- Email: [email protected]
Balancing Immunity and Yield in Crop Plants
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Review
Balancing Immunity and Yield in Crop Plants Yuese Ning,a Wende Liu,a,* and Guo-Liang Wanga,b,* Crop diseases cause enormous yield losses and threaten global food[217_TD$IF][ED1] security. The use of highly resistant cultivars can effectively control plant diseases, but in crops, genetic immunity to disease often comes with an unintended reduction in growth and yield. Here, we review recent advances in understanding how nucleotide-binding domain, leucine-rich repeat (NLR) receptors and cell wall-associated kinase (WAK) proteins function in balancing immunity and yield. We also discuss the role of plant hormones and transcription factors in regulating the trade-offs between plant growth and immunity. Finally, we describe how a novel mechanism of translational control of defense proteins can enhance immunity without the reduction in fitness. High Yield and Immunity to Pathogens Are Important Objectives in Plant Breeding, but Immunity Often Comes with Yield Penalties The demand for food is expected to increase by 70–100% by 2050, increasing concerns about food security worldwide [1]. In the last five decades, huge increases in crop yields were achieved due to new breeding methods and multiple cropping [2]. Because yields for major crops have now plateaued and the amount of arable land is being reduced due to urbanization, novel breeding methods, including molecular-assisted selection, transgenics, and gene-editing approaches, are being applied to increase yields. In agriculture, diverse and widespread microbial pathogens cause numerous diseases, and these diseases cause major losses in yield. Although crop diseases may be controlled by application of chemicals, chemical control is often expensive and has negative environmental consequences. The use of resistance (R) genes can provide an economical, environmentally safe method to control plant diseases [3] and selection of highly resistant cultivars is a priority in crop breeding programs. Although genetic resistance provides an economical method for the control of crop diseases, high levels of resistance usually carry yield penalties [4]. The cost of resistance was first reported by Vanderplank in the early 1960s for late blight disease of potato (Solanum tuberosum) [5] and has since been documented in other crops. For example, the wheat (Triticum aestivum) streak mosaic virus R gene Wsm1 is associated with a mean yield reduction of 21% [6], the wheat stem rust R gene Sr26 has a 9% yield penalty [4], and the barley (Hordeum vulgare) mlo R gene has a 4.2% yield penalty [7]. The cloning of R genes in model and crop plants in the last three decades has allowed us to study the molecular mechanisms underlying the trade-offs between yield and disease resistance. In this review, we summarize recent progress in understanding how plants balance disease resistance and growth, and we propose new breeding strategies for selecting high-yield cultivars with minimum fitness costs.
Trends High yield and immunity to pathogens are important objectives in plant breeding. However, plant growth and immunity pathways are intertwined and usually antagonistic. Hormones are important for plant growth; however, activation of immunity redirects and initiates hormone signaling that can impair plant growth. Transcription factors act as molecular integrators to regulate the trade-offs between immunity and growth. NLR and WAK immune receptors play dual roles in immunity and yield. Pathogen-inducible translational control strategies can enhance plant immunity without fitness costs. New breeding strategies should be developed to enhance immunity without sacrificing fitness and yield.
a State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China b Department of Plant Pathology, [215_TD$IF]Ohio State University, Columbus, OH 43210, USA
Plant Immunity and Growth Pathways Are Intertwined and Antagonistic Plants have evolved a two-layered innate immune system in which many cell surface patternrecognition receptors (PRRs) and cytoplasmic R proteins protect plants from diseases (Figure 1) [8]. The first layer of defense is governed by PRRs that recognize highly conserved pathogen-
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*[216_TD$IF]Corresponding author. Correspondence: [email protected] (W. Liu) and [email protected] (G.L. Wang). .
http://dx.doi.org/10.1016/j.tplants.2017.09.010 © 2017 Elsevier Ltd. All rights reserved.
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Figure 1. Balancing Immunity and Crop Yield with Transcription Factors and Plant Hormones. During infection, the pathogen-associated molecular pattern (PAMP) from pathogens can be detected by plant pattern-recognition receptors (PRRs), leading to PAMP-triggered immunity (PTI). Effectors from pathogens are recognized by plant R proteins resulting in effector-triggered immunity (ETI). PTI and ETI are the major mechanisms of crop immunity to pathogens. The number of panicles per plant, number of grains per panicle, and grain weight are the major yield components of cereal crops. The members of different transcription factor families (MYB, WRKY, NAC, bZIP, bHLH, MADS, etc.) and plant hormones (SA, BR, JA, GA, ABA, CK, AU, ET, etc.) are involved in both immunity and yield regulation in crop plants. ABA, abscisic acid; AU, auxin; BR, brassinosteroid; CK, cytokinin; ET, ethylene; GA, gibberellic acid; JA, jasmonate; SA, salicylic acid.
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associated molecular patterns (PAMPs); this recognition leads to a relatively weak PAMPtriggered immunity (PTI) that wards off most invading organisms. The second layer is initiated by archetypical R proteins that directly or indirectly recognize highly variable pathogen avirulence (Avr) effectors, resulting in the onset of effector-triggered immunity (ETI). Most cloned R genes in plants encode nucleotide-binding domain, leucine-rich repeat (NLR)-containing proteins. Genetic loci controlling plant immunity usually act antagonistically with genes involved in the regulation of plant growth and development [4,9]. DNA mutations and alternations in the expression of immunity-related genes often reduce plant growth and yield. Thus, immunity signaling must be precisely regulated to ensure that in the absence of pathogen infection, the plant allocates resources to growth. Plants undergoing pathogen attack must integrate multiple signaling pathways and reallocate resources to initiate immunity; [29_TD$IF]this usually involves the activation of hormone signaling, which can negatively affect plant growth. Changes in plant growth can affect the production of vegetative biomass and, in grasses, the yield of grain. Grain yield is a complex agronomic trait that is determined by many factors. In cereal crops, grain yield is mainly determined by the number of panicles per plant (NPP), the number of grains per panicle (NGP), and grain weight (GW; Figure 1) [10,11]. NPP is mainly determined by the tiller number, NGP is determined by the number of spikelets and the seedsetting rate, while GW is mainly influenced by the degree of filling and grain size [10].
