BRIC-National Institute of Plant Genome Research

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BRIC-National Institute of Plant Genome Research

An Autonomous Institute of Biotechnology Research and Innovation Council
Deptartment of Biotechnology, Ministry of Science and Technology
Government of India

Sowing seeds for a better tomorrow

Dr. Pinky Agarwal

Staff Scientist V

Ph. D. (Plant Molecular Biology – South Campus Delhi University)

Profile

Research Area

Enhancing Rice Grain Yield and Nutritional Quality

(Deciphering the molecular mechanisms underlying seed development to enhance rice productivity and improve grain quality by increasing protein and optimizing amylose content)

Research Interests

Context

Rice is the primary staple food for more than half of the world’s population, with the grain serving as the edible and nutritionally important component. The major constituent of rice grain is starch, which is composed of two polysaccharides: amylose and amylopectin. Rice varieties with a higher amylose-to-amylopectin ratio generally have a lower glycemic index, resulting in slower starch digestion and a more gradual release of glucose into the bloodstream. Such varieties are therefore considered a healthier dietary option, particularly for managing blood sugar levels.

Beyond providing dietary energy, rice is also an important source of protein, especially in low- and middle-income countries where it forms a substantial part of the daily diet. Enhancing grain protein content while optimizing starch composition can significantly improve the nutritional value of rice and contribute to better public health outcomes.

Simultaneously, meeting the food demands of a growing global population requires sustained improvements in rice productivity. Increasing grain yield remains a major agricultural priority, particularly under the constraints of limited arable land and changing climatic conditions.

Our research is driven by the vision of developing next-generation rice lines that combine high grain yield with superior nutritional quality. By increasing grain protein content and optimizing the amylose-to-amylopectin ratio, we aim to contribute to the development of rice lines that address the dual challenges of food security and nutritional security

Research Highlights

Our laboratory investigates the molecular mechanisms that regulate rice seed development, with the long-term goal of improving grain yield and nutritional quality. Through genetic, molecular, and functional genomics approaches, we have identified key developmental stages, regulatory genes, and transcriptional networks that control grain size, starch accumulation, and seed storage protein synthesis.

(A) Defining the Stages of Rice Seed Development

┬а

To provide a framework for studying grain development, we classified rice seed development into five distinct stages (S1тАУS5) based on characteristic morphological and physiological changes. This staging system has facilitated systematic analyses of gene expression, starch biosynthesis, and protein accumulation during seed development.

Figure: Agarwal et al., 2011. Morphological and physiological changes during the five stages (S1тАУS5) of rice grain development (DAP = Days After Pollination

Subsequent studies from our laboratory demonstrated progressive starch accumulation in the developing endosperm of different rice varieties and revealed the temporal expression patterns of seed storage proteins using transcriptome analysis and qRT-PCR.

Figure: Mahto et al., 2023. Starch accumulation during seed development.
Figure: Yadav et al., 2026. Expression profiles of seed storage proteins

(B) Transcriptional Regulation of Rice Grain Development

Rice grain development is orchestrated by complex transcriptional regulatory networks. Our research has focused on identifying and characterizing transcription factors that coordinate grain size, starch biosynthesis, and nutrient accumulation.

(i) C2H2 Zinc Finger Transcription Factors

We performed a genome-wide analysis of the C2H2 zinc finger transcription factor family, identifying 189 members in rice. Among these, ZOS5-09 and ZOS1-15 exhibited strong seed-specific expression during grain development, suggesting important regulatory functions

Figure: Agarwal et al., 2007. Expression profiles of ZOS5-09 and ZOS1-15 during the S1тАУS5 stages of seed development.

┬аUsing CRISPR/Cas9-mediated genome editing and gene knockdown approaches, we demonstrated that ZOS5-09 functions as a positive regulator of grain size and grain nutritional traits, establishing it as a promising target for rice improvement.

Our studies further revealed that ZOS5-09 functions as a DLN-type transcriptional repressor. We identified that the rice genome contains 266 DLN repressor proteins and developed the rGAL4 vector system as a versatile tool for studying transcriptional repression in plants.

