1. Post-Doctorate at International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Hyderabad, India.
2. Ph.D. in molecular biology and biotechnology, Faculty of Science, University of Kalyani, India.
3. M.Phil. in Oceanography and coastal management, Jadavpur University, India.
4. M.Sc. in Industrial Biotechnology, Berhampur University, India.
RESEARCH, TEACHING, or OTHER INTERESTS
Agricultural and Biological Sciences, Biochemistry, Genetics and Molecular Biology, Agronomy and Crop Science, Soil Science
12
Scopus Publications
426
Scholar Citations
8
Scholar h-index
8
Scholar i10-index
Scopus Publications
Utilizing X-ray radiography for non-destructive assessment of paddy rice grain quality traits Murugesan Tharanya, Debarati Chakraborty, Anand Pandravada, Raman Babu, Mahantesh Gangashetti, Swapna Paidi, Sunita Choudhary, Kaliamoorthy Sivasakthi, Krithika Anbazhagan, Bhavani Vaditandra, Michael Waininger, Mareike Weule, Eva Hufnagel, Joelle Claußen, Jiří Vaněk, Thomas Wittenberg, Jana Kholova, Stefan Gerth Plant Methods, 2025 Background Agricultural systems are under extreme pressure to meet the global food demand, hence necessitating faster crop improvement. Rapid evaluation of the crops using novel imaging technologies coupled with robust image analysis could accelerate crops research and improvement. This proof-of-concept study investigated the feasibility of using X-ray imaging for non-destructive evaluation of rice grain traits. By analyzing 2D X-ray images of paddy grains, we aimed to approximate their key physical Traits (T) important for rice production and breeding: (1) T 1 chaffiness, (2) T 2 chalky rice kernel percentage (CRK%), and (3) T 3 head rice recovery percentage (HRR%). In the future, the integration of X-ray imaging and data analysis into the rice research and breeding process could accelerate the improvement of global agricultural productivity. Results The study indicated, computer-vision based methods (X-ray image segmentation, features-based multi-linear models and thresholding) can predict the physical rice traits (chaffiness, CRK%, HRR%). We showed the feasibility to predict all three traits with reasonable accuracy (chaffiness: R 2 = 0.9987, RMSE = 1.302; CRK%: R 2 = 0.9397, RMSE = 8.91; HRR%: R 2 = 0.7613, RMSE = 6.83) using X-ray radiography and image-based analytics via PCA based prediction models on individual grains. Conclusions Our study demonstrated the feasibility to predict multiple key physical grain traits important in rice research and breeding (such as chaffiness, CRK%, and HRR%) from single 2D X-ray images of whole paddy grains. Such a non-destructive rice grain trait inference is expected to improve the robustness of paddy rice evaluation, as well as to reduce time and possibly costs for rice grain trait analysis. Furthermore, the described approach can also be transferred and adapted to other grain crops.
Mangroves as an Effective Tool of Phytoremediation and Its Implications on Agricultural Land in Estuarine Zones Debarati Chakraborty Phytoremediation and Biofortification Strategies for Sustainable Environmental and Health Management, 2024 Phytoremediation, a treatment technique for getting rid of toxic trace metal pollution is being explored for a long time owing to its low-cost compared to physicochemical methods. Mangrove estuaries are often high metal pollution due to the high affinity of sedimentary organic matter (OM) for trace metals and capacity of mangroves to efficiently trap suspended material from the water and sediments. The functionality of mangroves to store metallic pollutants have been proven to be an effective natural purification process for toxic wastewater treatment. The Hooghly estuary supporting world’s largest continuous mangrove forest, the Sundarbans have also reported significantly high trace metal pollution. Particularly Al, As, Cd, Cr, Cu, Co, Fe, Hg, Pb, Mn, Ni, V, and Zn have shown higher shale values when compared with the global standard. Regular disposal of domestic sewage, semi treated industrial effluents, surface, and agricultural run-off are the potential sources of contamination in the zone. Studies have proven some of the dominant mangroves of Sundarbans namely Avicennia officinalis, Sonneratia apetala and Excoecaria agallocha have high toxic metal phytoremediation ability. This is of particular significance as Indian Sundarbans is home to over 4.5 million people and trace metals are non-biodegradable, 132shows bioaccumulation tendency in flora and fauna and toxic on exposure above threshold limits. Agriculture is the main occupation among the inhabitants and hence a balance between mangrove population and metal toxic waste free agricultural land is of baffling importance. Lastly, the post-harvest management of phytoremediation derived waste have received scarce focus to date. Hence strategies for removal of mangrove plant biomass with concentrated metal wastes are discussed as a way forward.
