RNAi and Agriculture

DNA is the genetic code that determines all the characteristics of an organism. Cells convert the information contained in DNA into proteins by means RNAs that acts as an interpreter.  For many decades, it was believed the primary function of RNA is to translate the information from DNA to make proteins which impart specific traits to the organism. However, now we know that RNAs have multitude of functions, they catalyze biochemical reactions like enzymes and regulates complex pathways governing normal cellular processes as well as during biotic (insects, pests, diseases) and abiotic (drought, heat, cold, nutrient) stresses. RNA interference (RNAi) or RNA silencing is one such mechanism which controls gene expression in living cells.

RNA silencing is a natural phenomenon that cells use to turn off, or to reduce the activity of specific genes. It is also a defense mechanism that targets and destroys foreign genomes like viruses and transposons that invade living cells.  For example, double stranded RNA (dsRNA) formed during virus replication in plant cells can trigger RNAi.  dsRNA is targeted by RNAi machinery and cleaved into small RNA called short silencing RNAs (siRNA) in a sequence specific manner. siRNA made in plant cells can target incoming virus genome to which it has homology and degrade it via RNAi, eventually resulting in the recovery of plants from virus infections. siRNA that is formed in the cells against a virus can not only seek and destroy viruses of the same kind from establishing subsequent infections but also those viruses that share genome similarity with the first invading virus.

The principle of dsRNA targeting via RNAi is exploited by scientists to create plants that are resistant to pathogens and pests.  siRNAs synthesized in these modified plants interfere with RNA accumulation and protein production from the target genes (pests or host) leading to either dysfunction or destruction of the invaders thereby offering protection. RNAi approach  is used to develop  virus (Cucumber mosaic virus , Tobacco mosaic virus, Tomato spotted wilt virus, Bean golden mosaic virus, Banana bract mosaic virus, Rice tungro bacilliform virus, Potato virus X, Papaya ringspot virus etc ) insect ( corn root worm , cotton bollworm, Colorado potato beetle) nematodes(root knot nematode) , pathogenic fungi (Fusarium , Aspergillus, Verticillium, Phytophthora  sp etc) , and weed ( striga) resistant crop varieties.

Development of gossypol free cotton seed oil, soybean oil   with reduced levels of saturated fatty acids , allergen -free peanuts, decaffeinated coffee beans, tomato that is slow ripening and  with better shelf life , tomato with higher levels of antioxidants- lycopene, beta carotene , slow ripening apples and non browning potatoes,  etc  are few  other examples  where RNAi is deployed to create improved varieties of crops. Two RNAi enabled products–the now-browning Arctic Apple and the non-bruising Simplot potato–are being sold. Male sterile lines which are very valuable in the hybrid seed industry have also been generated via RNAi.

siRNAs generated during RNA silencing are also capable of targeting DNA and this is called RNA directed DNA methylation (RdRM) and is very important in genome regulation, chromosome modeling and is vital in trait inheritance.

MicroRNAs (miRNAs) are another type of short silencing RNAs that is the product of RNA silencing mechanism that regulates gene function in both unicellular and multi cellular organisms. miRNA are noncoding (do not code for proteins) RNAs that regulates the expression of genes in a tissue specific and timely manner.  MiRs also have various applications in agriculture.  For example; levels of plant hormones that are critical for cell division, differentiation, growth and development are controlled by microRNAs. By miRs based manipulation of genes involved in phytohormone pathways, seedless fruits with higher market value can be developed. miRs are also imperative in disease and abiotic stress mitigation

RNAi has been regulating agriculturally important traits in crop species for millions of years. Understanding of this innate mechanism has allowed scientists to produce crops with desirable traits more precisely, cheaply and quickly. Few crop varieties developed by RNAi are already deregulated in countries like USA, Brazil etc and available in markets. Many scientists in India are also using RNAi to create improved crop plants. However, taking this new technology from the laboratory to field in India will require concerted efforts and knowledge sharing between scientists, regulators and common man to ease public concerns regarding its safety.  Here’s hoping that India will realize the benefits of RNAi in agriculture before it’s too late and adopt them without any inhibitions.

By Radha Anandalakshmi, Scientist, Mahyco