Figure: Jaiswal et al., 2025. Proposed working model illustrating the regulatory role of ZOS5-09.
Figure: Singh et al., 2019. The rGAL4 vector and its application for analyzing DLN repressor activity.
Figure: Mathew et al., 2018. Functional roles of NAC transcription factors in plants
Figure: Mathew et al., 2018. Functional roles of NAC transcription factors in plants

(ii) NAC Transcription Factors

The NAC family represents another major class of plant-specific transcription factors that regulate growth, development, and stress responses. Our work has highlighted their diverse functions during rice grain development.

Among these, we identified SUPER STARCHY1 (ONAC025) as a key regulator influencing grain development and starch accumulation, providing new insights into the molecular control of rice grain quality.

┬а

(iii) NF-Y Transcription Factors

We further demonstrated that OsNF-YB9, a homolog of LEAFY COTYLEDON1 (LEC1), plays an important role in regulating rice plant development and seed traits.

Figure: Das et al., 2019. Working model describing the function of OsNF-YB9.
Figure: Verma et al., 2021. Seed-development genes downstream to GW2.

(iv) Beyond Transcription Factors

Our research also extends to other regulatory proteins involved in grain development. We showed that GW2, an E3 ubiquitin ligase, acts as a negative regulator of grain size and influences the expression of numerous seed development genes, highlighting the importance of ubiquitin-mediated regulation during grain development.

Current Projects

Our current research focuses on the functional characterization of transcription factors and other regulatory proteins that govern rice grain size, yield, and nutritional quality. We aim to unravel the interconnected regulatory networks that control seed development and determine key agronomic and nutritional traits.

To achieve this, we employ CRISPR/Cas9-based genome editing, gene knockdown, and overexpression approaches to generate transgenic rice lines for candidate genes. These plants are evaluated across successive generations through comprehensive phenotypic analyses, with particular emphasis on grain size, seed morphology, and yield-related traits.

We further investigate grain nutritional quality by quantifying starch composition, protein content, and other biochemical characteristics. To understand the molecular basis of these traits, we integrate transcriptomic, metabolomic, and proteomic analyses to identify downstream target genes, interacting protein partners, and the biological pathways regulated by these factors. In parallel, we characterize upstream microRNAs (miRNAs) that modulate the expression of these regulatory genes.

By combining functional genomics with multi-omics approaches, our research seeks to construct comprehensive regulatory networks underlying rice grain development. These insights will facilitate the development of rice varieties with enhanced grain yield, improved nutritional quality, and greater potential to contribute to global food and nutritional security.

Career

Scientist V, BRIC-NIPGR (2022 тАУ present)

Scientist IV, NIPGR (2018 тАУ 2022)

Staff Scientist III, NIPGR (2014 тАУ 2018)

Scientist II, NIPGR (2011 – 2014)

Research Scientist, DBTтАЩs Center of Excellence, Department of Plant Molecular Biology, Delhi University (2010 тАУ 2011)

Senior Research Fellow, DBTтАЩs Center of Excellence, Department of Plant Molecular Biology, Delhi University (2009 тАУ 2010)

Ph. D., Department of Plant Molecular Biology, Delhi University (2003-09)

M. Sc., Department of Plant Molecular Biology, Delhi University (2001-03)

B. Sc. (Botany-Hons.), Gargi College, Delhi University (1998-2001)

Awards & Honors

DBT-CTEP Travel Grant (2024)

Future hope in Vigyan Vidushi:75 Women Trailblazers of Science by Vigyan Prasar (2023)

Women in STEM: Vanguards of India @75 by Confederation of Indian Industries (CII) and Department of Science and Technology (DST) (2022)

Travel grant award by American Society of Plant Biologists (ASPB) (not availed) (2018)

Selected for the 1st EMBO research leadership course in India by DBT India Alliance (2018)

SERB 'Women Excellence Award' by Science and Research Engineering Board, India and was felicitated with the same on Women's Day, 2013 at the Department of Science and Technology, New Delhi (2013)

INSA Young Scientist's Award (2012)

Special mention in Indian Women Scientist's Association (IWSA) newsletter (December 2012)

Junior and senior research fellowships from UGC (2001)

President of Gargi College Botanical Society (2000)

Openings in Laboratory

If your thoughts are in sync with above mentioned research and goals, please drop in a mail.

