Kutubuddin Mollaa and K C Bansalb
aScientist, Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack. Odisha
bFormer Director, ICAR-National Bureau of Plant Genetic Resources, New Delhi
The recent review article in ‘Nature Plants’ by Indian scientists and others (Molla et al 2021) covers both the base editing and the prime editing technologies in a concise yet comprehensive way and gives the current status of base editors and prime editors in plants, technological developments in the field and their biological applications for crop improvement.
Traditional plant breeding has been instrumental in increasing the food production by developing improved crop varieties since long. It involves crossing of parental lines and selection of individual plants with desired traits and improved plant characteristics. Selection is based mostly on yield as a parameter without the knowledge of genetic composition of the selected plants. Development of high yielding wheat and rice varieties which gave birth to Green Revolution around mid-1960s is an example of this approach. The advent of molecular biology in 1970s and the development of DNA based molecular markers in 1980s facilitated screening of large breeding population for individual plants with desired genes and traits in a cost-effective manner. Marker assisted selection (MAS) thus permitted the identification of desired individual plants on the basis of genetic composition. This was followed by the identification of quantitative trait loci (QTLs) for complex agronomic traits governed by multiple genetic loci in several crop plants of agricultural and economic importance. Structural and functional genomics studies in crops such as rice, tomato, potato, etc. and other biological organisms led to the identification of causal genes and alleles related with key agronomic features. This became the basis of genetic engineering and consequently transgenic crops were developed with several improved traits like resistance to herbicide, nutritional quality improvement, resistance to insect and pathogens, etc.
Currently, we are witnessing the use of a versatile technology –CRISPR-Cas9 mediated genome editing with huge potential to accelerate crop improvement by facilitating targeted modifications of individual or multiple genes (Figure 1). The 2020 Chemistry Nobel Prize was awarded to the developers of this technology – Emmanuelle Charpentier and Jennifer Doudna. This novel technology has a tremendous promise for basic biological research, human therapeutics, agriculture and environmental sustainability. Consequently, we see a great opportunity ahead for another revolution in agriculture, particularly by developing smart crops with desired attributes to bring sustainability in crop production.
CRISPR is used to make a desirable change at a precise spot within the DNA of a plant. Scientists with this tool in their hand can remove or alter plants’ own DNA for making them more useful. CRISPR is not the first method invented to change DNA. Spontaneous change in plant DNA is a natural process, that happens at a slow pace. Some changes result in the development of beneficial traits. When plant breeders learned the fact, they started trying to induce changes in DNA artificially in 1940s. Plant breeders have been using radiation like X-rays and gamma rays, and chemicals like alkylating agents to randomly modify plant’s DNA. To see if the random changes cause the generation of any useful trait, the whole lot of radiation/chemical-treated plants must be evaluated. According to a data by FAO, nearly 2500 plant varieties have been developed by radiation-induced DNA modification.
What are the advantages CRISPR-Cas system brings to the breeder’s tool bag? CRISPR allows breeders to make changes precisely at a desired spot in the DNA instead of inducing random changes here and there. Additionally, it saves a great deal of efforts and time. CRISPR works by generating a cut at a targeted location in the DNA. Once the cut is recognized, plant cell often inadvertently introduces small changes while repairing the cut.
Today, scientists across the globe are engaged in improving crops for both consumers and growers. Rice with higher yield and bacterial disease resistance, rice that grow in less water, wheat with reduced gluten level, tomato with a special component that reduces blood pressure, soybeans with reduced unhealthy fats, bananas that can fight deadly virus and fungus or enriched with beta-carotene, non-browning mushroom, cassava with reduced neurotoxin and many more are the type of improvements that breeders rapidly achieve with CRISPR.
More recently, the invention of two powerful advanced genome editing technologies, base editing and prime editing, has further enhanced the precision and the efficiency in generating edited plants with improved traits. The review article by Molla et al (2021) covers both the base editing and the prime editing technologies in a concise yet comprehensive way and gives the current status of base editors and prime editors in plants, technological developments in the field and their biological applications for crop improvement. If conventional CRISPR-Cas tools are like scissors to make DNA cut at a predefined position, base editing tools are like pencils to rewrite single DNA letter, and prime editing tools are like word processors that search for specific DNA sequence and precisely replace them. Together these two tools give us more power for precision breeding like never before.