Hormone-Regulated Plant Growth and Immunity Converge on Signaling Pathways Plant growth is regulated by several hormones that interact in complex networks, which directly or indirectly affect plant immunity [12,13]. Upon pathogen attack, plants synthesize a complex blend of hormones leading to the activation of distinct sets of defense-related genes [12,14]. Plant hormones, including salicylic acid (SA), brassinosteroid (BR), jasmonates (JAs), ethylene (ET), gibberellic acid (GA), abscisic acid (ABA), and auxin (AU), act as signals to trigger and mediate plant immune responses (Figure 1) [15]. The SA and JA pathways often interact in an antagonistic manner, and interact with other phytohormone pathways, including the ABA, GA, BR, and AU pathways, forming a large network that coregulates the trade-offs between growth and immunity [16,17]. Advances in our understanding of the molecular crosstalk between these hormones and plant resistance in the model dicot arabidopsis (Arabidopsis thaliana) have been summarized [18–21]. Here, we focus on recent advances in the roles of plant hormones regulating immunity and yields in the model monocot crop rice (Oryza sativa). Unlike arabidopsis, rice synthesizes a high level of SA that does not significantly change during pathogen attack [22]. However, treatment of rice plants with exogenous SA or synthetic SA analogs induces defense responses to a wide range of pathogens with different life cycles and infection strategies [23,24]. These results indicate that SA signaling, rather than SA synthesis, mediates defense signaling transduction in rice. The SA signaling pathway in rice branches into two subpathways regulated by WRKY45 and OsNPR1. Several pathogenesis-related (PR) genes and transcription factor (TF) genes, such as OsWRKY62, OsNAC4, and OsHSF1, are upregulated by the SA functional analog benzothiadiazole (BTH) and are dependent on WRKY45 [25]. By contrast, many genes that are downregulated by BTH are dependent on OsNPR1 [25,26]. In addition, many genes involved in photosynthesis and protein synthesis are also downregulated in OsNPR1 knockout lines upon BTH stimulation [26]. Moreover, transgenic rice plants that overexpressed OsNPR1 (OsNPR1-OX) show [23_TD$IF]strongly inhibited growth and development but enhanced resistance to the rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) [27]. Interestingly, the GH3 family gene OsGH3.8, which encodes an indole-3-acetic acid (IAA)-amido synthetase, [24_TD$IF]is significantly up-regulated in OsNPR1-OX plants, while RNA interference of OsGH3.8 partially [25_TD$IF]restores IAA levels and largely [26_TD$IF]rescues
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the restrained growth and development phenotypes. These results revealed that OsNPR1 affects rice growth and development by interfering with the AU pathway, at least partially, through indirectly upregulating OsGH3.8 expression [27]. JAs are a group of lipid-derived hormones that are essential for plant defense and development. Unlike in dicots, in monocots, JA contributes to resistance against pathogens with different life cycles [28–31]. JAs are also important for rice spikelet development, and therefore grain yield [32]. The mechanism underlying the balance of JA-mediated defense and growth has been best characterized for the plant shade avoidance syndrome (SAS) mediated by photoreceptor phytochromes [33]. While SAS allows plants to grow taller and project out from the canopy, biomass, yields, and defense responses to pathogens are attenuated in plants with strong SAS. For instance, the rice phyA phyB phyC triple-mutant plants show prematurely extended internodes and very early flowering under long-day conditions, produce small panicles, and set very few seeds [34]. Further characterization of the rice phyA phyB phyC triple mutant revealed the involvement of both JA and SA signaling pathways in immunity and growth because the mutant confers enhanced susceptibility to the rice blast fungus Magnaporthe oryzae and shows transcript suppression of SA- and JA-related defense genes [35]. These results collectively indicate that phytochromes play vital roles in maximizing photosynthetic abilities and SA- and JA-mediated defense responses in rice. GA promotes plant growth and defense when bioactive GA ligands bind to cognate receptors, leading to 26S proteasome-mediated degradation of nuclear growth-repressing proteins, called DELLAs [12]. The DELLA protein Slender Rice1 (SLR1) is essential for resistance against hemibiotrophic pathogens, but not necrotrophic pathogens, in rice [36,37]. In addition, SLR1 is a key regulator of multiple hormone signaling pathways. For instance, SLR1 is important for the induction of JA-responsive genes, such as OsMPK7; therefore, it appears to be a major target of JA-mediated growth inhibition and immunity [38]. A recent finding indicated that SLR1mediated pathogen resistance is partly due to its ability to activate both SA- and JA-mediated rice defenses [36]. SA and JA treatments reduced GA metabolism and stabilized SLR1 [36]. Together, these findings suggest that SLR1 acts as a positive regulator of hemibiotrophic pathogen resistance by integrating and amplifying SA- and JA-dependent defense signaling in rice. ET has diverse functions in plants. In rice, the accumulation of ET and the activation of ET signaling enhance disease resistance to M. oryzae [39,40]. A recent study revealed that the homeodomain TF OsBIHD1 coordinates with [27_TD$IF]NLR-type rice blast R protein Pik-H4 to balance resistance to the rice blast fungus and growth by integrating the ET–BR pathways [41]. In the Pik-H4 background, knockout of OsBIHD1 reduced resistance to M. oryzae, and overexpression of OsBIHD1 increased resistance to M. oryzae [28_TD$IF][[ED3] 41]. In addition, OsBIHD1 knockout and overexpressing transgenic lines show [29_TD$IF]dwarfism and insensitivity to BR [41]. This might be because OsBIHD1 binds to the sequence-specific cis-elements of the promoter of CYP734A2 to repress BR biosynthesis and BR signaling, and thus, to suppress plant growth under fungal invasion. These findings indicate that by coordinating the ET–BR pathways, OsBIHD1 contributes to Pik-H4-mediated immunity and mediates the trade-offs between resistance and growth. Although the aforementioned proteins are involved in the regulation of hormone and growth pathways in rice, several important questions remain to be answered, such as the role of these regulators in compatible and incompatible interactions, how they interact with their partners to balance immunity and yield in crop plants with or without pathogen infections, and their relationship with PRRs and NLRs.
