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.