Introduction
World population is expected to reach 9.7 billion by 2050 from 7.9 in 2030 hence, at least 40% more staple food grains like rice will have to be produced in order to ensure that the global needs are secured in the 21st century and beyond (Khush 2001). The cultivation of rice as a major food crop is constantly challenged by the negative impacts of pathogens, insect herbivores and other parasites. These biotic stressors particularly the pathogens account for 20-30% losses in global yields (Savary et al. 2019).
Pathogens and their host plants continuously compete for their dominance in the co-evolutionary battle. Plants have evolved multi-layered defense strategies against pathogen invasion (Dangl, Horvath & Staskawicz 2013; Jones, Vance & Dangl 2016). Plants induce complex defense mechanisms by activating or suppressing a large array of genes in response to pathogen attack (Jones & Dangl 2006). Such mechanisms are facilitated by the ability of host plant to recognize an array of pathogen-associated molecular patterns (PAMPs) or damage-associated molecular patterns (DAMPs) during the initial stages of pathogen or herbivore invasion (Dodds & Rathjen 2010). The pathogen-triggered PAMP or DAMP is usually recognized by pattern-recognition receptors (PRRs) present on the surface of the host cell. The PAMPs or DAMPs in turn activate the PAMP-triggered immunity (PTI) by inducing many different types of defense-related genes (Zhang & Zhou 2010; Zipfel 2014).
The strong immunity of the host plant depends on successful activation of defence-related genes by the pathogens. Successful virulent pathogens could often overcome the PTI by mediating effector-triggered susceptibility (ETS), which then leads to disease development (Hatsugaiet al. 2017). In response, the host plants develop a secondary immune response, known as effector-triggered immunity (ETI) that is mediated by intracellular receptor proteins encoded by R-genes (Tsuda & Katagiri 2010). The product of R-genes binds to specific pathogen effectors producing more complex, robust and specific response called hypersensitive response (HR), which further mediates cell death to restrict the growth of the pathogen at the sites of infection (Danglet al. 2013). In rice, many R-genes have been cloned and characterized against pathogens and insect-pests. Most of these R-genes are being effectively utilized for the enhancement of resistance through introgression breeding. However, the efficacy of these R-genes is normally overcome within a certain period of time due to development of new resistant races that can no longer be recognized by the R-gene products. Moreover, unregulated expression of R-genes imposes substantial demand of resources that negatively affect plant growth and grain yield (Huot, Yao, Montgomery & He 2014; Ning, Liu & Wang 2017; Nelson, Wiesner-Hanks, Wisser & Balint-Kurti 2018). Therefore, identification and use of the intrinsic genetic defense mechanism against pathogen and insect herbivores in rice may be an important strategy for efficient disease and pest management and sustainable rice production.
MicroRNAs (miRNAs) are short, endogenous, single-stranded, non-coding RNAs that form a characteristic stem-loop structure. These RNAs act as crucial modulators of various cellular and biological processes including plant growth, development, reproduction and responses to biotic and abiotic stresses (Katiyar-Agarwal & Jin 2010; Khraiwesh, Zhu & Zhu 2012; Tang & Chu 2017). The processed miRNAs are approximately 22 nucleotides (nt) in length derived from the stem-loop structure, which then regulate the expression of their target genes through the degradation of complementary or partially complementary target mRNAs leading to post-transcriptional gene silencing (Chen 2009; Voinnet 2009). Plant miRNAs are transcribed as a primary miRNA (pri-miRNA) from miRNA-encoding genomic loci by RNA polymerase II (Lee et al.2004). The stem of the looped pri-miRNAs are subsequently processed by RNAse III DICER-like 1 (DCL1 ) proteins into double stranded miRNA-miRNA* duplex (Kurihara & Watanabe 2004; Kim 2005). The miRNA/miRNA* duplex from the stem-loop is transported from the nucleus into the cytoplasm where mature miRNA duplex is excised form pri-miRNA and are methylated by HUA ENHANCER 1 (HEN1 ) to prevent degradation (Mee, Wu, Gonzalez-Sulser, Vaucheret & Poethig 2005). The guide miRNA is loaded into ARGONAUTE1 (AGO1 ) to form a functional RNA induced silencing complex (RISC) (Voinnet 2009). A suitable complementarity between miRNA and target mRNA allows the RISC complex to trigger complete inhibition of protein expression by either degradation of mRNA or by inhibition of translation.
In the past few years, rapid development of next-generation sequencing (NGS) technologies and continually refined algorithms for bioinformatic prediction has opened a new path in miRNA discovery. Molecular approaches like 5’RACE, degradome sequencing, stem-loop RT-PCR, reporter gene analysis, loss- or gain-of-function mutation experiments become the powerful tools to unravel the function of miRNA (Basso et al.2019). In rice, numerous miRNAs that fine-tune the immune response mechanisms and regulate plant growth have been identified, cloned, and functionally validated through loss- or gain-of-function mutation experiments. This review focuses on the regulatory impacts of functionally characterized immune-responsive miRNAs in fine-tuning complex traits of agronomic importance. Cautionary aspects of innovative strategies for miRNA manipulation for understanding the balance and trade-offs between defense and productivity in terms of yield are discussed.