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TFs Act as Molecular Integrators to Regulate the Trade-Offs between Plant Growth and Immunity TFs function at the intersection of plant growth and immunity [42] (Figure 1). The bHLH-type TF BZR1 is a major regulator of BR-induced growth [43]. A recent study reported that BRactivated BZR1 is sufficient to block PTI signaling by interacting with and transcriptionally regulating diverse WRKY TFs in arabidopsis. The BZR1-mediated suppression of immunity is particularly pronounced when plants are growing rapidly [44], suggesting that BZR1 prioritizes growth over immunity under certain conditions. BZR1 is not affected by PAMP signals, indicating that the downstream targets of BZR1 might be the major factors that balance the PTI and BR pathways [42,45]. The bHLH TF HBI1, a direct transcriptional target of BZR1, is induced by BR treatment but suppressed by PAMP treatments [45,46]. As with overexpression of BZR1, overexpression of HBI1 in arabidopsis inhibits PTI signaling. HBI1-overexpressing plants also exhibit increased BR responses and enhanced plant growth [45,46]. These results demonstrate that HBI1 is downstream of BZR1 and modulates the trade-offs between immunity and BR-regulated growth. BRZ1 also associates with the bHLH TF PIF4 to switch between thermosensory growth and immunity at elevated temperature [47,48]. Like BZR1 and HBI1, PIF4 promotes growth and reduces immunity [44–46]. These studies suggest that BZR1, along with its target HBI1 and its interactor PIF4, plays a central role in balancing BR environment-induced growth and basal immunity. The heat[23_TD$IF]-shock factor-like TF TBF1 in arabidopsis is a major component in the balance of growth and immunity related to SA signaling [49]. TBF1 specifically binds to the TL1 cis element of endoplasmic-reticulum genes that are required for antimicrobial protein secretion in arabidopsis. Genome-wide transcriptional profiling indicates that TBF1 may be involved in the growth-to-defense transition. The tbf1 mutant partially compromises the SA- and PAMPinduced arrest in growth and disease resistance. The transcription of AtNPR1 exhibits an interdependent and feedback regulation with TBF1 [49], which confirms that SA signaling also contributes to the trade-offs in growth and immunity. The atypical E2F TF DEL1 is another molecule related to plant growth, immunity, and SA signaling [50]. del1-mutant plants have slightly impaired growth and enhanced resistance to pathogens. In addition, the SA transporter EDS5 is a direct target of DEL1, indicating that DEL1 may target EDS5 to modulate SA levels, thus favoring growth over immunity in growing tissues [42,50]. The rice TF WRKY45 is induced by BTH and SA [24] and contributes to PTI against Xoo and M. oryzae [24,51]. Moreover, WRKY45 interacts with the CC–NBS–LRR protein Pb1 and is required for Pb1-mediated rice blast resistance [52]. Recent studies also showed that WRKY45 associates with R proteins including Pi36, Pit, Pib, Pi-ta, and Piz-t, suggesting that WRKY45 functions as a common module of rice ETI [53]. However, overexpression of WRKY45 leads to defects in plant growth and fitness costs [24,54,55]. To minimize the negative effect on plant growth, researchers tested 16 rice promoters to optimize the expression of WRKY45 in transgenic rice [54]. Field evaluations of inoculated plants showed that the WRKY45 overexpressing lines driven by the OsUbi7 promoter (POsUbi7) had the best balance of agronomic performance and disease resistance [54]. These studies suggest that an optimized expression of WRKY45 can minimize the negative effects of the defense gene on growth. Recently, bsr-d1, a naturally occurring allele of the C2H2-type TF Bsr-d1, was identified through a genome-wide association study [23_TD$IF][56]. The bsr-d1 mutant confers non-race-specific resistance to M. oryzae. Sequence and phenotypic analyses showed that a single-base A to G change in the promoter region of Bsr-d1 is tightly linked with the broad-spectrum resistance in the donor cultivar Digu. BSR-D1 directly binds to the promoter of the peroxidase gene
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Os10g39170, which is involved in H2O2 accumulation and basal resistance to M. oryzae. By contrast, the TF MYSB1 binds to the promoter of Bsr-d1, and the A to G change in the Bsr-d1 promoter leads to enhanced affinity with MYSB1, which negatively regulates Bsr-d1 gene expression. Since the bsr-d1 mutant confers broad-spectrum resistance, but does not confer obvious yield penalties, identification of novel BSR-D1 alleles in rice germplasm might provide a new approach for selecting resistant rice cultivars. The aforementioned results demonstrate that TFs can play a positive or negative role in balancing immunity and plant growth, and the optimum expression of some TF genes in transgenic plants can produce strong resistance with minimal effects on plant growth and yield. More research should be conducted to identify the targets of these TFs, functionally analyze their target genes, and search for suitable promoters to drive these TF genes to obtain effective, broad-spectrum resistance against diverse pathogens.
Immune Receptors NLR and Cell Wall-Associated Kinase Have Dual Roles in Balancing Immunity and Yield In the last half-century, R genes have been widely used to combat plant diseases [236_TD$IF][57]. Empirical evidence for the fitness costs of R genes is still controversial because some R genes may be tightly linked to other yield-reducing genes [65_TD$IF][58] and because fitness costs are affected by environmental conditions and may vary by evaluation method [6_TD$IF][59]. Therefore, the pairs of transgenic lines with and without cloned single R genes may be the most useful materials for understanding the fitness costs of individual R genes. For example, using a pair of isogenic arabidopsis lines, researchers estimated that the RPM1 and RPS5 loci had fitness costs of 5– 10% in the absence of pathogen infection [237_TD$IF][60,61]. However, another study that compared resistant alleles and sensitive alleles of Rps2 located in another genomic region in arabidopsis reported that Rps2 has no fitness costs, suggesting a fundamental effect of genetic architecture on the manifestation of costs of resistance [238_TD$IF][62]. Cooperative and antagonistic relationships between NLR genes have been reported in arabidopsis and rice [70_TD$IF][63]. For example, the arabidopsis NLR protein pair RPS4/RRS1 is required for resistance against both bacterial and fungal pathogens, and the rice NLR pair RGA4/RGA5 is required for resistance against the fungus M. oryzae [239_TD$IF][64,65]. The formation of heterodimers of the two NLR pairs is essential for effector recognition and subsequent defense activation. A good example for the antagonistic relationship is the combination of NLR DM1 alleles at two loci, which induce hybrid heterosis in arabidopsis [240_TD$IF][66]. The rice blast R gene Pi-ta is associated with decreased seed weight, which may explain why U.S. rice varieties containing Pi-ta are not competitive in their yield potentials with those without the gene [73_TD$IF][67]. It is unclear if the negative effect of Pi-ta on yield is due to effects of the gene itself or another yield-reducing gene located in the same genomic region. Deng [241_TD$IF]et al. [68] found that two NLR genes at the Pigm locus have opposing functions: one confers resistance against M. oryzae, and the other increases yield [24_TD$IF]Figure 2A). Pigm, which was identified in a Chinese cultivar, Gumei 4, confers durable resistance to M. oryzae and was mapped to the Pi2/Pi9/Piz-t cluster on chromosome 6 [243_TD$IF][69,70]. Molecular characterization revealed that PigmR is responsible for the durable resistance in Gumei 4 and that enhanced expression of PigmS reduces PigmR-mediated resistance [74_TD$IF][68]. Heterodimerization of PigmR and PigmS prevents the formation of the PigmR homodimers required for defense activation. Expression of PigmS is strictly regulated by an epigenetic mechanism in plants carrying Pigm. In leaves, expression of PigmS is suppressed by the transposons MITE1 and MITE2, as well as by DNA methylation in the PigmS promoter through RNA-directed DNA methylation. In addition to their opposing effects on pathogen defenses, PigmR and PigmS also have opposing effects on rice yield; PigmR decreases GW in the absence of rice blast infection,
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Figure 2. Novel Functions of NLR and WAK Proteins in Balancing Immunity and Yield. (A) The balance of rice yield and resistance to Magnaporthe oryzae (M. oryzae) mediated by the NLR immune receptor Pigm. PigmR is constitutively expressed at a low level in the whole plant, while PigmS is tightly and epigenetically regulated by miniature transposons (MITEs) and is mainly expressed in pollen and panicles. PigmR and PigmS form homodimers and PigmR–PigmS heterodimers. In field-grown plants, PigmS can directly or indirectly activate growth-related (GR) gene expression to increase the number of grains per panicle (NGP), while PigmR may slightly elevate pathogenesis-related (PR) gene expression, which leads to decreased grain weight (GW), that is, a yield penalty. In plants carrying PigmR and PigmS, the PigmR-mediated yield penalty can be compensated for by the PigmS-mediated increase in NGP. (B) Xanthomonas oryzae pv. oryzae (Xoo) resistance and yield balance mediated by the WAK immune receptor XA4. XA4 is a cell wall-associated kinase that may recognize the ligands from rice or Xoo. XA4-carrying plants enhance CesAs (cellulose synthases) expression and suppress EXPA (expansin) expression to reinforce cell walls, which may directly or indirectly lead to increased NGP and decreased GW without compromising yield under field conditions. When rice is challenged by an incompatible Xoo isolate, the bacterial effectors secreted into rice cells rapidly activate XA4, which activates CesAs expression and inhibits EXPA expression; this strengthens the cell wall and induces JAR2 expression to increase the JA-IIe concentration, which may contribute to XA4-mediated resistance to Xoo. ETI, effector-triggered immunity; NLR, nucleotide-binding domain, leucine-rich repeat; WAK, cell wall-associated kinase.