X-ray driven peanut trait estimation: computer vision aided agri-system transformation Martha Domhoefer, Debarati Chakraborty, Eva Hufnagel, Joelle Claußen, Norbert Wörlein, Marijn Voorhaar, Krithika Anbazhagan, Sunita Choudhary, Janila Pasupuleti, Rekha Baddam, Jana Kholova, Stefan Gerth Plant Methods, 2022 Background In India, raw peanuts are obtained by aggregators from smallholder farms in the form of whole pods and the price is based on a manual estimation of basic peanut pod and kernel characteristics. These methods of raw produce evaluation are slow and can result in procurement irregularities. The procurement delays combined with the lack of storage facilities lead to fungal contaminations and pose a serious threat to food safety in many regions. To address this gap, we investigated whether X-ray technology could be used for the rapid assessment of the key peanut qualities that are important for price estimation. Results We generated 1752 individual peanut pod 2D X-ray projections using a computed tomography (CT) system (CTportable160.90). Out of these projections we predicted the kernel weight and shell weight, which are important indicators of the produce price. Two methods for the feature prediction were tested: (i) X-ray image transformation (XRT) and (ii) a trained convolutional neural network (CNN). The prediction power of these methods was tested against the gravimetric measurements of kernel weight and shell weight in diverse peanut pod varieties1. Both methods predicted the kernel mass with R2 > 0.93 (XRT: R2 = 0.93 and mean error estimate (MAE) = 0.17, CNN: R2 = 0.95 and MAE = 0.14). While the shell weight was predicted more accurately by CNN (R2 = 0.91, MAE = 0.09) compared to XRT (R2 = 0.78; MAE = 0.08). Conclusion Our study demonstrated that the X-ray based system is a relevant technology option for the estimation of key peanut produce indicators (Figure 1). The obtained results justify further research to adapt the existing X-ray system for the rapid, accurate and objective peanut procurement process. Fast and accurate estimates of produce value are a necessary pre-requisite to avoid post-harvest losses due to fungal contamination and, at the same time, allow the fair payment to farmers. Additionally, the same technology could also assist crop improvement programs in selecting and developing peanut cultivars with enhanced economic value in a high-throughput manner by skipping the shelling of the pods completely. This study demonstrated the technical feasibility of the approach and is a first step to realize a technology-driven peanut production system transformation of the future.
Biodiversity and Importance of Plant Bioprospecting in Cosmetics K. Sri Manjari, Debarati Chakraborty, Aakanksha Kumar, Sakshi Singh Bioprospecting of Plant Biodiversity for Industrial Molecules, 2021 Bioprospecting is a methodical search for natural ingredients and genes in wildlife that have the potential to be turned into industrial products by biological, genetic, and chemical manipulation and without harming nature. Bioprospecting in cosmetics has made leaps from utilizing plant seeds to fungi, from traditional and herbal cosmetics to vegan and natural products made from seaweed and oats. The undiscovered potential of our ecosystem and diverse species has never-ending possibilities of biological value. The chapter aims to outline the various aspects of bioprospecting in cosmetic industry addressing the need to keep in line with various ethical guidelines and enlisting various natural products in use in cosmetic industry.
A Critical Evaluation Revealed the Proto-indica Model Rests on a Weaker Foundation and Has a Minimal Bearing on Rice Domestication Avik Ray, Debarati Chakraborty, Surajit Ghosh Ancient Asia, 2020 We have evaluated the proto-indica model that is the proponent of multiple domestication of rice but a single origin of the key genes in japonica. Attainment of non-shattering, a marker; appeared least integral to the initial phases of domestication. The other archeological determinants were less discernible in specimens. Existence of the key domestication genes in the wild rice and absence of introgression signature in indica further weakened the hypothesis. Moreover, japonica introduction from China happened in a backdrop of a culture exploiting domesticated rice. Summarizing, we propose that proto-indica model has a little bearing on rice domestication.
