and quality control measures. The antifungal efficacy testing and cell death assay are employed to determine inhibitory concentrations via spectrophotometry and to quantify hyphal death through fluorescence microscopy, respectively. In addition, detailed procedures for inoculum preparation, antifungal agent dilution, incubation conditions, and statistical analysis are described.
Quantification of mitochondrial pyrroline-5-carboxylate in Arabidopsis under Pseudomonas Syringae infection
(Springer Nature Publishing AG, 2026) Qamar, Aarzoo; Senthil-Kumar, Muthappa
Pyrroline-5 carboxylic acid (P5C) is an intermediary metabolite formed during proline synthesis and catabolism. Proline catabolism in two steps occurs in mitochondria where proline dehydrogenase (ProDH) catabolizes proline into P5C, and finally, pyrroline-5 carboxylate dehydrogenase catabolizes P5C into glutamate. Estimating mitochondrial P5C is essential to know how the metabolism of P5C in mitochondria via proline catabolism genes is responsible for causing disease and defense reaction in the case of Pseudomonas syringae–Arabidopsis interaction. There is no protocol available in the literature to estimate mitochondrial P5C due to which its role is masked and not properly deciphered. Here, we describe the protocol for estimating mitochondrial P5C from Arabidopsis leaves infected with bacterial pathogen P. syringae. Mitochondria was isolated from Arabidopsis leaf samples by percoll gradient centrifugation method. Mitochondrial amino acids and their derivatives were extracted in 80% methanol and without derivatization directly used for LC-MS analysis with standard labeled amino acids acting as internal control. P5C was detected as the daughter ion of the parent ion proline and quantified from the internally labeled proline standard.