and PigmS increases yield due to increased seed setting. Transgenic plants carrying both genes have the same yield as the wild type in the absence of infection. These exciting findings have provided mechanistic insight into how tandemly repeated NLRs in a complex locus can balance the trade-offs between immunity and yield. Pigm is allelic to five R genes (Pi2, Pi9, Piz-t, Pi40, and Piz) located on rice chromosome 6 [24_TD$IF][71,72]. To evaluate and compare the resistance frequency mediated by these six resistance alleles, researchers developed near-isogenic lines (NILs) of the six genes in indica cv. Yangdao 6 and japonica cv. 07GY31 backgrounds [245_TD$IF][73,74]. Because total spikelets per plant were
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reduced, the yield of NIL-Pi2 in the Yangdao 6 background and of NIL-Pi9 in the 07GY31 background was decreased, while other NILs in both backgrounds had similar yields and other agronomic traits [246_TD$IF]with the recurrent parents [245_TD$IF][73,74]. These results suggest that regulation of gene expression and genetic background may help mitigate the balance between immunity and yield in crops [247_TD$IF][75]. XA4 is another immune receptor that improves multiple traits of agronomic importance without compromising grain yield [83_TD$IF][76] (Figure 2B). XA4 encodes a cell wall-associated kinase (WAK) and confers race-specific durable resistance against Xoo without a loss in yield potential. In an incompatible reaction, the expression of Xa4 is rapidly increased while cell wall synthesis genes are induced and cell expansion genes are repressed. Xa4-carrying transgenic lines have slightly reduced plant height but suffer no yield penalty in the field. By strengthening the cell wall, Xa4 confers enhanced resistance to Xoo infection and also increased mechanical strength of the culm, which may decrease lodging. The unique features of Xa4 may account for its long and widespread use in rice breeding. The orthologs of XA4 in maize (Zea mays), ZmWAK and ZmWAK-RLK1, confer quantitative resistance to the fungal pathogens Sporisorium reilianum and Exserohilum turcicum [248_TD$IF][77,78]. However, ZmWAK may have a fitness cost because lines without the gene have persisted and spread in maize germplasm [84_TD$IF][77]. Nevertheless, the identification of Xa4 in rice and ZmWAK in maize was significant in plant breeding because these genes are present in many popular cultivars. Identification of the ligand of their encoded proteins will be useful for increasing our understanding of the WAK-mediated mechanism for balancing immunity and yield in rice and maize [249_TD$IF][79]. Precise regulation of R genes may help alleviate the fitness costs associated with their expression, and the genomic organization of NLR genes into coregulatory modules reduces fitness costs in arabidopsis [247_TD$IF][75]. In rice, identification of the R genes PigmR/PigmS and XA4 has opened an avenue for better understanding the molecular mechanisms of R genes and designing approaches to mitigate immunity–yield trade-offs to engineer plants with durable resistance. However, it remains unknown how the interaction between PigmR and PigmS compromises rice resistance to M. oryzae and what the upstream and downstream components of XA4 are in rice immunity to Xoo.
Breeding Strategies for Obtaining High-Yielding Crop Cultivars with BroadSpectrum, Durable Disease Resistance Breeding high yielding and resistant cultivars with no or minimal fitness costs is challenging. Ideally, immune receptors would be in the ‘off’ status in the absence of pathogen infection, and the expression of immune-responsive genes would be strictly controlled so they are only induced when the plant is attacked by pathogens. A recent study demonstrated the usefulness of the TF TBF1 for minimizing the fitness penalties associated with enhanced disease resistance in arabidopsis and rice [25_TD$IF][80] (Figure 3). TBF1 is an important TF for the growth-to-defense switch upon immune induction [49]. The researchers used the ‘TBF1 cassette’ containing the immune-inducible promoter and two pathogen-responsive upstream open reading frames (uORFs) of the TBF1 gene to drive the NLR snc1 (suppressor of npr1) gene in arabidopsis and the AtNPR1 gene in rice. Surprisingly, the translational control of the two genes mediated by the TBF1 uORFs resulted in broad-spectrum disease resistance without compromising plant fitness. Because the uORF sequences are conserved in many plants, this strategy has opened a new avenue to engineering crop plants with broad-spectrum resistance and with minimal adverse effects on plant growth and development. Although this approach is effective for biotrophic and hemibiotrophic pathogens, further research should be conducted to determine the effect of uORF-mediated resistance to necrotrophic pathogens that can extract nutrients from dead or dying cells during infection.
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Figure 3. Translational Control of the Immunity Regulator AtNPR1 to Balance Immunity and Yield in Rice. (A) AtNPR1 is the master immune regulatory gene in arabidopsis. When ectopically expressed in rice under the control of the 35S promoter and the mutated TBF1 50 leader, AtNPR1 is transcribed and translated. High levels of AtNPR1 proteins lead to the induction of PR gene expression and then to enhanced immunity. However, the strong immunity to pathogens is associated with a yield penalty. (B) When AtNPR1 is expressed under the control of the TBF1 promoter and its 50 leader with uORF1 and uORF2, both AtNPR1 transcription and translation are tightly controlled. In the absence of pathogen infection, the translational repression of AtNPR1 by uORF1 and uORF2 is turned on, and the synthesis and degradation of AtNPR1 reach a balance, which has a minimal effect on crop yield. When a pathogen infects rice plants, the translational repression of AtNPR1 by uORF1 and uORF2 is alleviated. The accumulation of higher levels of AtNPR1 activates PR gene expression to enhance broad-spectrum immunity against different pathogens. PR, pathogenesis related; uORF, upstream open reading frame.