Population genetics analyses of North-East Indian indigenous rice landraces revealed divergent history and alternate origin of aroma in aus group Debarati Chakraborty, Avik Ray Plant Genetic Resources Characterisation and Utilisation, 2019 The rice-based agriculture of the Indian subcontinent has been interwoven in the rich socio-cultural fabric of the country. Of which, bio-culturally diverse North-Eastern states nurture thousands of landraces with poorly tapped agronomic traits. In the present study, 27 standard microsatellite data from 171 rice landraces from six states were analysed to understand their genetic diversity and population structure. Further, combining with a global dataset, we determined subpopulation identity using both model-based and multivariate analyses to uncover their history. We found moderate to high genetic diversity and high differentiation [standardized G”ST = 0.57]. The AMOVA partitioned overall variance into within population (75%) and among population (25%). The landraces from six states remained at various degrees of differentiation (pairwise FST = 0.09–0.41). We have detected a preponderance of aus-type in a majority of aromatic landraces. Rests were japonica and admixed with a little representation of indica. The presence of aromatic aus probably implied assimilation into local culture from the primary aus growing region of Bangladesh and India. Likewise, the arrival of japonica may stem from the exchange of goods among neighbouring dynasties via Southern and Southwestern Silk routes. The shared ancestry may reflect a merger of two ancient cultures. Our analyses also uncovered the existence of aus-type short and medium grain aromatic rice predicting an origin of aroma in aus subpopulation. Collectively, it demonstrated the diversity and divergent history of the rice landraces have been shaped by various socio-cultural interactions operative over time and space.
Origin of the Aromatic Group of Cultivated Rice (Oryza sativa L.) Traced to the Indian Subcontinent Peter Civáň, Sajid Ali, Riza Batista-Navarro, Konstantina Drosou, Chioma Ihejieto, Debarati Chakraborty, Avik Ray, Pierre Gladieux, Terence A Brown Genome Biology and Evolution, 2019 The aromatic group of Asian cultivated rice is a distinct population with considerable genetic diversity on the Indian subcontinent and includes the popular Basmati types characterized by pleasant fragrance. Genetic and phenotypic associations with other cultivated groups are ambiguous, obscuring the origin of the aromatic population. From analysis of genome-wide diversity among over 1,000 wild and cultivated rice accessions, we show that aromatic rice originated in the Indian subcontinent from hybridization between a local wild population and examples of domesticated japonica that had spread to the region from their own center of origin in East Asia. Most present-day aromatic accessions have inherited their cytoplasm along with 29–47% of their nuclear genome from the local Indian rice. We infer that the admixture occurred 4,000–2,400 years ago, soon after japonica rice reached the region. We identify aus as the original crop of the Indian subcontinent, indica and japonica as later arrivals, and aromatic a specific product of local agriculture. These results prompt a reappraisal of our understanding of the emergence and development of rice agriculture in the Indian subcontinent.
But does it taste good? A plea to consider the importance of flavor in managing plant genetic resources EJB von Wettberg, CR Banks, D Chakraborty, T Getahun, M Bakir, ... Plants, people, planet 7 (6), 1585-1595 , 2025 2025 Citations: 1
Utilizing X-ray radiography for non-destructive assessment of paddy rice grain quality traits M Tharanya, D Chakraborty, A Pandravada, R Babu, M Gangashetti, ... Plant Methods 21 (1), 94 , 2025 2025 Citations: 2
Utilizing X-ray radiography fornon-destructive assessment ofpaddy rice grain quality traits M Tharanya, D Chakraborty, A Pandravada, R Babu, M Gangashetti, ... 2025