In addition to the DNA present in the nucleus, plants also have DNA in their chloroplasts and mitochondria. Chloroplast DNA is crucial in plant’s productivity, while mitochondrial DNA plays important role in generating hybrid crop varieties. Molla et al (2021) describes how base editing tool has been repurposed for modifying plants’ chloroplast and mitochondrial DNAs. Base editors enhance mitochondrial and chloroplast genetic diversity, which could fulfill the long-sought desire of the breeders to enhance our food supply. It is desired that these tools are employed for developing high yielding and resilient crop cultivars in the face of climate change. Moreover, these advanced technologies provide ample opportunities to improve crops with various complex agronomic traits. Examples of crop improvement by base editing and prime editing include, i) herbicide tolerance by modifying amino acids in enzymes that are targeted by herbicides, ii) improved nutrient composition by modifying biosynthetic pathway genes, splice sites or uORFs, iii) accelerated domestication by editing domestication genes in wild relatives of crop species, iv) converting a susceptible allele into a disease resistant allele, v) reducing the time required for the removal of deleterious alleles, vi) yield increase by targeted modification of endogenous genes, and vi) increased nutrient uptake, transport and utilization for increasing resource input-use efficiency (Molla et al, 2021). Final plant varieties created with conventional CRISPR-Cas, base editing, or prime editing technologies are practically indistinguishable from that of traditional selective breeding or mutation breeding.
It is highly recommended that we develop integrated breeding strategies combining the traditional breeding methods with advanced genome editing tools for sustainable agriculture and for ultimately meeting the United Nations Sustainable Development Goals (SDGs-2030). Importantly, we need to create an enabling policy space for effective use of these technologies for crop improvement for the benefit of Indian agriculture.
Molla, K.A., Sretenovic, S., Bansal, K.C. & Qi, Y. Precise plant genome editing using base editors and prime editors. Nat. Plants 7, 1166–1187 (2021). https://doi.org/10.1038/s41477-021-00991-1
Prof K C Bansal
Prof. Bansal obtained his doctoral degree from the Indian Agricultural Research Institute (IARI), New Delhi. He pursued advanced research from Harvard University, Cambridge, USA. Since his return from the USA, he served as Professor (Plant Biotechnology) at IARI; Coordinator, National Project on Transgenics in Crops; and Director, National Bureau of Plant Genetic Resources (ICAR), New Delhi. He was the first to get selected for the prestigious Norman Borlaug Chair (ICAR-National Professor) for crop improvement. Currently, Prof. Bansal is Secretary of the National Academy of Agricultural Sciences, and Member, Board of Directors, Global Plant Council. He is on the Editorial Board of Plant Biotechnology Journal (UK).
His research interests include genome engineering and functional genomics for enhancing abiotic stress tolerance in crop plants. Prof. Bansal has supervised over 20 doctoral students, and imparted training to over 500 scientists and scholars at national and international level. Many of his students got national level awards like Jawaharlal Nehru best thesis award of the ICAR, National Young Scientist awards and the IARI Gold Medal. Prof. Bansal is a recipient of several awards, and is Fellow of the National Academy of Agricultural Sciences, and the National Academy of Sciences, India.
Dr Kutubuddin Molla
Dr. Kutubuddin Molla is a scientist at the ICAR-National Rice Research Institute, Cuttack. He has obtained his Ph.D. from the University of Calcutta, Kolkata. Dr. Molla is the recipient of the prestigious Fulbright fellowship. He has done his post-doctoral research on genome editing at the Pennsylvania State University, USA, from 2017-2019. Dr. Molla has recently received the ‘INSA Medal for Young Scientist-2020’ award from the Indian National Science Academy, New Delhi. He is also the recipient of the AAAS/Science Program for Excellence in Science from the American Association for the Advancement of Science (AAAS), Washington D.C.
Dr. Molla has several publications in high impact factor journals. His research interests include precise genome editing, CRISPR-Cas system and other advanced editing technologies for crop improvement.