Concluding Remarks and Future Perspectives Much progress has been made in the last decade in the use of the model plant arabidopsis to understand the trade-offs between immunity and plant growth. Although much less is known in crop plants, our understanding of the cost of resistance on yield has improved in recent years. For the foreseeable future, plant breeders will continue to use R genes to combat plant diseases because they are effective against pathogen infection in the field and because molecular markers linked to the R genes are available. Given the yield penalty associated with some R genes, breeders must select genotypes closest to the Pareto front that have minimal yield penalties [253_TD$IF][63]. Although Deng et al. [68], Hu et al. [76], Xu et al. [80], and others have provided new knowledge and novel strategies to minimize fitness costs in arabidopsis and rice, developing new crop cultivars that have strong, durable disease resistance and that lack a yield penalty in the field remains difficult. The following research themes may emerge from these studies. First, researchers should determine which R genes currently used in crop production carry a yield penalty. Second, natural genotypes in the crop germplasm that suffer from
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autoimmunity and reduced growth but that carry pleiotropic broad-spectrum resistance against a wide range of pathogens might be useful for crop breeding and should be identified. Third, researchers should determine whether there are any susceptible NLR alleles, like PigmS, that have the opposite effect of R genes on yield. Fourth, the influence of genetic background and environment should be investigated for R genes with fitness costs. Fifth, identification of uORF-like sequences, or other mechanisms that can provide fine control of translation in crop plants, can be useful for engineering cultivars with broad-spectrum resistance. Finally, future advances that increase our understanding of the trade-offs between immunity and yield (see Outstanding Questions) will provide plant breeders with novel strategies to rapidly and efficiently select highly resistant cultivars without yield penalties to feed the increasing world population.
Outstanding Questions
Acknowledgments
Are there other genes like TBF1 that control the expression of defense genes at the translational level for genetic engineering of broad-spectrum resistance without a yield penalty in crop plants?
We thank the National Natural Science Foundation [256_TD$IF]of China (31571944 and 31422045), the National Key Research and Development Program [257_TD$IF]of China (2016YFD0100600), and the Young Elite Scientist Sponsorship of China Association for Science and Technology (2015QNRC001) for providing funding. In addition, the authors would like to apologize to those authors whose work could not be cited because of space limitations.
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How can the fitness costs of resistance be accurately evaluated in different genetic backgrounds and environments? What are the mechanisms underlying resource reallocation during pathogen infection, particularly for metabolites? What are the roles of plant hormones and TFs in minimizing R gene-mediated yield penalties?
Can we fine-tune R gene expression to balance defense–yield trade-offs? What are the master regulatory genes that influence the balance between immunity and yield in crop plants for breeding selection? What is the role of the phytobiome in ameliorating the cost of immunity and its effect on yield?
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Review
Balancing Immunity and Yield in Crop Plants Yuese Ning,a Wende Liu,a,* and Guo-Liang Wanga,b,* Crop diseases cause enormous yield losses and threaten global food[217_TD$IF][ED1] security. The use of highly resistant cultivars can effectively control plant diseases, but in crops, genetic immunity to disease often comes with an unintended reduction in growth and yield. Here, we review recent advances in understanding how nucleotide-binding domain, leucine-rich repeat (NLR) receptors and cell wall-associated kinase (WAK) proteins function in balancing immunity and yield. We also discuss the role of plant hormones and transcription factors in regulating the trade-offs between plant growth and immunity. Finally, we describe how a novel mechanism of translational control of defense proteins can enhance immunity without the reduction in fitness. High Yield and Immunity to Pathogens Are Important Objectives in Plant Breeding, but Immunity Often Comes with Yield Penalties The demand for food is expected to increase by 70–100% by 2050, increasing concerns about food security worldwide [1]. In the last five decades, huge increases in crop yields were achieved due to new breeding methods and multiple cropping [2]. Because yields for major crops have now plateaued and the amount of arable land is being reduced due to urbanization, novel breeding methods, including molecular-assisted selection, transgenics, and gene-editing approaches, are being applied to increase yields. In agriculture, diverse and widespread microbial pathogens cause numerous diseases, and these diseases cause major losses in yield. Although crop diseases may be controlled by application of chemicals, chemical control is often expensive and has negative environmental consequences. The use of resistance (R) genes can provide an economical, environmentally safe method to control plant diseases [3] and selection of highly resistant cultivars is a priority in crop breeding programs. Although genetic resistance provides an economical method for the control of crop diseases, high levels of resistance usually carry yield penalties [4]. The cost of resistance was first reported by Vanderplank in the early 1960s for late blight disease of potato (Solanum tuberosum) [5] and has since been documented in other crops. For example, the wheat (Triticum aestivum) streak mosaic virus R gene Wsm1 is associated with a mean yield reduction of 21% [6], the wheat stem rust R gene Sr26 has a 9% yield penalty [4], and the barley (Hordeum vulgare) mlo R gene has a 4.2% yield penalty [7]. The cloning of R genes in model and crop plants in the last three decades has allowed us to study the molecular mechanisms underlying the trade-offs between yield and disease resistance. In this review, we summarize recent progress in understanding how plants balance disease resistance and growth, and we propose new breeding strategies for selecting high-yield cultivars with minimum fitness costs.
Trends High yield and immunity to pathogens are important objectives in plant breeding. However, plant growth and immunity pathways are intertwined and usually antagonistic. Hormones are important for plant growth; however, activation of immunity redirects and initiates hormone signaling that can impair plant growth. Transcription factors act as molecular integrators to regulate the trade-offs between immunity and growth. NLR and WAK immune receptors play dual roles in immunity and yield. Pathogen-inducible translational control strategies can enhance plant immunity without fitness costs. New breeding strategies should be developed to enhance immunity without sacrificing fitness and yield.
a State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China b Department of Plant Pathology, [215_TD$IF]Ohio State University, Columbus, OH 43210, USA
Plant Immunity and Growth Pathways Are Intertwined and Antagonistic Plants have evolved a two-layered innate immune system in which many cell surface patternrecognition receptors (PRRs) and cytoplasmic R proteins protect plants from diseases (Figure 1) [8]. The first layer of defense is governed by PRRs that recognize highly conserved pathogen-
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*[216_TD$IF]Corresponding author. Correspondence: [email protected] (W. Liu) and [email protected] (G.L. Wang). .
http://dx.doi.org/10.1016/j.tplants.2017.09.010 © 2017 Elsevier Ltd. All rights reserved.
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MYB
NAC
WR KY bZIP
MADS
bH
LH
etc.
Transcripon factors PAMPs
Effectors
PRRs
R Proteins
PTI
ETI
Panicles per plant Grains per panicle Grain weight
Plant hormones
SA CK
ABA
BR JA
GA
AU ET
etc.
Figure 1. Balancing Immunity and Crop Yield with Transcription Factors and Plant Hormones. During infection, the pathogen-associated molecular pattern (PAMP) from pathogens can be detected by plant pattern-recognition receptors (PRRs), leading to PAMP-triggered immunity (PTI). Effectors from pathogens are recognized by plant R proteins resulting in effector-triggered immunity (ETI). PTI and ETI are the major mechanisms of crop immunity to pathogens. The number of panicles per plant, number of grains per panicle, and grain weight are the major yield components of cereal crops. The members of different transcription factor families (MYB, WRKY, NAC, bZIP, bHLH, MADS, etc.) and plant hormones (SA, BR, JA, GA, ABA, CK, AU, ET, etc.) are involved in both immunity and yield regulation in crop plants. ABA, abscisic acid; AU, auxin; BR, brassinosteroid; CK, cytokinin; ET, ethylene; GA, gibberellic acid; JA, jasmonate; SA, salicylic acid.