Mangroves as an effective tool of phytoremediation and its implications on agricultural land in estuarine zones D Chakraborty Phytoremediation and Biofortification, 131-146 , 2024 2024 Citations: 7
Use of Allele-Specific Amplification for Rapid Identification of Aromatic and Non-aromatic Rice Germplasms D Chakraborty Plant Comparative Genomics, 269-279 , 2022 2022
X-ray driven peanut trait estimation: computer vision aided agri-system transformation D Martha, C Debarati, H Eva, C Joelle, W Norbert, V Marijn, A Krithika, ... Plant Methods 18 (76) , 2022 2022 Citations: 15
Biodiversity and importance of plant bioprospecting in cosmetics KS Manjari, D Chakraborty, A Kumar, S Singh Bioprospecting of plant biodiversity for industrial molecules, 189-210 , 2021 2021 Citations: 8
An Investigation Of Genetic And Biochemical Characters Of Aroma In Traditional Indian Rice Landraces, And Its Larger Ecological Role In Plants C D University of Kalyani , 2021 2021
A Critical Evaluation Revealed the Proto-indica Model Rests on a Weaker Foundation and Has a Minimal Bearing on Rice Domestication A Ray, D Chakraborty, S Ghosh Ancient Asia 11 , 2020 2020 Citations: 1
Awn reduction and the domestication of Asian rice: a syndrome or crop improvement trait? S Svizzero, A Ray, D Chakraborty Economic Botany 73 (4), 477-488 , 2019 2019 Citations: 18
Population genetics analyses of North-East Indian indigenous rice landraces revealed divergent history and alternate origin of aroma in aus group D Chakraborty, A Ray Plant Genetic Resources 17 (5), 437-447 , 2019 2019 Citations: 20
Origin of the Aromatic Group of Cultivated Rice ( Oryza sativa L.) Traced to the Indian Subcontinent P Civáň, S Ali, R Batista-Navarro, K Drosou, C Ihejieto, D Chakraborty, ... Genome biology and evolution 11 (3), 832-843 , 2019 2019 Citations: 70
Assessment of potentially toxic metal (PTM) pollution in mangrove habitats using biochemical markers: A case study on Avicennia officinalis L. in and around Sundarban, India M Bakshi, S Ghosh, D Chakraborty, S Hazra, P Chaudhuri Marine pollution bulletin 133, 157-172 , 2018 2018 Citations: 86
The winged Guardians of rice fields: stories of Dragonflies and Damselflies D Chakraborty 10.13140/RG.2.2.22763.03364 , 2018 2018
Climate risks adaptation strategies for Indian Sundarbans MPP Ghosh S, Chakraborty D, Dash P, S Patra, NandyP https://peerj.com/preprints/26963/ , 2018 2018
Assessment of Flood-Emanated Impediments to Kaziranga National Park Grassland Ecosystem—A Binocular Vision with Remote Sensing and Geographic Information System SP Surajit Ghosh, Subrata Nandy, Debarati Chakraborty, Raj Kumar, Vishal ... Geospatial applications for natural resources management, 275-290 , 2018 2018 Citations: 3
Shattering or not shattering: that is the question in domestication of rice (Oryza sativa L.) A Ray, D Chakraborty Genetic Resources and Crop Evolution, 1-5 , 2017 2017 Citations: 15
An analysis of variation of the aroma gene in rice (Oryza sativa L. subsp. indica Kato) landraces D Chakraborty, D Deb, A Ray Genetic Resources and Crop Evolution 63 (6), 953-959 , 2016 2016 Citations: 20
Bio-monitoring of Heavy Metal Pollution of Mangrove Ecosystem using Biochemical-Markers D Chakraborty School of Oceanographic Studies. Jadavpur University , 2014 2014 Citations: 2
Reduction of Copper using Agricultural Waste SD S Mukherjee, Hasanuryaman, D Chakraborty, S Dutta, Papita Saha International conference on Food security and Environmental Sustainability … , 2009 2009
MOST CITED SCHOLAR PUBLICATIONS
A study of the thermodynamics and kinetics of copper adsorption using chemically modified rice husk H Jaman, D Chakraborty, P Saha CLEAN–Soil, Air, Water 37 (9), 704-711 , 2009 2009 Citations: 158
Assessment of potentially toxic metal (PTM) pollution in mangrove habitats using biochemical markers: A case study on Avicennia officinalis L. in and around Sundarban, India M Bakshi, S Ghosh, D Chakraborty, S Hazra, P Chaudhuri Marine pollution bulletin 133, 157-172 , 2018 2018 Citations: 86
