Understanding the Plant-microbe Interactions in CRISPR/Cas9 Era: Indeed a Sprinting Start in Marathon

Abstract

: Plant-microbe interactions can be either beneficial or harmful depending on the nature of interaction. Multifaceted benefits of plant-associated microbes in crops are well documented. Specifically, management of plant diseases using beneficial microbes is considered to be eco-friendly and the best alternative for sustainable agriculture. Diseases caused by various phytopathogens are responsible for significant reduction in crop yield and causes substantial economic losses globally. In an ecosystem, there is always an equally daunting challenge for the establishment of disease and development of resistance by pathogens and plants, respectively. In particular, comprehending the complete view of complex biological system of plant-pathogen interactions, co-evolution and plant growth promotions (PGP) at both genetic and molecular levels require novel approaches to decipher the function of genes involved in their interaction. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 (CRISPR-associated protein 9) is a fast, emerging, precise, eco-friendly and efficient tool to address the challenges in agriculture and decipher plant-microbe interaction in crops. Nowadays, CRISPR/Cas9 approach is receiving major attention in the field of functional genomics and crop improvement. Consequently, the present review updates the prevailing knowledge in the deployment of CRISPR/Cas9 techniques to understand plantmicrobe interactions,; genes edited for the development of fungal, bacterial and viral disease resistance,; to elucidate the nodulation processes, plant growth promotion, and future implications in agriculture. Further, CRISPR/Cas9 would be a new tool for the management of plant diseases and increasing productivity for climate resilience farming.

Realities and hopes in the application of microbial tools in agriculture

“…Gene editing tools such as CRISPR‐Cas9 (clustered regularly interspaced short palindromic repeats) and RNAi (RNA interference) have the potential to contribute towards these goals (Sudheer et al ., 2020). Recently, CRISPR‐Cas9 has been used to elucidate genes involved in the mutual recognition between N‐fixing bacteria and legumes (Prabhukarthikeyan et al ., 2020). For example, the gene Rfg1 , responsible for restricting the nodulation by the N‐fixing Sinorhizobium fredii to specific soybean genotypes, was identified and validated using CRISPR‐Cas9 (Fan et al ., 2017).…”

Ribozyme-mediated CRISPR/Cas9 gene editing in pyrethrum (Tanacetum cinerariifolium) hairy roots using a RNA polymerase II-dependent promoter

“…The most damaging foliar disease of pyrethrum is ray blight caused by Stagonosporopsis tanaceti [ 48 ]. The emergence of CRISPR/Cas9 technology provides a new approach to address this problem, and this technology has worked to achieve resistance to pathogens in various crops [ 49 – 51 ]; however, to reduce the negative effects of a transgene on the whole plant, the most efficient way to confer resistance is to restrict its expression only to infected cells. Pathogen-induced promoters are unique and valuable tools for engineering resistance to plant disease [ 52 , 53 ].…”

Coping with salt stress-interaction of halotolerant bacteria in crop plants: A mini review

“…Recent advancements in “rhizosphere engineering” could mitigate salt stress by engineering the rhizosphere microbiome. For example, genome editing technology, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), is a fast, eco-friendly, and effective way to understand the plant–PGPR interactions, in particular, to target pathways involved in various metabolites (Prabhukarthikeyan et al, 2020 ). Another approach is to unravel the “blackbox” of PGPRs using next-generation sequencing (NGS) to explore microbial diversity under salinity stress.…”