Current Members

Our laboratory brings together researchers with diverse expertise in molecular biology, genetics, genomics, and plant biotechnology. We are committed to fostering a collaborative, inclusive, and intellectually stimulating research environment while training the next generation of plant scientists

Current Research Team

Antima Yadav

Research Associate, DBT Indo-Canada Project (2026 тАУ present)

Ph. D. тАУ BRIC-NIPGR

Aswathi P.V

Ph. D. (2020 тАУ present)

Falah Qasim

Ph. D. (2022 - present)

Upasana Das

Ph. D. (2022 - present)

Tripti Avinash

Ph. D. (2023 - present)

Ritama Kundu

Ph. D. (2024 - present)

Nitika

Project Associate (2025-present), BRIC-NIPGR STRF Scheme

Former Lab Members Ph. D. Alumni

Naveen Malik

Ph. D., 2017

Assistant Professor-III, Amity Institute of Biotechnology, Amity University Rajasthan

Rajeev Ranjan

Ph. D., 2017

Postdoctoral Researcher at Purdue University, USA

Iny Mathew

Ph. D., 2018

Postdoctoral Researcher at USDA/ARS Children's Nutrition Research Centre, Texas

Sweta Das

Ph. D., 2018

Functional Characterization of Rice Homologues of LEAFY COTYLEDON1 in Seed Development

Arunima Mahto

Ph. D., 2019

Research associate III, Indian Sugarcane Research Institute (ISRI), Lucknow

Ankit Verma

Ph. D., 2021

Food Safety Officer, Commissionerate of Food Safety and Drug Control, Jaipur, Rajasthan

Priya Jaiswal

Ph. D., 2024

Postdoctoral Researcher at University of Cambridge, UK

Richa Priyadarshini

Ph. D., 2024

Assistant Professor (Botany) at Tilka Manjhi University, Bhagalpur, Bihar

Antima Yadav

Ph. D., 2026

Research Associate , BRIC-NIPGR

Research Alumni

Priya Jaiswal, RA

Afsana Parveen, RA

Ankur Vichitra, RA

Shubhra Rastogi, RA

Shuaib Malik, SRF

Rashmi Renu Sahoo, SRF

Akanksha Panwar, SRF

Purnima Singh, SRF

Megha Varshney, SRF

Sanjoli Jain, JRF

Swarnmala Samal, JRF

Veena K. Sinha, JRF

Poonam Ray, JRF

┬а

Publications

Yadav A, Jaiswal P, Mathew IE, Panwar A, Agarwal P (2026) Decoding rice seed storage proteins: from gene identification to structural prediction. Annals of Botany (accepted) DOI: 10.1093/aob/mcag124

Jaiswal P, Qasim F, Mahto A, Vichitra A, Tyagi AK, Agarwal P (2025) Zinc finger transcriptional repressor ZOS5-09 regulates grain filling and development in rice. Physiologia Plantarum 177(4):e70376 DOI:┬а1111/ppl.70376

Jaiswal P,┬аPriyadarshini R,┬аYadav A,┬аAswathi PV,┬аMahto A,┬аMathew IE,┬аDas U,┬аQasim F,┬аVichitra A,┬аPanwar A,┬аVerma A,┬аTyagi AK, Agarwal P (2024) A novel repressor-activator-competitor module comprising C2H2 zinc finger and NAC transcription factors regulates rice grain development. bioRxiv (preprint)┬а doi: 2024.07.15.603577

Mahto A, Yadav A, Aswathi PV, Parida SK, Tyagi AK, Agarwal P (2023) Cytological, transcriptome and miRNome temporal landscapes decode enhancement of rice grain size. BMC Biology 21:91 DOI:┬а1186/s12915-023-01577-3

Verma A, Prakash G, Ranjan R, Tyagi A K, Agarwal P (2021) Silencing of an ubiquitin ligase increases grain width and weight in indica rice. Frontiers in Genetics 11:600378 DOI:┬а3389/fgene.2020.600378

Mathew IE, Priyadarshini R, Mahto A, Jaiswal P, Parida SK, Agarwal P (2020) SUPER STARCHY1/ONAC025 participates in rice grain filling. Plant Direct 4:e00249 DOI:┬а1002/pld3.249

Malik N, Ranjan R, Parida SK,┬аAgarwal P, Tyagi AK (2020) Mediator subunit OsMED14_1 plays an important role in rice development.┬аPlant Journal┬а101:1411.

