Publications of NIPGR Scientists

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    Assessing cold stress resilience in wild chickpea accessions using physiological, biochemical, and reproductive traits
    (Springer Nature, 2025) Kaur, Sarbjeet; Padhiar, Deeksha; Singh, Mohar; Parida, Swarup K.; Jha, Uday C.; Sharma, Kamal Dev; Prasad, P. V. Vara; Siddique, Kadambot H. M.; Nayyar, Harsh
    Domesticated chickpea (Cicer arietinum L.) exhibits high sensitivity to temperatures below 20/10 °C during its reproductive phase resulting in substantial loss of flowers, pods and crop yields. With the aim to add new sources of cold tolerance and elucidate mechanism of cold-tolerance in wild species of chickpea, the present study evaluated 36 wild accessions of three Cicer species (Cicer judaicum, Cicer pinnatifidum, Cicer reticulatum) at the reproductive stage for yield, and reproductive, physiological and biochemical traits under cold stress (15/7 °C) for two consecutive years. Cluster analysis based on yield-related traits such as pod number, seed weight, and total seed count categorized these accessions as cold-tolerant and cold-sensitive. Six C. judaicum accessions (ILWC 256, ICC 13852, ILWC 263, ILWC 20, ILWC 223, and ILWC 30) were tolerant to cold whereas the remaining ones were cold-sensitive. Under cold stress, cold-tolerant accessions exhibited lower impairment of physiological processes as compared to the cold-sensitive accessions e.g. lower tissue damage and electrolyte leakage, and higher chlorophyll content, carotenoid content, chlorophyll fluorescence, and leaf water content, thereby resulting in higher photosynthetic efficiency and carbohydrate accumulation in cold-tolerant accessions. At the biochemical level, the tolerant accessions demonstrated significantly higher amounts of cryoprotectants and enhanced activities of enzymatic and non-enzymatic antioxidants resulting in substantially lower levels of reactive oxygen species. Cold-tolerant accessions also accumulated more proline and trehalose compared to their sensitive counterparts. Slight disruptions in physiological processes, low oxidative stress and accumulation of cryoprotectants under cold stress were associated with higher pollen viability, pollen germination, pollen load, ovule receptivity, pod set, number of pods and seed yield in cold-tolerant accessions while opposite was true for cold-sensitive accessions. The wild chickpea accessions exhibiting high seed yield under cold stress are promising candidates for breeding programs aimed at cold tolerance.
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    Deciphering shared attributes of plant long non-coding RNAs through a comparative computational approach
    (Springer Nature Publishing AG, 2023) Yadav, Vikash Kumar; Jalmi, Siddhi Kashinath; Tiwari, Shalini; Kerkar, Savita
    Over the past decade, long non-coding RNA (lncRNA), which lacks protein-coding potential, has emerged as an essential regulator of the genome. The present study examined 13,599 lncRNAs in Arabidopsis thaliana, 11,565 in Oryza sativa, and 32,397 in Zea mays for their characteristic features and explored the associated genomic and epigenomic features. We found lncRNAs were distributed throughout the chromosomes and the Helitron family of transposable elements (TEs) enriched, while the terminal inverted repeat depleted in lncRNA transcribing regions. Our analyses determined that lncRNA transcribing regions show rare or weak signals for most epigenetic marks except for H3K9me2 and cytosine methylation in all three plant species. LncRNAs showed preferential localization in the nucleus and cytoplasm; however, the distribution ratio in the cytoplasm and nucleus varies among the studied plant species. We identified several conserved endogenous target mimic sites in the lncRNAs among the studied plants. We found 233, 301, and 273 unique miRNAs, potentially targeting the lncRNAs of A. thaliana, O. sativa, and Z. mays, respectively. Our study has revealed that miRNAs, which interact with lncRNAs, target genes that are involved in a diverse array of biological and molecular processes. The miRNA-targeted lncRNAs displayed a strong affinity for several transcription factors, including ERF and BBR-BPC, mutually present in all three plants, advocating their conserved functions. Overall, the present study showed that plant lncRNAs exhibit conserved genomic and epigenomic characteristics and potentially govern the growth and development of plants.
