Publications of NIPGR Scientists

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    The developmental dynamics in cool season legumes with focus on chickpea
    (Springer Nature Publishing AG, 2023) Basu, Udita; Parida, Swarup K.
    Chickpea is one of the most widely consumed grain legume world-wide. Advances in next-generation sequencing and genomics tools have led to genetic dissection and identification of potential candidate genes regulating agronomic traits in chickpea. However, the developmental particularities and its potential in reforming the yield and nutritional value remain largely unexplored. Studies in crops such as rice, maize, tomato and pea have highlighted the contribution of key regulator of developmental events in yield related traits. A comprehensive knowledge on the development aspects of a crop can pave way for new vistas to explore. Pea and Medicago are the close relatives of genus Cicer and the basic developmental events in these legumes are similar. However, there are some distinct developmental features in chickpea which hold potential for future crop improvement endeavours. The global chickpea germplasm encompasses wide range of diversities in terms of morphology at both vegetative and reproductive stages. There is an immediate need for understanding the genetic and molecular basis of this diversity and utilizing them for the yield contributing trait improvement. The review discusses some of the key developmental events which have potential in yield enhancement and the lessons which can be learnt from model legumes in this regard.
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    Transcriptome landscape of early inflorescence developmental stages identifies key flowering time regulators in chickpea
    (Springer Nature Publishing AG, 2022) Basu, Udita; Hegde, Venkatraman S.; Daware, Anurag; Jha, Uday Chand; Parida, Swarup K.
    The early stages of inflorescence development in plants are as crucial as the later floral developmental stages. Several traits, such as inflorescence architecture and flower developmental timings, are determined during those early stages. In chickpea, diverse forms of inflorescence architectures regarding meristem determinacy and the number of flowers per node are observed within the germplasm. Transcriptome analysis in four desi chickpea accessions with such unique inflorescence characteristics identifies the underlying shared regulatory events leading to inflorescence development. The vegetative to reproductive stage transition brings about major changes in the transcriptome landscape. The inflorescence development progression associated genes identified through co-expression network analysis includes both protein-coding genes and long non-coding RNAs (lncRNAs). Few lncRNAs identified in our study positively regulate flowering-related mRNA stability by acting competitively with miRNAs. Bulk segregrant analysis and association mapping narrowed down an InDel marker regulating flowering time in chickpea. Deletion of 11 bp in first exon of a negative flowering time regulator, Early Flowering 3a gene, leads to early flowering phenotype in chickpea. Understanding the key players involved in vegetative to reproductive stage transition and floral meristem development will be useful in manipulating flowering time and inflorescence architecture in chickpea and other legumes.
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    Variety-specific transcript accumulation during reproductive stage in drought- stressed rice
    (John Wiley & Sons, 2022) Gour, Pratibha; Kansal, Shivani; Agarwal, Priyanka; Mishra, Bhuwaneshwar Sharan; Sharma, Deepika; Mathur, Saloni; Raghuvanshi, Saurabh
    The divergence of natural stress tolerance mechanisms between species is an intriguing phenomenon. To study it in rice, a comparative transcriptome analysis was carried out in ‘heading’ stage tissue (flag leaf, panicles and roots) of Nagina 22 (N22; drought-tolerant) and IR64 (drought-sensitive) plants subjected to field drought. Interestingly, N22 showed almost double the number of differentially expressed genes (DEGs) than IR64. Many DEGs colocalized within drought-related QTLs responsible for grain yield and drought tolerance and also associated with drought tolerance and critical drought-related plant traits such as leaf rolling, trehalose content, sucrose and cellulose content. Besides, co-expression analysis of the DEGs revealed several ‘hub’ genes known to actively regulate drought stress response. Strikingly, 1366 DEGs, including 21 ‘hub’ genes, showed a distinct opposite regulation in the two rice varieties under similar drought conditions. Annotation of these variety-specific DEGs (VS-DEGs) revealed that they are distributed in various biological pathways. Furthermore, 103 VS-DEGs were found to physically interact with over 1300 genes, including 32 that physically interact with other VS-DEGs as well. The promoter region of these genes have sequence variations among the two rice varieties, which might be in part responsible for their unique expression pattern.
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    Petal abscission in roses is associated with the activation of a truncated version of the animal PDCD4 homologue, RbPCD1
    (Elsevier B.V., 2019) Singh, Priya; Singh, Amar Pal; Tripathi, Siddharth Kaushal; Kumar, Vinod; Sane, Aniruddha P.
    Abscission is a developmental process that leads to shedding of organs not needed by the plant. Apart from wallhydrolysis, the cells of the abscission zone (AZ) are also believed to undergo programmed cell death (PCD). Weshow that ethylene-induced petal abscission inRosa bourbonianais accompanied with the activation ofRbPCD1(PROGRAMMED CELL DEATH LIKE 1) encoding a protein of 78 amino acids. Its expression increases duringnatural and ethylene-induced petal abscission. Its transcription in most tissues is up-regulated by ethylene.RbPCD1 shows similarity to the N-terminal domain of animal PDCD4 (PROGRAMMED CELL DEATH PROTEIN 4)proteins that are activated during apoptosis and function as transcriptional and translational repressors. RbPCD1resides in the nucleus and cytoplasm and acts as a transcriptional repressor. Constitutive expression ofRbPCD1intransgenic Arabidopsis is seedling lethal. Heat-induced expression ofRbPCD1under the soybean heat-shockpromoter affects leaf function, inflorescence development, silique formation, seed yield and reduces survival.Nuclear localization of RbPCD1 is necessary for manifestation of its effects. RbPCD1 may be necessary to mediatesome of the ethylene-induced changes during abscission and senescence in specific tissues.