Das S, Parida SK, Agarwal P#, Tyagi AK# (2019) Transcription factor OsNFтАСYB9 regulates reproductive growth and development in rice. Planta 250: 1849 (#-equal corresponding author) DOI:┬а1007/s00425-019-03268-2

Singh P, Mathew IE, Verma A, Tyagi AK, Agarwal P (2019) Analysis of rice proteins with DLN repressor Motif/S. International Journal of Molecular Sciences 20:1600 DOI:┬а3390/ijms20071600

Mathew I E, Agarwal P (2018) May the fittest protein evolve: favoring the plant-specific origin and expansion of NAC transcription factors. Bioessays 40: e1800018 DOI:┬а1002/bies.201800018

Malik N,┬аAgarwal P, Tyagi A K (2017)┬а Emerging functions of multi-protein complex Mediator with special emphasis on plants.┬аCritical Reviews in Biochemistry and Molecular Biology┬а52:475.

Mathew IE, Das S, Mahto A, Agarwal P (2016) Three rice NAC transcription factors heteromerize and are associated with seed size. Frontiers in Plant Science 7:1638. DOI:┬а3389/fpls.2016.01638

Daware A, Das S, Srivastava R, Badoni S, Singh AK,┬аAgarwal P, Parida SK, Tyagi AK (2016) An efficient strategy combining SSR markers- and advanced QTL-seq-driven QTL mapping unravels candidate genes regulating grain weight in rice.┬аFront Plant Sci┬а7:1535.

Malik N, Dwivedi N, Singh A K, Parida S K,┬аAgarwal P, Thakur J K, Tyagi A K (2016) An integrated genomic strategy delineates candidate mediator genes regulating grain size and weight in rice.┬аSci Rep┬а6:23253.

Agarwal P, Parida S K, Raghuvanshi S, Kapoor S, Khurana P, Khurana J P, Tyagi A K (2016) Rice improvement through genome-based functional analysis and molecular breeding in India.┬аRice (N Y)┬а9 (1):1.

Sharma NK, Gupta SK, Dwivedi V,┬аChattopadhyay D┬а(2020) Lignin deposition in chickpea root xylem under drought.┬аPlant Signal. Behav.┬а15(6):e1754621

Daware A, Das S, Srivastava R, Badoni S, Singh AK,┬аAgarwal P, Parida SK, Tyagi AK (2016) An efficient strategy combining SSR markers- and advanced QTL-seq-driven QTL mapping unravels candidate genes regulating grain weight in rice.┬аFrontiers in Plant Sciences┬а7:1535.

Malik N, Dwivedi N, Singh A K, Parida S K,┬аAgarwal P, Thakur J K, Tyagi A K (2016) An integrated genomic strategy delineates candidate mediator genes regulating grain size and weight in rice.┬аScientific Reports┬а6:23253.

Badoni S, Das S, Sayal YK, Gopalakrishnan S, Singh AK, Rao AR,┬аAgarwal P, Parida SK, Tyagi AK (2016) Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice.┬аScientific Reports┬а6:23765.

Agarwal P, Parida S K, Mahto A, Das S, Mathew I E, Malik N, Tyagi A K (2014)┬аExpanding frontiers in plant transcriptomics in aid of functional genomics and molecular breeding.┬аBiotechnol J┬а9:1480-1491.

Thakur J K,┬аAgarwal P, Parida S, Bajaj D, Pasrija R (2013) Sequence and expression analyses of KIX domain proteins suggest their importance in seed development and determination of seed size in rice, and genome stability in Arabidopsis.┬аMolecular Genetics and Genomics┬а288:329-46.