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    Low soil moisture predisposes field-grown chickpea plants to dry root rot disease: evidence from simulation modeling and correlation analysis
    (Springer Nature Publishing AG, 2021) Sinha, Ranjita; Irulappan, Vadivelmurugan; Patil, Basavanagouda S.; Reddy, Puli Chandra Obul; Ramegowda, Venkategowda; Mohan‑Raju, Basavaiah; Rangappa, Krishnappa; Singh, Harvinder Kumar; Bhartiya, Sharad; Senthil-Kumar, Muthappa
    Rhizoctonia bataticola causes dry root rot (DRR), a devastating disease in chickpea (Cicer arietinum). DRR incidence increases under water defcit stress and high temperature. However, the roles of other edaphic and environmental factors remain unclear. Here, we performed an artifcial neural network (ANN)-based prediction of DRR incidence considering DRR incidence data from previous reports and weather factors. ANN-based prediction using the backpropagation algorithm showed that the combination of total rainfall from November to January of the chickpea-growing season and average maximum temperature of the months October and November is crucial in determining DRR occurrence in chickpea felds. The prediction accuracy of DRR incidence was 84.6% with the validation dataset. Field trials at seven diferent locations in India with combination of low soil moisture and pathogen stress treatments confrmed the impact of low soil moisture on DRR incidence under diferent agroclimatic zones and helped in determining the correlation of soil factors with DRR incidence. Soil phosphorus, potassium, organic carbon, and clay content were positively correlated with DRR incidence, while soil silt content was negatively correlated. Our results establish the role of edaphic and other weather factors in chickpea DRR disease incidence. Our ANN-based model will allow the location-specifc prediction of DRR incidence, enabling efcient decision-making in chickpea cultivation to minimize yield loss.
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    Regulatory feedback response mechanisms to phosphate starvation in rice
    (Nature Publishing Group, 2018) Ajmera, Ishan; Shi, Jing; Giri, Jitender; Wu, Ping; Stekel, Dov J.; Lu, Chungui; Hodgman, T. Charlie
    Phosphorus is a growth-limiting nutrient for plants. The growing scarcity of phosphate stocks threatens global food security. Phosphate-uptake regulation is so complex and incompletely known that attempts to improve phosphorus use efficiency have had extremely limited success. This study improves our understanding of the molecular mechanisms underlying phosphate uptake by investigating the transcriptional dynamics of two regulators: the Ubiquitin ligase PHO2 and the long non-coding RNA IPS1. Temporal measurements of RNA levels have been integrated into mechanistic mathematical models using advanced statistical techniques. Models based solely on current knowledge could not adequately explain the temporal expression profiles. Further modeling and bioinformatics analysis have led to the prediction of three regulatory features: the PHO2 protein mediates the degradation of its own transcriptional activator to maintain constant PHO2 mRNA levels; the binding affinity of the transcriptional activator of PHO2 is impaired by a phosphate-sensitive transcriptional repressor/inhibitor; and the extremely high levels of IPS1 and its rapid disappearance upon Pi re-supply are best explained by Pi-sensitive RNA protection. This work offers both new opportunities for plant phosphate research that will be essential for informing the development of phosphate efficient crop varieties, and a foundation for the development of models integrating phosphate with other stress responses.
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    A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea
    (Nature Publishing Group, 2015) Kujur, Alice; Bajaj, Deepak; Upadhyaya, Hari D.; Das, Shouvik; Ranjan, Rajeev; Shree, Tanima; Saxena, Maneesha S.; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C.L.L.; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K.; Parida, Swarup K.
    We identified 44844 high-quality SNPs by sequencing 92 diverse chickpea accessions belonging to a seed and pod trait-specific association panel using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays. A GWAS (genome-wide association study) in an association panel of 211, including the 92 sequenced accessions, identified 22 major genomic loci showing significant association (explaining 23–47% phenotypic variation) with pod and seed number/plant and 100-seed weight. Eighteen trait-regulatory major genomic loci underlying 13 robust QTLs were validated and mapped on an intra-specific genetic linkage map by QTL mapping. A combinatorial approach of GWAS, QTL mapping and gene haplotype-specific LD mapping and transcript profiling uncovered one superior haplotype and favourable natural allelic variants in the upstream regulatory region of a CesA-type cellulose synthase (Ca_Kabuli_CesA3) gene regulating high pod and seed number/plant (explaining 47% phenotypic variation) in chickpea. The up-regulation of this superior gene haplotype correlated with increased transcript expression of Ca_Kabuli_CesA3 gene in the pollen and pod of high pod/seed number accession, resulting in higher cellulose accumulation for normal pollen and pollen tube growth. A rapid combinatorial genome-wide SNP genotyping-based approach has potential to dissect complex quantitative agronomic traits and delineate trait-regulatory genomic loci (candidate genes) for genetic enhancement in crop plants, including chickpea.