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About the Programme

The focus of the Biotechnology programme at MSSRF is to undertake strategic and anticipatory research to develop socially relevant products from our locally adapted natural resources, to address issues related to environmental degradation, changing climate scenarios such as sea level rise, reduced precipitation and deteriorating soil and water quality. This is achieved by utilising cutting-edge science and relevant technologies particularly genomics, proteomics and molecular breeding tools, while also focusing on bioprospecting niche specific biological resources: microbes and plants and utilise them for improving soil and plant health.

The nutri-garden approach is expected to provide multiple benefits including bridging the disconnect between agriculture and nutrition, growing nutritionally important crops in farms, increase awareness on nutrition-related issues among consumers, and increase consumption of a nutritive and balanced diet by the people for a healthy society.

Major activities therefore focus on understanding genetic and genomic architecture of naturally stress tolerant species using whole transcriptomic profiling, functional characterisation of abiotic stress responsive genes and transgenic characterization of selected genes in limited field trials. The group has been executing effective lab-to-land transition intervention to address the technology needs of small and marginal farmers in addressing plant and soil health and improving crop productivity by an integrated approach.

An outreach programme for the school students, ‘The Every Child A Scientist’ aims at inculcating a scientific temper among middle-school students studying in Corporation schools to make learning a joyful experience.

About 48 PhD theses on the above anticipatory areas of research have been submitted to the University of Madras and Doctoral degrees awarded. The group has also published more than 170 peer-reviewed research articles in high impact peer reviewed journals of national and international repute and presented their findings in many national and international conferences.

The Biotechnology Programme Area has established robust collaborations with national and international organisations in the chosen area of research for the past 30 years and continues to work in this collaborative mode through exchange programmes for scientists and research scholars. The team collectively identifies gaps and leads (successes) to formulate and develop new proposals, and thus has been able receive continuous support from the funding agencies.

Vision: The vision of the programme is to enhance resilience of agricultural production systems to abiotic stress and contribute to nutrition security.

Mission: The mission of the programme is to utilise cutting edge biotechnological tools to generate and extend new knowledge and products to add value to existing farming systems. anticipating changing scenarios of climate and chronic levels of malnutrition.


  • Increased crop productivity (rice) under abiotic stress
  • Bridge the disconnect between farming system and nutrition through adoption of elite nutri-rich plants
  • Improved nutrient status of soils and increased crop productivity of millets and spices

Our Focus

The programme is engaged in the application of cutting-edge biotechnological tools for improving agriculture productivity under increasing abiotic stress (salinity), enhancing soil nutrients and promoting elite nutri-rich plants to address malnutrition. Enhancing the scientific knowledge base for suitable application in the areas of plant abiotic stress tolerance, soil health management and nutritional security is another area of research.

Core working areas include:

  • Utilising molecular, bioinformatics, plant breeding technologies and microbial products to addressing plant biotic and abiotic stresses, enhancing soil nutrients and quality and quantity of produce.
  • Capacity building and creating a cadre of skilled human resources (research scholars) in advanced areas of biotechnology and knowledge management (peer reviewed publications/patents).
  • Collaborating with suitable institutions and also with other programme areas at MSSRF for product and model development.

This is achieved through four core thematic areas of research:

Theme 1: Abiotic stress tolerant crops for resilient agriculture under changing climate

The Biotechnology programme aims to develop locale-specific products for abiotic stress against the backdrop of climate change. This research is mostly anticipatory and uses cutting-edge tools to delineate basic mechanisms of abiotic stress tolerance in rice species. In addition, it also examines natural variation in crop landraces with regard to abiotic stress tolerance to identify products that address local needs. The group has produced pioneering research data on genetic fingerprinting of saline tolerant mangrove and associate species as well as detailed characterisation of specific genes from mangroves that are highly cited in that area of research. The group has now moved into examining the function of transporter genes in relation to salinity tolerance in mangroves and rice.

Theme 2: Addressing hidden hunger through nutri-rich plants and biofortified crops

The nutri-garden programme is expected to address United Nation Sustainable Developmental Goals (UN SDG) Goal 2 ‘Zero Hunger’ and aims to use food-based strategies to improve diets (including availability of nutri-rich food, dietary diversification) in both quantity and quality in order to overcome and prevent malnutrition throughout the lifecycle of an individual. The nutri-garden approach is expected to provide multiple benefits, including bridging the disconnect between agriculture and nutrition, growing nutritionally important crops in farms, increase awareness on nutrition related issues among consumers and increase consumption of a nutritive and balanced diet by the people, leading towards a healthy society.