Sharma R*,┬аAgarwal P*, Ray S, Deveshwar P, Sharma P, Sharma N, Nijhawan A, Jain M, Singh A K, Singh V P, Khurana J P, Tyagi A K, Kapoor S.┬а(2012)┬аExpression dynamics of metabolic and regulatory components across stages of panicle and seed development in┬аindica┬аrice.┬аFunct Integr Genomics┬а12:229-248 (*-equal contribution)

Agarwal P, Kapoor S, Tyagi A K.┬а(2011)┬аTranscription factors regulating the progression of monocot and dicot seed development.┬аBioEssays┬а33:189-202.

Chauhan H, Khurana N,┬аAgarwal P, Khurana P (2011) Heat shock factors in rice (Oryza sativa┬аL.): genome-wide expression analysis during reproductive development and abiotic stress.┬аMolecular Genetics and Genomics┬а286:171-187.

Ray S, Dansana, P K, Giri J, Deveshwar P, Arora R,┬аAgarwal P, Khurana J P, Kapoor S, Tyagi A K. (2011). Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice.┬аFunctional and Integrative Genomics┬а11:157-78.

Agarwal P, Arora R, Ray S, Singh A K, Singh V P, Takatsuji H, Kapoor S, Tyagi A K.┬а(2007)┬аGenome-wide identification of C2H2 zinc-finger gene family in rice and their phylogeny and expression analysis.┬аPlant Mol Biol┬а65:467-485.

Ray S,┬аAgarwal P, Arora R, Kapoor S, Tyagi A K. (2007) Expression analysis of calcium- dependent protein kinase gene family during reproductive development and abiotic stress conditions in rice (Oryza sativa┬аL. ssp.┬аindica).┬аMolecular Genetics and Genomics┬а278:493-505.

Arora R,┬аAgarwal P, Ray S, Singh A K, Singh V P, Tyagi A K,┬а Kapoor S. (2007) MADS-box gene family in rice: Genome wide identification, organization and expression profiling during reproductive development and stress.┬аBMC Genomics┬а8:242.

Jain M, Nijhawan A, Arora R,┬аAgarwal P, Ray S, Sharma P, Kapoor S, Tyagi A K, Khurana J P.┬а(2007)┬аF-box proteins in rice: Genome-wide analysis, classification, spatial and temporal gene expression during panicle and seed development, and regulation by light and abiotic stress.┬аPlant Physiol┬а143:1467-1483.

Other Publications

Agarwal P, Parida S K, Raghuvanshi S, Kapoor S, Khurana P, Khurana J P, Tyagi A K (2016) Rice improvement through genome-based functional analysis and molecular breeding in India. Rice (N Y) 9 (1):1.

Agarwal P, Parida S K, Mahto A, Das S, Mathew I E, Malik N, Tyagi A K (2014) Expanding frontiers in plant transcriptomics in aid of functional genomics and molecular breeding. Biotechnol J 9:1480-1491.

Prusty A, Malik N, Ranjan R, Agarwal P, Parida SK, Kapoor S, Tyagi AK (2025) The Mediator complex subunit, OsMED26_2, modulates plant growth, seed set and seed traits related to starch quality in rice. Plant Science 364:112941

Jain M, Nijhawan A, Arora R,┬аAgarwal P, Ray S, Sharma P, Kapoor S, Tyagi A K, Khurana J P.┬а(2007)┬аF-box proteins in rice: Genome-wide analysis, classification, spatial and temporal gene expression during panicle and seed development, and regulation by light and abiotic stress.┬аPlant Physiol┬а143:1467-1483.

