A Plant's Pathology, Physiology And Productivity

An international team of scientists has developed a machine learning-based computational software to design small RNA. The software is freely available as a web service at https://plantgrn.noble.org/pssRNAit/  to design small RNA for more than 160 plants. The pssRNAit helps scientists to identify the function behind plant properties. The tool will also allow researchers to develop a high yield crop variety suitable for growing in the desert and harsh climatic conditions. This work has been published in the “breakthrough technology” section of the September 2020 issue of the international journal Plant Physiology. Plant Physiology is one of the world's oldest and most well-respected plant science journals published by the American Society of Plant Biologists.

Food security for the growing global population of humans and livestock is a big challenge. Everybody requires sufficient and nutritious food for maintaining a healthy lifestyle. Farmers are losing crop output (agriculture production) because of less rainfall, high global temperature, and floods—these climatic changes reducing crop quality, food security, and agriculture economy worldwide. Furthermore, vast desert land is not suitable for farmers for agriculture purposes. Interestingly, several wild plants have been identified that can tolerate and grow in harsh climatic conditions; however, the details understanding behind these properties are not clearly known. “The pssRNAit helps scientists to identify the reasons behind plant tolerance against harsh climatic condition and pathogens. The tool will also help researchers to implement the identified properties in a plant to grow them in harsh climatic condition. Thus, the farmers will achieve maximum agriculture production with high nutritional value,” said senior author Dr. Kiran Mysore. He is a professor of Molecular-Plant Microbe laboratory and a Fellow of the American Association for the Advancement of Science (AAAS).

Genes are the heredity materials and responsible for the production of different proteins. These proteins are required for the structure and function of a plant.A plant produces small RNA molecules inside a cellto prevent protein production. However, small RNA is specific for a particular gene. This mechanism helps the plant selectively regulate the level of different proteins to perform the desired function and respond to its environment. Scientists exploited this mechanism for basics and applied studies in modern biology. When scientists want to understand a gene’s role behind a plant property, they artificially produce the small RNA against it that stops its protein production, resulting in a change in the properties. However, designing small RNAs against the desired gene without affecting other proteins' production is a big challenge. The pssRNAit software could create better small RNAs for a specific gene and thus provides a path to study gene functions in plants.

“In pssRNAit, we have implemented rules and computational models mimicking the small RNA production and binding properties to a gene. Besides, this software selects the pool of highly functional small RNA. In this way, pssRNAit designed highly effective and specific small RNA.The pssRNAit will help develop a better plant not only for securing food but also to clean environmental pollution,”said first author Dr. Firoz Ahmed, Assistant Professor at the University of Jeddah in Saudi Arabia. Originally hailing from Siwan, Bihar, Dr. Ahmed obtained B.Sc. (Hons) Biotechnology from Patna University, M.Sc. in Biotechnology from Aligarh Muslim University, and Ph.D. in Bioinformatics from Jawaharlal Nehru University, New Delhi.

( Dr Firoz Ahmed)

Prof. Patrick X. Zhao from Noble Research Institute at Ardmore, USA, is the project's principal investigator.“The pssRNAit software runs on a powerful, high-performance computing platform with more than 1,000 CPU cores for quick analysis. This tool could help to achieve effective and specific gene silencing and thus allows scientists to identify the genes and pathways responsible for plant properties,” said Prof. Zhao.

“We verified experimentally that pssRNAit design small RNA can prevent the protein production in plant,” said co-author Dr. Vemanna S Ramu, Assistant Professor,Regional Center for Biotechnology, Faridabad, India

This collaborative work was funded by the Noble Research Institute, Oklahoma Center for the Advancement of Science and Technology, and the National Science Foundation of the USA.

*F Ahmed, M Senthil-Kumar, X Dai, VS Ramu, S Lee, KS Mysore, PX Zhao,pssRNAit-a web server for designing effective and specific plant siRNAs with genome-wide off-target assessment,Plant Physiology (September 2020). DOI: https://doi.org/10.1104/pp.20.00293.