Theme 3: Microbial products for sustainable agro-ecosystems

The microbiology group focuses on research, development and dissemination of eco-friendly technologies through innovative delivery models to promote sustainable agricultural practices. The research focus is technology specific (eg. biofertilizers, biopesticides, and biocontrol agents) and need based solutions to address problems encountered at farm level that integrate nutrient and disease management practices. Through intensive training, demystified technologies for bioproduct manufacture have been transferred to community managed enterprises. The key strengths of the group have been in executing effective lab-to-land transition of microbial products, demonstration of their efficacy in field trials, validation of field data in the form of peer reviewed publications and transfer of the technology to farmers for utilisation in fields.

Theme 4: Genetic Literacy

The ‘Every Child A Scientist’ (ECAS)” programme at the M.S. Swaminathan Research Foundation aims to kindle scientific temper among middle school students studying in Corporation schools. The ECAS Programme. revived after the Covid-19 pandemic with support from L&T Chennai. and is being implemented using modern digital teaching tools such as interactive smart boards, personal computers and internet that reinforces and provides deeper understanding of STEM (Science, Technology, Engineering and Mathematics) concepts. Further ‘learning science by doing’, improves the creative thinking of students. Hence, a laboratory to conduct basic experiments is also available under the programme. This encourages students to study independently by exploring and researching and instils self-confidence and also enhances learning opportunities.

Achievements & Publications

Theme 1 – Abiotic stress tolerance in crops and lessons for Resilient Agriculture under changing climate

The Plant Molecular Biology Laboratory at MSSRF has been working in the area of abiotic stress tolerance over the last three decades. The major activities of the programme, therefore, have focused on understanding mechanisms of abiotic stress tolerance in naturally stress tolerant species and to apply these learnings to crop species. The laboratory has specialised in the area of salinity stress tolerance in plants.

The pioneering work carried out at MSSRF with regard to mangrove phylogeny over two decades ago is now being extended to examine mangrove development and growth traits in relation to salinity and to examine gene networks governing these traits. Excessive sodium in soil is toxic to plant species as it competes with potassium (a major macronutrient) in plants, inhibiting overall metabolic activity, thereby impacting growth and photosynthesis (ionic component).

Salinity tolerance is a complex trait and the gene networks, transporters governing ion movement are conserved in both salt sensitive (glycophytic) and salt tolerant (halophytic) species. What perhaps differentiates glycophytic and halophytic species is how these genetic networks or transporters function to allow halophytes to adapt to excess sodium (and also chloride) as a way of life. Salinity tolerance in glycophytes relies primarily on ‘shoot ion exclusion’ mechanisms: limiting sodium entry to the shoot. On the other hand, halophytes have remarkable ‘tissue tolerance’ i.e. the ability to accumulate sodium in the osmotic component of salinity stress water uptake tissues and utilize it to drive growth driven processes, otherwise requiring potassium. The approaches used in the laboratory include classical gene/promoter isolation and characterization methods, stress physiology, cellular microscopy, and biochemical methods as well as natural variation screening in rice. The pioneering work carried out at MSSRF with regard to mangrove phylogeny over two decades ago is now being extended to examine mangrove development and growth traits in relation to salinity and to examine gene networks governing these traits.

Exhaustive characterization of transporter gene function from mangrove associate species – We have used halophytic model species (mangroves and mangroves associates eg. Avicennia marina and Oryza coarctata) to understand transporter gene function in relation to salinity tolerance. These include the vacuolar antiporter gene (NHX1) and the plasma membrane localized High-Affinity Potassium Transporter (HKT1;5) from O. coarctata. Some learnings from the research in the halophytic wild rice O. coarctata is now being extended to understand salinity tolerance in the cultivated rice, Oryza sativa. These studies showed that halophytic species differ from their glycophytic counterparts in the tissue specific expression patterns of genes as well as in extensive post-transcriptional control in expression of these genes. Further, specific amino acid residue determinants in orthologous transporters from related species may be crucial determinants of sodium transport and hence salinity tolerance.