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associated molecular patterns (PAMPs); this recognition leads to a relatively weak PAMPtriggered immunity (PTI) that wards off most invading organisms. The second layer is initiated by archetypical R proteins that directly or indirectly recognize highly variable pathogen avirulence (Avr) effectors, resulting in the onset of effector-triggered immunity (ETI). Most cloned R genes in plants encode nucleotide-binding domain, leucine-rich repeat (NLR)-containing proteins. Genetic loci controlling plant immunity usually act antagonistically with genes involved in the regulation of plant growth and development [4,9]. DNA mutations and alternations in the expression of immunity-related genes often reduce plant growth and yield. Thus, immunity signaling must be precisely regulated to ensure that in the absence of pathogen infection, the plant allocates resources to growth. Plants undergoing pathogen attack must integrate multiple signaling pathways and reallocate resources to initiate immunity; [29_TD$IF]this usually involves the activation of hormone signaling, which can negatively affect plant growth. Changes in plant growth can affect the production of vegetative biomass and, in grasses, the yield of grain. Grain yield is a complex agronomic trait that is determined by many factors. In cereal crops, grain yield is mainly determined by the number of panicles per plant (NPP), the number of grains per panicle (NGP), and grain weight (GW; Figure 1) [10,11]. NPP is mainly determined by the tiller number, NGP is determined by the number of spikelets and the seedsetting rate, while GW is mainly influenced by the degree of filling and grain size [10].
Hormone-Regulated Plant Growth and Immunity Converge on Signaling Pathways Plant growth is regulated by several hormones that interact in complex networks, which directly or indirectly affect plant immunity [12,13]. Upon pathogen attack, plants synthesize a complex blend of hormones leading to the activation of distinct sets of defense-related genes [12,14]. Plant hormones, including salicylic acid (SA), brassinosteroid (BR), jasmonates (JAs), ethylene (ET), gibberellic acid (GA), abscisic acid (ABA), and auxin (AU), act as signals to trigger and mediate plant immune responses (Figure 1) [15]. The SA and JA pathways often interact in an antagonistic manner, and interact with other phytohormone pathways, including the ABA, GA, BR, and AU pathways, forming a large network that coregulates the trade-offs between growth and immunity [16,17]. Advances in our understanding of the molecular crosstalk between these hormones and plant resistance in the model dicot arabidopsis (Arabidopsis thaliana) have been summarized [18–21]. Here, we focus on recent advances in the roles of plant hormones regulating immunity and yields in the model monocot crop rice (Oryza sativa). Unlike arabidopsis, rice synthesizes a high level of SA that does not significantly change during pathogen attack [22]. However, treatment of rice plants with exogenous SA or synthetic SA analogs induces defense responses to a wide range of pathogens with different life cycles and infection strategies [23,24]. These results indicate that SA signaling, rather than SA synthesis, mediates defense signaling transduction in rice. The SA signaling pathway in rice branches into two subpathways regulated by WRKY45 and OsNPR1. Several pathogenesis-related (PR) genes and transcription factor (TF) genes, such as OsWRKY62, OsNAC4, and OsHSF1, are upregulated by the SA functional analog benzothiadiazole (BTH) and are dependent on WRKY45 [25]. By contrast, many genes that are downregulated by BTH are dependent on OsNPR1 [25,26]. In addition, many genes involved in photosynthesis and protein synthesis are also downregulated in OsNPR1 knockout lines upon BTH stimulation [26]. Moreover, transgenic rice plants that overexpressed OsNPR1 (OsNPR1-OX) show [23_TD$IF]strongly inhibited growth and development but enhanced resistance to the rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) [27]. Interestingly, the GH3 family gene OsGH3.8, which encodes an indole-3-acetic acid (IAA)-amido synthetase, [24_TD$IF]is significantly up-regulated in OsNPR1-OX plants, while RNA interference of OsGH3.8 partially [25_TD$IF]restores IAA levels and largely [26_TD$IF]rescues
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the restrained growth and development phenotypes. These results revealed that OsNPR1 affects rice growth and development by interfering with the AU pathway, at least partially, through indirectly upregulating OsGH3.8 expression [27]. JAs are a group of lipid-derived hormones that are essential for plant defense and development. Unlike in dicots, in monocots, JA contributes to resistance against pathogens with different life cycles [28–31]. JAs are also important for rice spikelet development, and therefore grain yield [32]. The mechanism underlying the balance of JA-mediated defense and growth has been best characterized for the plant shade avoidance syndrome (SAS) mediated by photoreceptor phytochromes [33]. While SAS allows plants to grow taller and project out from the canopy, biomass, yields, and defense responses to pathogens are attenuated in plants with strong SAS. For instance, the rice phyA phyB phyC triple-mutant plants show prematurely extended internodes and very early flowering under long-day conditions, produce small panicles, and set very few seeds [34]. Further characterization of the rice phyA phyB phyC triple mutant revealed the involvement of both JA and SA signaling pathways in immunity and growth because the mutant confers enhanced susceptibility to the rice blast fungus Magnaporthe oryzae and shows transcript suppression of SA- and JA-related defense genes [35]. These results collectively indicate that phytochromes play vital roles in maximizing photosynthetic abilities and SA- and JA-mediated defense responses in rice. GA promotes plant growth and defense when bioactive GA ligands bind to cognate receptors, leading to 26S proteasome-mediated degradation of nuclear growth-repressing proteins, called DELLAs [12]. The DELLA protein Slender Rice1 (SLR1) is essential for resistance against hemibiotrophic pathogens, but not necrotrophic pathogens, in rice [36,37]. In addition, SLR1 is a key regulator of multiple hormone signaling pathways. For instance, SLR1 is important for the induction of JA-responsive genes, such as OsMPK7; therefore, it appears to be a major target of JA-mediated growth inhibition and immunity [38]. A recent finding indicated that SLR1mediated pathogen resistance is partly due to its ability to activate both SA- and JA-mediated rice defenses [36]. SA and JA treatments reduced GA metabolism and stabilized SLR1 [36]. Together, these findings suggest that SLR1 acts as a positive regulator of hemibiotrophic pathogen resistance by integrating and amplifying SA- and JA-dependent defense signaling in rice. ET has diverse functions in plants. In rice, the accumulation of ET and the activation of ET signaling enhance disease resistance to M. oryzae [39,40]. A recent study revealed that the homeodomain TF OsBIHD1 coordinates with [27_TD$IF]NLR-type rice blast R protein Pik-H4 to balance resistance to the rice blast fungus and growth by integrating the ET–BR pathways [41]. In the Pik-H4 background, knockout of OsBIHD1 reduced resistance to M. oryzae, and overexpression of OsBIHD1 increased resistance to M. oryzae [28_TD$IF][[ED3] 41]. In addition, OsBIHD1 knockout and overexpressing transgenic lines show [29_TD$IF]dwarfism and insensitivity to BR [41]. This might be because OsBIHD1 binds to the sequence-specific cis-elements of the promoter of CYP734A2 to repress BR biosynthesis and BR signaling, and thus, to suppress plant growth under fungal invasion. These findings indicate that by coordinating the ET–BR pathways, OsBIHD1 contributes to Pik-H4-mediated immunity and mediates the trade-offs between resistance and growth. Although the aforementioned proteins are involved in the regulation of hormone and growth pathways in rice, several important questions remain to be answered, such as the role of these regulators in compatible and incompatible interactions, how they interact with their partners to balance immunity and yield in crop plants with or without pathogen infections, and their relationship with PRRs and NLRs.