Mohanty JK, Yadav A, Narnoliya L, Thakro V, Rathore D, Tripathi S, Sinharoy S, Agarwal P, Parida SK (2025) Trans-QTL alliance of HKT1 and PHL7 modulate salinity stress tolerance and enhance crop yield endurance. Plant Biotechnology Journal 24: 1166

Mohanty JK, Yadav A, Narnoliya L, Thakro V, Nayyar H, Dixit GP, Jha UC, Vara Prasad PV, Agarwal P, Parida SK (2025) A next-generation combinatorial genomic strategy scans genomic loci governing heat stress tolerance in chickpea. Plant Cell and Environment 48(4):2706

Mohanty J, Thakro V, Nair H, Dixit GP, Jha UC, Yadav A, Agarwal P, Parida SK (2024) Delineation of genes for a major QTL governing heat stress tolerance in chickpea. Plant Molecular Biology 114(2):19

Prusty A, Mehra P, Sharma S, Malik N, Agarwal P, Parida SK, Kapoor S, Tyagi AK (2024) OsMED14_2, a tail module subunit of Mediator complex, controls rice development and involves jasmonic acid. Plant Science 346:112146

Ranjan, R, Malik, N, Sharma S, Agarwal P, Kapoor S, Tyagi AK (2022) OsCPK29 interacts with MADS68 to regulate pollen development in rice. Plant Science 321:111297

Kumar A, Mir RR, Sehgal D, Agarwal P, Carter A. (2021) Editorial: Genetics and genomics to enhance crop production, towards food security. Frontiers in Genetics 12:798308

Plant Cell Atlas Consortium, Jha SG, Borowsky AT, Cole BJ, Fahlgren N, Farmer A, Huang SC, Karia P, Libault M, Provart NJ, Rice SL, Saura-Sanchez M, Agarwal P, Ahkami AH, Anderton CR, Briggs SP, Brophy JA, Denolf P, Di Costanzo LF, Exposito-Alonso M, Giacomello S, Gomez-Cano F, Kaufmann K, Ko DK, Kumar S, Malkovskiy AV, Nakayama N, Obata T, Otegui MS, Palfalvi G, Quezada-Rodr├нguez EH, Singh R, Uhrig RG, Waese J, Van Wijk K, Wright RC, Ehrhardt DW, Birnbaum KD, Rhee SY (2021) Vision, challenges and opportunities for a Plant Cell Atlas.eLife 10:e66877.

Malik N, Ranjan R, Parida SK, Agarwal P, Tyagi AK (2020) Mediator subunit OsMED14_1 plays an important role in rice development. Plant J 101(6):1411-1429.

Malik N, Agarwal P, Tyagi A K (2017) Emerging functions of multi-protein complex Mediator with special emphasis on plants. Crit Rev Biochem Mol Biol 52: 475-502.

Daware A, Das S, Srivastava R, Badoni S, Singh AK, Agarwal P, Parida SK, Tyagi AK (2016) An efficient strategy combining SSR markers- and advanced QTL-seq-driven QTL mapping unravels candidate genes regulating grain weight in rice. Front Plant Sci 7:1535.

Badoni S, Das S, Sayal Y K, Gopalakrishnan S, Singh A K, Rao AR, Agarwal P, Parida S K, Tyagi A K (2016) Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice. Sci Rep 6:23765.

Malik N, Dwivedi N, Singh A K, Parida S K, Agarwal P, Thakur J K, Tyagi A K (2016) An integrated genomic strategy delineates candidate Mediator genes regulating grain size and weight in rice. Sci Rep 6:23253.

Thakur J K, Agarwal P, Parida S, Bajaj D, Pasrija R (2013) Sequence and expression analyses of KIX domain proteins suggest their importance in seed development and determination of seed size in rice, and genome stability in Arabidopsis. Mol Genet Genomics 288:329-46.

Chauhan H, Khurana N, Agarwal P, Khurana P (2011) Heat shock factors in rice (Oryza sativa L.): genome-wide expression analysis during reproductive development and abiotic stress. Mol Genet Genomics 286:171-187.

Ray S, Dansana, P K, Giri J, Deveshwar P, Arora R, Agarwal P, Khurana J P, Kapoor S, Tyagi A K. (2011). Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice. Funct Integr Genomics 11:157-78.

Ray S, Agarwal P, Arora R, Kapoor S, Tyagi A K. (2007). Expression analysis of calcium- dependent protein kinase gene family during reproductive development and abiotic stress conditions in rice (Oryza sativa ssp. indica). Mol Genet Genomics 278:493-505.