Genotyping and Phenotyping coastal rice landraces for salinity tolerance – The vast coastline of India is host to an enormous diversity of naturally evolved saline tolerant rice landraces that are a valuable genomic resource to explore the complex and polygenic nature of salinity tolerance in rice. Rice landraces (including tolerant and sensitive checks) originating from geographically divergent coastal regions of India have been genotyped using a set of genome wide Simple Sequence Repeat (SSR) markers. Phenotyping of rice landraces in hydroponics using using morpho-physiological and biochemical parameters has resulted in the identification of novel genotypes as potential sources of salinity tolerance (including tissue tolerance). Four marker trait associations (accounted for phenotypic variations in the range of 20.97- 39.82%. A significant increase in root endodermal and exodermal suberization was observed in selected rice landraces under salinity. Within salt tolerant landraces, the Saltol/SKC1 locus is a major determinant of shoot sodium concentration. allelic variation in the sodium transporter gene OsHKT1;5 within the Saltol/SKC1 locus) contributes to specific codon changes (SNPs) that correlate with differences in salinity tolerance of rice varieties. Cleavage Amplified Polymorphic Sequence (CAPS) marker (OsHKT1;5V395) that targets one of these codons in OsHKT1;5 has been developed along with an additional CAPS marker that targets an indel in the OsHKT1;5 promoters and validated in this set of landraces.

Bio-saline agriculture revival of Kagga cultivation – Kagga crop is a paddy variety growing in saline soils of Ghazini area (Aghanashini estuary) in coastal Karnataka. The paddy variety has longer internodes, growing up 160 cm in height and has a long panicle with awns on the seeds. Kagga paddy also shows high submergence and salinity tolerance, tolerating flooding for up to even days. Seven different types of Kagga paddy variants with distinct plant and grain type along with productivity were identified. All these Kagga varieties have red kernels but differ in grain type and awn characters. Under the crop improvement programme, we now are evaluating a segregating population for desirable traits like high yield, short stature, high tiller numbers, non-lodging character, awnless plants as well as tolerance to salinity and submergence conditions. Lines with suitable agronomic traits will be selected and further evaluated under different saline conditions.

Theme 2 – Addressing hidden hunger through nutri-rich plants and biofortified crops

Prof. M. S. Swaminathan recommends a food-based approach to eradicate malnutrition by increasing the availability and consumption of micronutrient-rich foods as, in the long-term, these approaches are more sustainable. MSSRF is advocating and demonstrating ‘Farming System for Nutrition’ or Food Diversity for Nutrition – a movement, to eradicate malnutrition, using locale specific nutri rich crop species.

Food based nutritional security through Nutri- Garden approach – Nutri-gardens have been established in four agro-ecological zones of the country in collaboration with Krishi Vigyan Kendras (KVKs) at Palghar, Maharashtra; Tirur, Tamil Nadu; Kanpur (Dehat), Uttar Pradesh and Jeypore (MSSRF Campus), Odisha. Each nutri-garden has sections for a micronutrient and relevant seasonal and annual plants that can supply the micronutrient to ensure nutrition security all year round. All nutri-gardens have an interpretation centre and a mother nursery for the multiplication of nutrient-rich plants. The mother nurseries provide training to farmers for seedling production and distribute the nutrient-rich plants to farmers and households.

Advocating nutrition literacy – Creating awareness on the importance of the nutri-garden is very vital by advertising the nutri-garden concept through pamphlets, posters, and booklets. Target groups include farmers, anganwadi workers, adolescent girls, pregnant and lactating women, and children under the age of five. Booklets titled “Nutrition through the Lifecycle’ in different vernacular languages (Tamil, Hindi, Marathi, Odia, and English), have been released, emphasizing the role and importance of nutrition at various stages of life, as well as the dietary sources to be included to meet these nutritional requirements.

Toolkit for Establishing a Nutri-Garden – A booklet titled “Toolkit for Establishing a Nutri-Garden” provides complete information on the whole process of setting up a nutri-garden, right from field preparation to making a healthy plate. It includes designing the layout, selection of locale specific nutri-rich plants, crop and pest and disease management practices. MSSRF has developed a web page with details of 150 nutrient-rich crops that can be included in the nutri-garden, with crop nutrition profiles and cultivation aspects that serves as a knowledge source of nutri-rich crops. A nutrition intervention study scrutinizing the impact of nutri-garden and trainings on the nutritional status of beneficiary farmers is in progress.