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TFs Act as Molecular Integrators to Regulate the Trade-Offs between Plant Growth and Immunity TFs function at the intersection of plant growth and immunity [42] (Figure 1). The bHLH-type TF BZR1 is a major regulator of BR-induced growth [43]. A recent study reported that BRactivated BZR1 is sufficient to block PTI signaling by interacting with and transcriptionally regulating diverse WRKY TFs in arabidopsis. The BZR1-mediated suppression of immunity is particularly pronounced when plants are growing rapidly [44], suggesting that BZR1 prioritizes growth over immunity under certain conditions. BZR1 is not affected by PAMP signals, indicating that the downstream targets of BZR1 might be the major factors that balance the PTI and BR pathways [42,45]. The bHLH TF HBI1, a direct transcriptional target of BZR1, is induced by BR treatment but suppressed by PAMP treatments [45,46]. As with overexpression of BZR1, overexpression of HBI1 in arabidopsis inhibits PTI signaling. HBI1-overexpressing plants also exhibit increased BR responses and enhanced plant growth [45,46]. These results demonstrate that HBI1 is downstream of BZR1 and modulates the trade-offs between immunity and BR-regulated growth. BRZ1 also associates with the bHLH TF PIF4 to switch between thermosensory growth and immunity at elevated temperature [47,48]. Like BZR1 and HBI1, PIF4 promotes growth and reduces immunity [44–46]. These studies suggest that BZR1, along with its target HBI1 and its interactor PIF4, plays a central role in balancing BR environment-induced growth and basal immunity. The heat[23_TD$IF]-shock factor-like TF TBF1 in arabidopsis is a major component in the balance of growth and immunity related to SA signaling [49]. TBF1 specifically binds to the TL1 cis element of endoplasmic-reticulum genes that are required for antimicrobial protein secretion in arabidopsis. Genome-wide transcriptional profiling indicates that TBF1 may be involved in the growth-to-defense transition. The tbf1 mutant partially compromises the SA- and PAMPinduced arrest in growth and disease resistance. The transcription of AtNPR1 exhibits an interdependent and feedback regulation with TBF1 [49], which confirms that SA signaling also contributes to the trade-offs in growth and immunity. The atypical E2F TF DEL1 is another molecule related to plant growth, immunity, and SA signaling [50]. del1-mutant plants have slightly impaired growth and enhanced resistance to pathogens. In addition, the SA transporter EDS5 is a direct target of DEL1, indicating that DEL1 may target EDS5 to modulate SA levels, thus favoring growth over immunity in growing tissues [42,50]. The rice TF WRKY45 is induced by BTH and SA [24] and contributes to PTI against Xoo and M. oryzae [24,51]. Moreover, WRKY45 interacts with the CC–NBS–LRR protein Pb1 and is required for Pb1-mediated rice blast resistance [52]. Recent studies also showed that WRKY45 associates with R proteins including Pi36, Pit, Pib, Pi-ta, and Piz-t, suggesting that WRKY45 functions as a common module of rice ETI [53]. However, overexpression of WRKY45 leads to defects in plant growth and fitness costs [24,54,55]. To minimize the negative effect on plant growth, researchers tested 16 rice promoters to optimize the expression of WRKY45 in transgenic rice [54]. Field evaluations of inoculated plants showed that the WRKY45 overexpressing lines driven by the OsUbi7 promoter (POsUbi7) had the best balance of agronomic performance and disease resistance [54]. These studies suggest that an optimized expression of WRKY45 can minimize the negative effects of the defense gene on growth. Recently, bsr-d1, a naturally occurring allele of the C2H2-type TF Bsr-d1, was identified through a genome-wide association study [23_TD$IF][56]. The bsr-d1 mutant confers non-race-specific resistance to M. oryzae. Sequence and phenotypic analyses showed that a single-base A to G change in the promoter region of Bsr-d1 is tightly linked with the broad-spectrum resistance in the donor cultivar Digu. BSR-D1 directly binds to the promoter of the peroxidase gene
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Os10g39170, which is involved in H2O2 accumulation and basal resistance to M. oryzae. By contrast, the TF MYSB1 binds to the promoter of Bsr-d1, and the A to G change in the Bsr-d1 promoter leads to enhanced affinity with MYSB1, which negatively regulates Bsr-d1 gene expression. Since the bsr-d1 mutant confers broad-spectrum resistance, but does not confer obvious yield penalties, identification of novel BSR-D1 alleles in rice germplasm might provide a new approach for selecting resistant rice cultivars. The aforementioned results demonstrate that TFs can play a positive or negative role in balancing immunity and plant growth, and the optimum expression of some TF genes in transgenic plants can produce strong resistance with minimal effects on plant growth and yield. More research should be conducted to identify the targets of these TFs, functionally analyze their target genes, and search for suitable promoters to drive these TF genes to obtain effective, broad-spectrum resistance against diverse pathogens.
