Our foundation is involved in a number of research initiatives. Most of our current activities are in areas identified as scientifically relevant and important in consultation with our scientific advisory board, but typically not funded by government agencies. We hope to publish our findings from these studies in top peer reviewed journals and in the process generate enough data to attract further support from funding bodies.

Our ongoing research activities cover areas of Agriculture, Animal health, Biodiversity, Genomics and Human Health.

The ongoing projects include the genomics of colored rice, metagenomics of rivers in India, wild elephant viral disease genomics, tea looper biocontrol agent development, familial cancer genomics and human genome variation studies.

Colored rice genomics

Rice is staple food for over half of the world population. Over 40,000 varieties are known. While rice genomes have been published, many traditional or wild varieties have not been sequenced. One such example is the Purple Puttu variety of rice, which is cultivated in Tamil Nadu and is used in the preparation of a traditional South Indian type of breakfast called ‘puttu’. The grains and leaves of this crop are purple, which indicate robust anthocyanin metabolic pathways.

In this project we aim to understand the molecular regulation of colour development, domestication and responses to stresses like drought, salt, cold and submergence of this rice. We also aim to produce a genome assembly that can serve as a reference for the indica varieties

SGRF has completed the genome sequencing. Studies on the regulation of anthocyanin synthesis in this crop are currently underway.

Metagenomics of Rivers in India

About 1.24 billion people, 17% of the world’s population, live in India and consume approximately half of India’s freshwater resources. Periyar River is the main source of drinking and irrigation water for the Idukki and Ernakulam districts in Kerala, India, home to 4 million people. The demand for water from Periyar will likely increase, as Kerala’s population is expected to grow by 7% from 2011 to 2026, and India’s total water demand is estimated to increase from 680 Bm3 in 2000 to 833 Bm3 in 2025. It is important to examine the health of the freshwater systems to efficiently manage and conserve them. Recent advances in DNA sequencing allows the metagenomic examination of the microbial flora of rivers and can provide a benchmark on environmental health of the river and the region. Metagenomic surveys can be used to track microbial populations in freshwater as climate, pollution, and usage of freshwater changes. Understanding microbial diversity is also important for the discovery of new genes and compounds for biotechnology since bacterial proteins have been used in drug therapies. Though a few freshwater metagenomes have been examined in general through out the world, there was no available metagenomic data from India.

Next-generation sequencing (NGS) technologies have enabled microbial communities to be studied in unprecedented detail and depth, increasing our understanding of microbial diversity in various environments by providing valuable information about microbial community structure, function, and diversity. NGS has enabled 16S rRNA gene sequencing to be used for taxonomic and phylogenetic analyses of microbial communities by generating more data at less cost, thus allowing researchers to survey more areas and sequence deeper.

We have in this study collected samples along the highly populated and thinly populated protected course of the Periyar River and performed a metagenomic analysis. The sequencing data is being analyzed to understand the metagenome of the Periyar river.

Wild Elephant Viral Disease Genomics

The largest remaining wild Asian elephant population inhabits the Nilgiri’s biosphere reserve. About 5000-8000 elephants are estimated to inhabit this area. Besides threat from human activities, elephants in the wild succumb to various diseases. More recently, a fatal haemorrhagic disease caused by Elephant Endotheliotropic Herpes Viruses (EEHVs) that infect elephant endothelial cells in the wild has been reported Kerala Forest Department (Journal of Wildlife Disease, 2013, 49:381). The disease affects mainly young Asian elephants and has a mortality rate of > 80%. We are in the process of isolating and sequencing the EEHV genome from India to fully understand the virus. Hopefully, this will allow development of rapid diagnostics tests and better management of the disease in the wild.

Tea Looper Biopesticide development

India is the second largest producer of tea (Camellia sinensis). Assam and West Bengal account for close to two-thirds of the total tea production in India. Buzura suppressaria - a common tea looper caterpillar has become a major tea defoliator and causes considerable damage to tea plants in the North-eastern part of India. Currently the pest is managed through use of conventional chemical pesticides adding to the cost of tea leaf production. Also, heightened concerns about residual pesticide levels affect pricing and marketability. Recently, Nuclear Polyhedrosis Virus (NPV) infection affecting tea loopers was reported. NPV have the potential for development as a biopesticide and can help reduce the use of chemical pesticides. We aim to sequence the tea looper genome to better characterize it and help develop it as a biopesticide

Human variation Project

Next generation sequencing (NGS) technologies have reduced the cost of sequencing while increasing the throughput. In contrast to the 3 billion USD and 10 years it took to complete the sequencing of the first human genome, today one can obtain a whole genome or exome (coding part of the genomes) sequence for under 5000 USD in a matter of 2-3 weeks. This dramatic progress in sequencing technologies has enabled assessment of population genetic diversity. Such information, besides being of scientific importance, is useful in managing human health and disease. Working with academic institutes and medical research groups we intend to sample genomic variations in the Indian subcontinent. A database of such variants will be valuable in understanding medically relevant variants in India