Nutrition Garden in the Chennai City for the urban community – A model nutri-garden Thiruvanmiyur, Chennai has been established for promoting nutritional awareness in the urban areas. Fifty species of fruits and vegetables rich in vitamin A, E, K, C, B and minerals like iron, calcium, phosphorus, zinc are being cultivated in the garden. MSSRF is a knowledge partner in setting up a nutri-garden at the premises of Chengalpattu Medical College Hospital (CMCH). The innovative garden design (shape of a foetus) emphasises the nutritional requirement of a child in the first 1000 days of life and also dietary sources of each nutrient.

Theme 3 – Microbial products for sustainable Agro-ecosystems

The microbiology laboratory for the last three decades, has carried out pioneering research on exploring the crop rhizosphere associated beneficial plant growth promoting bacteria (PGPB) communities for eco-friendly management of plant and soil health and to reduce chemical inputs. The group has identified and characterized more than 80 strains of PGRB, with multiple beneficial traits such as nitrogen fixation, phosphate solubilization, phytohormone production and biocontrol activities etc. Overall, about 500 microbial isolates from agricultural as well as from mangroves ecosystems are being maintained at MSSRF.

Beneficial microbes for soil and plant health management – Around twenty zinc and iron mobilising bacteria isolates that enhanced grain zinc and iron  content have been identified and the efficacy of the isolates tested in pot experiments. Biocontrol efficiency of thirty isolates for the control of phytopathogens such as Fusarium oxysporum, Fusarium solani, Fusarium graminearum, Pyricularia grisea, Rhizoctonia solani, Gaeumannomyces graminis, Xanthomonas campestris has been examined.

Pseudomonas sp. Plant growth promoting bacteria – Pseudomonas sp. MSSRFD41, a novel isolate from the finger millet rhizosphere shows several plant growth traits and biocontrol activity. This isolates tested positive for the production of antibiotics, 2,4-Diacetylphloroglucinol- (2,4,-DAPG), Pyrrolnitrin (PRN) and Pyoluteorin (PLT) siderophores and hydrolytic enzymes like cellulase. chitinase, glucanase. Whole genome sequencing of this isolate reveals genes governing additional traits:  genes for osmotic tolerance, cobalt-zinc-cadmium resistance genes, Phosphodiesterase/alkaline phosphatase, acid phosphatase, and Na+/H+ antiporter genes. Molecular tracer tool targeting the key functional gene PhlD specific to Pseudomonas sp. MSSRFD41 was developed to study the population density, colonization efficiency and the survivability period.

Field testing of mycorrhizal and pseudomonas consortia – The isolate was extensively tested for five successive years under multi-location field trials as dual inoculation with AMF, in finger millet and pigeon pea crops that conferred increased grain yield and was more effective than single inoculations. Compared to direct sowing, the line transplanting of pigeon pea increased average grain yield significantly across the site, and the yield gains due to biofertilization and the transplanting system were additive. These technologies thus offer a toolbox for sustainable yield improvement of pigeon pea and finger millet.

Pilot scale production cum training unit of PGPR and AMF – A pilot-scale production model unit of Arbuscular Mycorrhizal Fungi (AMF) by root inoculation method in a polyhouse has been set up. Pilot scale production of PGPR by fermentation process has also been set up, using two fermentors with capacity of 50 litres each. This serves as a training facility for AMF as well as PGPR production.

Technology popularization – The MSSRF DBT-Biotech KISAN hub project is being implemented in three aspirational districts of Odisha namely Koraput, Malkangiri and Rayagada and one aspirational district, in Kerala (Wayanad) with a focus to promote eco-friendly technologies for improving farming practices using bioinoculants, improved varieties, crop yield, sustainable use of soil and water to enhance soil health and to create access to rural processing technologies, value addition and market. So far in this programme, 1127 farmers have directly benefited in participatory demonstration trials in an area covering 450 acres, with 16033 farmers benefiting from via multiple training and awareness programmes.

Exploration of Mangrove microbial diversity – Mangroves are highly productive unique ecosystems, harbouring diverse unexplored microbial communities that play crucial roles in nutrient cycling as well as in maintaining ecosystem services. The mangrove-associated microbial communities transform the dead vegetation into nutrient sources of nitrogen, phosphorus, potash, etc.