Arora R, Agarwal P, Ray S, Singh A K, Singh V P, Tyagi A K, Kapoor S. (2007). MADS-box gene family in rice: Genome wide identification, organization and expression profiling during reproductive development and stress. BMC Genomics 8:242.

Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, Sharma P, Kapoor S, Tyagi A K, Khurana J P. (2007). F-box proteins in rice: Genome-wide analysis, classification, spatial and temporal gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol 143:1467-1483.

Book Chapter

Jaiswal, P., Thakro, V., & Agarwal, P. (2026). The hidden hand: Exploring miRNA-mediated signaling in plantтАУmicrobe synergy. In V. Mishra, S. Pandey, V. Varshney, & C. Kole (Eds.), PlantтАУmicrobe interactions for sustainable growth and resilience (1st ed.). CRC Press. (corresponding author)

Mahto A, Mathew IE and┬аAgarwal┬аP┬а(2017). Decoding the transcriptome of rice seed during development. In Advances in Seed Biology, J. C. Jimenez-Lopez (Ed.), 25, InTech, Spain.

Agarwal P, Parida S, Kothari KS, Sharma G, Baranwal V, Kapoor S and Tyagi A. (2012). Transcriptome resources for function analysis and genetic enhancement of rice. In International Dialogue on Designer Rice for Future: Perception and Prospects EA Siddiq eds., 1-25, Patancheru, India

Kapoor S, Khurana R, Baranwal V,┬аAgarwal P, Ray S, and Tyagi AK (2011). Genome-wide strategies for genetic enhancement of rice. Proceedings of National Symposium on Genomics and Crop Improvement 2011 (In Press), Hyderabad, India.

Tyagi AK, Khurana JP, Khurana P, Kapoor S, Singh VP, Singh AK, Thakur JK, Gupta V, Anand S, Vij S, Jain M, Ray S,┬аAgarwal P, Arora R, Sharma P, Mukerjee S, Nijhawan A, Giri J, Khurana R (2007). Expression and functional analysis of rice genes involved in reproductive development and stress response.┬аRice Genetics V, 301-334, IRRI, Philippines.

Data and Research Resources

To support open science and facilitate research in plant biology, our laboratory has developed a database and generated publicly available transcriptomic datasets. These resources are freely accessible to the scientific community.

Rice Grain Development Database (RGDD)

The Rice Grain Development Database (RGDD) integrates gene expression data generated during rice seed development and serves as a valuable resource for researchers investigating grain development and related biological processes.

Indian Crop Phenome Database (ICPD)

Phenotypic datasets generated by our laboratory for seed development in two contrasting rice varietiesтАФSonasal (small-grained) and LGR (large-grained)тАФare publicly available through the Indian Crop Phenome Database (ICPD).

Available datasets include:

RNA-Seq Datasets (NCBI Sequence Read Archive)

┬а ┬а Our RNA sequencing datasets are publicly available through the NCBI Sequence Read Archive (SRA).

SRA Accession

Dataset Description

PRJNA540785

Transcriptome of one wild-type rice plantlet and two SUPER STARCHY1 overexpression lines (2.5-month-old plants).

PRJNA659415

RNA-seq of OsGW2 RNAi and wild-type rice seeds at the S4 developmental stage, with biological duplicates.

PRJNA605919

Transcriptomes of five rice seed developmental stages (S1тАУS5) and flag leaves from two rice genotypes (SN and LGR), with biological triplicates.

Small RNA-Seq Dataset

Small RNA sequencing data from five stages of rice seed development (S1тАУS5) and flag leaves of two rice genotypes (SN and LGR) are publicly available through the NCBI Sequence Read Archive.

  • SRA Accession: PRJNA616068
Rice C2H2 Zinc Finger Gene Family Resource

Our genome-wide analysis of the rice C2H2 zinc finger transcription factor family has been incorporated into the Rice Genome Annotation Project (formerly TIGR/JCVI) and is publicly available online (https://rice.uga.edu/cgi-bin/putative_function_search.pl).

Microarray Datasets

Microarray expression datasets generated from rice seed development and young root tissues have been deposited in the NCBI Gene Expression Omnibus (GEO).

  • Series ID: GSE6893
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