Origin of the Aromatic Group of Cultivated Rice ( Oryza sativa L.) Traced to the Indian Subcontinent P Civáň, S Ali, R Batista-Navarro, K Drosou, C Ihejieto, D Chakraborty, ... Genome biology and evolution 11 (3), 832-843 , 2019 2019 Citations: 70
Population genetics analyses of North-East Indian indigenous rice landraces revealed divergent history and alternate origin of aroma in aus group D Chakraborty, A Ray Plant Genetic Resources 17 (5), 437-447 , 2019 2019 Citations: 20
An analysis of variation of the aroma gene in rice (Oryza sativa L. subsp. indica Kato) landraces D Chakraborty, D Deb, A Ray Genetic Resources and Crop Evolution 63 (6), 953-959 , 2016 2016 Citations: 20
Awn reduction and the domestication of Asian rice: a syndrome or crop improvement trait? S Svizzero, A Ray, D Chakraborty Economic Botany 73 (4), 477-488 , 2019 2019 Citations: 18
X-ray driven peanut trait estimation: computer vision aided agri-system transformation D Martha, C Debarati, H Eva, C Joelle, W Norbert, V Marijn, A Krithika, ... Plant Methods 18 (76) , 2022 2022 Citations: 15
Shattering or not shattering: that is the question in domestication of rice (Oryza sativa L.) A Ray, D Chakraborty Genetic Resources and Crop Evolution, 1-5 , 2017 2017 Citations: 15
Biodiversity and importance of plant bioprospecting in cosmetics KS Manjari, D Chakraborty, A Kumar, S Singh Bioprospecting of plant biodiversity for industrial molecules, 189-210 , 2021 2021 Citations: 8
Mangroves as an effective tool of phytoremediation and its implications on agricultural land in estuarine zones D Chakraborty Phytoremediation and Biofortification, 131-146 , 2024 2024 Citations: 7
Assessment of Flood-Emanated Impediments to Kaziranga National Park Grassland Ecosystem—A Binocular Vision with Remote Sensing and Geographic Information System SP Surajit Ghosh, Subrata Nandy, Debarati Chakraborty, Raj Kumar, Vishal ... Geospatial applications for natural resources management, 275-290 , 2018 2018 Citations: 3
Utilizing X-ray radiography for non-destructive assessment of paddy rice grain quality traits M Tharanya, D Chakraborty, A Pandravada, R Babu, M Gangashetti, ... Plant Methods 21 (1), 94 , 2025 2025 Citations: 2
Bio-monitoring of Heavy Metal Pollution of Mangrove Ecosystem using Biochemical-Markers D Chakraborty School of Oceanographic Studies. Jadavpur University , 2014 2014 Citations: 2
But does it taste good? A plea to consider the importance of flavor in managing plant genetic resources EJB von Wettberg, CR Banks, D Chakraborty, T Getahun, M Bakir, ... Plants, people, planet 7 (6), 1585-1595 , 2025 2025 Citations: 1
A Critical Evaluation Revealed the Proto-indica Model Rests on a Weaker Foundation and Has a Minimal Bearing on Rice Domestication A Ray, D Chakraborty, S Ghosh Ancient Asia 11 , 2020 2020 Citations: 1
Utilizing X-ray radiography fornon-destructive assessment ofpaddy rice grain quality traits M Tharanya, D Chakraborty, A Pandravada, R Babu, M Gangashetti, ... 2025
Use of Allele-Specific Amplification for Rapid Identification of Aromatic and Non-aromatic Rice Germplasms D Chakraborty Plant Comparative Genomics, 269-279 , 2022 2022
An Investigation Of Genetic And Biochemical Characters Of Aroma In Traditional Indian Rice Landraces, And Its Larger Ecological Role In Plants C D University of Kalyani , 2021 2021
The winged Guardians of rice fields: stories of Dragonflies and Damselflies D Chakraborty 10.13140/RG.2.2.22763.03364 , 2018 2018
Climate risks adaptation strategies for Indian Sundarbans MPP Ghosh S, Chakraborty D, Dash P, S Patra, NandyP https://peerj.com/preprints/26963/ , 2018 2018
Publications
PREPRINT
Preprint
Ghosh S, Chakraborty D, Dash P et al. 2018. Climate risks adaptation strategies for Indian Sundarbans.
POPULAR SCIENCE ARTICLE
1. Chakraborty D. Winged Guardians of rice fields: stories of Dragonflies and Damselflies. CEiBa Newsletter Vol. 1, Issue 2, 2018, DOI: 10.13140/ .
03364.
2. Chakraborty D. The scented story of rice. MarcH25, 2020.
3. Chakraborty D. Bhoot Choturdoshi - An ancient Shaak eating ritual with ethnomedicinal importance. CEiBa Newsletter Vol. 3, Issue 1, 2020, DOI:10.13140/
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