Bacteria involved in biogeochemical cycling: Nitrogen cycle – A combination of both culturable and unculturable Polymerase Chain reaction -Denaturing Gradient Gel Electrophoresis approaches were adopted to explore the bacterial communities involved in nitrogen fixation by examining nifH genes, and denitrifiers by targeting the nirS and nosZ genes. Across the rhizospheres, gammaproteobacteria were found to be predominant, representing both nitrogen fixers and denitrifiers as revealed by culturable and unculturable analyses. Sequence analysis of soil nifH, nirS and nosZ genes clustered to unculturables, with few groups clustering with culturable groups, viz., Pseudomonas sp. and Halomonas sp. A total of 16 culturable genera were isolated and characterized in this study. Other phyla like firmicutes and actinobacteria were also observed. The PCR-DGGE analysis also revealed the presence of 29 novel nifH sequences that were not reported earlier.

Dimethylsulfoniopropionate (DMSP) biosynthesis – Communities involved in sulphur cycling -dimethylsulfoniopropionate (DMSP) biosynthesis and catabolism has been characterized. More than that 60 isolates harboured genes for the DMSP synthesis and catabolism process have been identified. Several acyl homoserine lactone and 1-aminocyclopropane -1- carboxylic acid (ACC) deaminase producing isolates have been reported.

DGGE analysis of archaea indicated the presence of 2 major groups such as Crenarchaeota and Euryarchaeota, which were further classified into 7 different genera.

Novel bacteria genus and species reported – Three Novel Genus and six – novel species were reported.

Genetic Literacy: Every Child A Scientist Programme – The Every Child A Scientist aims to kindle scientific temper Smart class room teaching/learning facilities with digital interactive smart boards, access to personal computers and the availability of internet resources reinforce understanding of Science, Technology, Engineering and Mathematics (STEM) concepts. This method of learning through smart devices also encourages students to study independently by exploring and researching, encourages creative thinking and instil self-confidence in students by adopting appropriate educational teaching tools. Accordingly, in the ECAS programme, innovative learning modules in Biology, Chemistry and Physics have been developed. These modules have been custom designed in alignment with the syllabi used for students in middle schools (6th, 7th, 8th and 9th grades) studying in the Corporation schools of Chennai.



Stories of Change

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Unexplored mangrove soils harbour novel microbial groups with multiple functions

Mangroves are highly productive unique ecosystems harbouring diverse unexplored microbial communities that play crucial roles in nutrient cycling as well as in maintaining ecosystem services. Research to uncover the microbe-mangrove interactions that maintain ecosystem services and resilience under changing conditions is urgently needed for successful conservation and rehabilitation of these fragile ecosystems as these communities play crucial roles in mangrove biogeochemistry and nutrient cycling.

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The dual benefits of Kagga cultivation cum aquaculture

Coastal agroecosystems have become more vulnerable due to climate change. Farm families in the Aghanashini Estuary region, Uttara Kannada district, Karnataka, are traditional cultivators of paddy that is always submerged in saline water. Unique to this ecosystem is the saline tolerant Kagga paddy that is cultivated in a growth cycle with marine shrimp/fish. However, area under Kagga is diminishing due to changes in land use, hyper-salinity, climate change, non-availability of quality Kagga seeds, low demand, and lack of modern agro-technologies.

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Raising awareness about Kagga rice

Kagga crop is a paddy variety cultivated in the saline soils of Ghazini area of the Aghanashini estuaries of coastal Karnataka. It has longer internodes (up to 140-160 cm in height) and a long panicle with an awn on the seeds. The dehusked rice grain is red-pigmented and slightly bigger in size. Kagga rice is a favourite food of local people, has several health benefits, is a rich source of nutrients, provides more energy to work for long hours, acts as coolant, prevents heat strokes, and is also used to treat diarrhoea and other digestive disorders.

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Beneficial bacteria for sustainable crop production in smallholder agroecosystems

Soil degradation restrains soil nutrition status and is considered as a significant cause to threaten global nutrition security. Soil management practices that enhance biological contributions to soil fertility and support sustainable farming systems is gaining more attention. One of the approaches for regenerative soil system is the use of cultured plant growth promoting microorganisms to achieve crop productivity.

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Adaptive traits for salinity tolerance in coastal rice landraces and halophytic rice wild relative

Soil salinization is identified as a major cause of land degradation, rendering land unsuitable for crop cultivation. Domestication of crops over the past 10,000 years has resulted in the loss of ancestral traits. Crop Wild Relatives (CWRs) can be important sources of salinity tolerance.

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Publications and Newsletters

International Conference 2021

This fortnight e-synergy has some of the eminent participants’ videos who speak on various issues related to food and agriculture.

MSSRF Annual Report 2020-2021

Thirty-First Annual Report

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