Genomics: Insight

CRISPR/Cas9 and Revolutions in Rice Crop Disease Resistance

Successful genetic modifications against rice blast and the Xoo pathogen.

Sabrina Zhang
April 11, 2022


With the development of CRISPR/Cas9, the technology’s transformational modifications to plant genes can significantly increase resistance to diseases affecting the production of rice crops. 



Rice is essential to the diets of 3.5 billion people around the world, serving as 50% of caloric intake and a significant portion of protein intake for 520 million impoverished people in Asia.1 However, around 10% and 30% of rice harvest is lost to rice blast disease each year with bacterial blight accounting for yield losses ranging from 20-80%.2 3 In order to best combat such epidemics, scientists have turned to the Nobel Prize Winning genetic engineering technology– the CRISPR/Cas9 system. CRISPR/Cas9 has enabled scientists to introduce mutated DNA sequences that are then inherited by the next generation of plants, illustrating how genome editing can shift the evolution of plants. 


Rice Blast

Rice blast, scientifically known as Magnathorpe Oryzae, attacks rice crops by forming lesions throughout the plant, spanning from panicles to roots. Researchers have observed that the most effective and economical way to combat rice blast is through genetic engineering which propagates beneficial mutations among breeding programs.4 The OsERF922 gene in rice plants is a transcription factor that reduces plant resistance when overly expressed. CRISPR/Cas9, a genetic engineering tool that adds, alters, and or removes sections of DNA, has proved effective in manipulating the gene. Scientists used the CRISPR/Cas9 technique to create mutations, alterations of the DNA sequences, in the OsERF922 genes. Contrasting the performance of C-ERF-922-induced mutated plants to those of wildtype rice with non-mutated OsERF922 genes, genetically modified plants proved more resistant in the presence of disease. Data revealed that the average area of lesions in the third leaf of inoculated crops indicated 30-50% reduction of lesion size among genetically edited plants in comparison to organically grown rice crops.4 Specifically, plants in the tillering phase saw lesion lengths of 3-4 mm in CRISPR/Cas9 mediated crops, almost two to three times smaller than the size of the wildtype rice crop which had lesions of nearly 9mm.5 The drastic difference in size and severity of rice blast symptoms signifies a substantial increase in resistance through mitigation of lesions, which harm crops by interference and or reduction of photosynthesis, absorption of nutrients, and respiration. Lesions, characterized by brown, gray, and yellow symptoms, directly shrink the available “green” area on rice plants, damage chloroplast, and deteriorate remaining leaf tissue, which, compounded with an increase in “dark-leaf” respiration for maintenance, impairs the plant’s ability to undergo photosynthesis at various stages. In addition to disruption of light reception, rice blast’s impairment of radiation interception and radiation use efficiency – the unit by which plant biomass accumulation can be quantified– are responsible for 50-70% of the decline in rice production.6 The destruction of plant tissue obstructs rice crops’ ability to transport and absorb nutrients such as water through the stomata, further inhibiting rice crop performance. After the appearance of lesions, spore production begins, which can last for 20-30 days. Major spore production (90% of all spores produced) during the initial 14-day window led to reduction in carbohydrate production was approximated to be 200kg formaldehyde per plant.6 Thus as significant stresses to plants in early life stages prolongs the tillering phase and delays proper maturation of rice plants, rice blast prevents proper harvesting and lowers yield.  

Genetically modified crops indicated 30-50% reduction of lesion size.


Bacterial Diseases In Rice

Another devastating disease of rice crops, Xanthomonas oryzae pv. Oryzae (Xoo) that causes bacterial blight and leaf streaks, most prominently seen in Asian and African countries, has also been addressed using the CRISPR/Cas9 system to target the OsSWEET14 gene which is associated with disease resistance. The genetically-altered OsSWEET14 gene resulted in greater resistance in plants against four strains of the Xoo pathogen, relative to the unaltered gene.7 Lesions created by the pathogen on unedited plants were highly concentrated for 15 cm along the leaves, streaking along the plant for an additional 15 cm; however, mutated plants demonstrated marked resistance to the Xoo pathogen as lesions across all genetically modified plants had an average lesion length under 2 cm.7 Furthermore, mutated rice crops experienced another advantage to OsSWEET14 modifications due to the gene’s primary expression in the vascular tissue like the stems. OsSWEET14 was found to have enhanced growth when in its newly mutated state: differences in plant height reached an 8% increase for mutated crops with a maximum improvement of 7 cm.7 

CRISPR/Cas9 editing improves disease resistance, thus lowering GHGs and aiding global hunger relief.



As a result of CRISPR/Cas9 editing to both OsERF922 transcription factors and OsSWEET14 sugar transporters, genetically modified rice crops display higher resistance to rice blast and the bacterial disease Xoo. With leaves, stems, and panicles vulnerable to pernicious infections, deterrence of consequent lesions and spores is crucial to maintaining the quality and health of rice plants. Due to the inheritable mutations created by CRISPR/Cas9 engineering, plants will not only survive and counteract infections but also become more readily able to reinforce resistance against different strains of diseases for generations to come. The impact of CRISPR/Cas9 technology extends beyond these diseases. Breakthroughs within the OsERF922 gene itself have proven that regulation of expression and modifications can improve tolerance to salt stress and acidic conditions.8 In the status quo, diseases are responsible for 14.1% of all crops lost worldwide and cost the global economy $220 billion each year.9 As global warming severely compromises the available land for rice production by 18-51% in the tropics in the next century, factors such as water scarcity, storms, and salinization further threaten global food security by directly diminishing yield and fostering prime conditions for new epidemics.10 Furthermore, rice waste releases large amounts of potent greenhouse gases such as methane and nitrous oxide, chemicals even more destructive than carbon dioxide.11 12 Counteracting deadly diseases is increasingly vital from both an environmental perspective and a humanitarian stance. With CRISPR/Cas9 innovations, rice crops can better curtail consequent greenhouse gas emissions and contribute to global hunger relief though higher yield. 



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  2. Saha, S., Garg, R., Biswas, A., & Rai, A. B. (2015). Bacterial Diseases of Rice: An Overview. Journal of Pure and Applied Microbiology, 9, 725–736. 
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  10. Srinivasan, B., & Gnanamanickam, S. S. (2005). Identification of a new source of resistance in wild rice, Oryza rufipogon to bacterial blight of rice caused by Indian strains of Xanthomonas oryzae pv. oryzae. Current Science, 88(8), 1229–1231.
  11. Yan, X., Akiyama, H., Yagi, K., & Akimoto, H. (2009). Global estimations of the inventory and mitigation potential of methane emissions from rice cultivation conducted using the 2006 intergovernmental panel on climate change guidelines. Global Biogeochemical Cycles, 23(2). 
  12. Cai, Z. C. (2012). Greenhouse gas budget for terrestrial ecosystems in China. Science China Earth Sciences, 55(2), 173–182. 

About the Author

Sabrina Zhang

Sabrina Zhang is a high school junior at Polytechnic School, California. Fascinated by biological breakthroughs and research, she is passionate about environmental protection and discovering less commonly known contributors to climate change such as food and harvest waste.