Immune Receptors NLR and Cell Wall-Associated Kinase Have Dual Roles in Balancing Immunity and Yield In the last half-century, R genes have been widely used to combat plant diseases [236_TD$IF][57]. Empirical evidence for the fitness costs of R genes is still controversial because some R genes may be tightly linked to other yield-reducing genes [65_TD$IF][58] and because fitness costs are affected by environmental conditions and may vary by evaluation method [6_TD$IF][59]. Therefore, the pairs of transgenic lines with and without cloned single R genes may be the most useful materials for understanding the fitness costs of individual R genes. For example, using a pair of isogenic arabidopsis lines, researchers estimated that the RPM1 and RPS5 loci had fitness costs of 5– 10% in the absence of pathogen infection [237_TD$IF][60,61]. However, another study that compared resistant alleles and sensitive alleles of Rps2 located in another genomic region in arabidopsis reported that Rps2 has no fitness costs, suggesting a fundamental effect of genetic architecture on the manifestation of costs of resistance [238_TD$IF][62]. Cooperative and antagonistic relationships between NLR genes have been reported in arabidopsis and rice [70_TD$IF][63]. For example, the arabidopsis NLR protein pair RPS4/RRS1 is required for resistance against both bacterial and fungal pathogens, and the rice NLR pair RGA4/RGA5 is required for resistance against the fungus M. oryzae [239_TD$IF][64,65]. The formation of heterodimers of the two NLR pairs is essential for effector recognition and subsequent defense activation. A good example for the antagonistic relationship is the combination of NLR DM1 alleles at two loci, which induce hybrid heterosis in arabidopsis [240_TD$IF][66]. The rice blast R gene Pi-ta is associated with decreased seed weight, which may explain why U.S. rice varieties containing Pi-ta are not competitive in their yield potentials with those without the gene [73_TD$IF][67]. It is unclear if the negative effect of Pi-ta on yield is due to effects of the gene itself or another yield-reducing gene located in the same genomic region. Deng [241_TD$IF]et al. [68] found that two NLR genes at the Pigm locus have opposing functions: one confers resistance against M. oryzae, and the other increases yield [24_TD$IF]Figure 2A). Pigm, which was identified in a Chinese cultivar, Gumei 4, confers durable resistance to M. oryzae and was mapped to the Pi2/Pi9/Piz-t cluster on chromosome 6 [243_TD$IF][69,70]. Molecular characterization revealed that PigmR is responsible for the durable resistance in Gumei 4 and that enhanced expression of PigmS reduces PigmR-mediated resistance [74_TD$IF][68]. Heterodimerization of PigmR and PigmS prevents the formation of the PigmR homodimers required for defense activation. Expression of PigmS is strictly regulated by an epigenetic mechanism in plants carrying Pigm. In leaves, expression of PigmS is suppressed by the transposons MITE1 and MITE2, as well as by DNA methylation in the PigmS promoter through RNA-directed DNA methylation. In addition to their opposing effects on pathogen defenses, PigmR and PigmS also have opposing effects on rice yield; PigmR decreases GW in the absence of rice blast infection,
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Figure 2. Novel Functions of NLR and WAK Proteins in Balancing Immunity and Yield. (A) The balance of rice yield and resistance to Magnaporthe oryzae (M. oryzae) mediated by the NLR immune receptor Pigm. PigmR is constitutively expressed at a low level in the whole plant, while PigmS is tightly and epigenetically regulated by miniature transposons (MITEs) and is mainly expressed in pollen and panicles. PigmR and PigmS form homodimers and PigmR–PigmS heterodimers. In field-grown plants, PigmS can directly or indirectly activate growth-related (GR) gene expression to increase the number of grains per panicle (NGP), while PigmR may slightly elevate pathogenesis-related (PR) gene expression, which leads to decreased grain weight (GW), that is, a yield penalty. In plants carrying PigmR and PigmS, the PigmR-mediated yield penalty can be compensated for by the PigmS-mediated increase in NGP. (B) Xanthomonas oryzae pv. oryzae (Xoo) resistance and yield balance mediated by the WAK immune receptor XA4. XA4 is a cell wall-associated kinase that may recognize the ligands from rice or Xoo. XA4-carrying plants enhance CesAs (cellulose synthases) expression and suppress EXPA (expansin) expression to reinforce cell walls, which may directly or indirectly lead to increased NGP and decreased GW without compromising yield under field conditions. When rice is challenged by an incompatible Xoo isolate, the bacterial effectors secreted into rice cells rapidly activate XA4, which activates CesAs expression and inhibits EXPA expression; this strengthens the cell wall and induces JAR2 expression to increase the JA-IIe concentration, which may contribute to XA4-mediated resistance to Xoo. ETI, effector-triggered immunity; NLR, nucleotide-binding domain, leucine-rich repeat; WAK, cell wall-associated kinase.
and PigmS increases yield due to increased seed setting. Transgenic plants carrying both genes have the same yield as the wild type in the absence of infection. These exciting findings have provided mechanistic insight into how tandemly repeated NLRs in a complex locus can balance the trade-offs between immunity and yield. Pigm is allelic to five R genes (Pi2, Pi9, Piz-t, Pi40, and Piz) located on rice chromosome 6 [24_TD$IF][71,72]. To evaluate and compare the resistance frequency mediated by these six resistance alleles, researchers developed near-isogenic lines (NILs) of the six genes in indica cv. Yangdao 6 and japonica cv. 07GY31 backgrounds [245_TD$IF][73,74]. Because total spikelets per plant were
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reduced, the yield of NIL-Pi2 in the Yangdao 6 background and of NIL-Pi9 in the 07GY31 background was decreased, while other NILs in both backgrounds had similar yields and other agronomic traits [246_TD$IF]with the recurrent parents [245_TD$IF][73,74]. These results suggest that regulation of gene expression and genetic background may help mitigate the balance between immunity and yield in crops [247_TD$IF][75]. XA4 is another immune receptor that improves multiple traits of agronomic importance without compromising grain yield [83_TD$IF][76] (Figure 2B). XA4 encodes a cell wall-associated kinase (WAK) and confers race-specific durable resistance against Xoo without a loss in yield potential. In an incompatible reaction, the expression of Xa4 is rapidly increased while cell wall synthesis genes are induced and cell expansion genes are repressed. Xa4-carrying transgenic lines have slightly reduced plant height but suffer no yield penalty in the field. By strengthening the cell wall, Xa4 confers enhanced resistance to Xoo infection and also increased mechanical strength of the culm, which may decrease lodging. The unique features of Xa4 may account for its long and widespread use in rice breeding. The orthologs of XA4 in maize (Zea mays), ZmWAK and ZmWAK-RLK1, confer quantitative resistance to the fungal pathogens Sporisorium reilianum and Exserohilum turcicum [248_TD$IF][77,78]. However, ZmWAK may have a fitness cost because lines without the gene have persisted and spread in maize germplasm [84_TD$IF][77]. Nevertheless, the identification of Xa4 in rice and ZmWAK in maize was significant in plant breeding because these genes are present in many popular cultivars. Identification of the ligand of their encoded proteins will be useful for increasing our understanding of the WAK-mediated mechanism for balancing immunity and yield in rice and maize [249_TD$IF][79]. Precise regulation of R genes may help alleviate the fitness costs associated with their expression, and the genomic organization of NLR genes into coregulatory modules reduces fitness costs in arabidopsis [247_TD$IF][75]. In rice, identification of the R genes PigmR/PigmS and XA4 has opened an avenue for better understanding the molecular mechanisms of R genes and designing approaches to mitigate immunity–yield trade-offs to engineer plants with durable resistance. However, it remains unknown how the interaction between PigmR and PigmS compromises rice resistance to M. oryzae and what the upstream and downstream components of XA4 are in rice immunity to Xoo.
Breeding Strategies for Obtaining High-Yielding Crop Cultivars with BroadSpectrum, Durable Disease Resistance Breeding high yielding and resistant cultivars with no or minimal fitness costs is challenging. Ideally, immune receptors would be in the ‘off’ status in the absence of pathogen infection, and the expression of immune-responsive genes would be strictly controlled so they are only induced when the plant is attacked by pathogens. A recent study demonstrated the usefulness of the TF TBF1 for minimizing the fitness penalties associated with enhanced disease resistance in arabidopsis and rice [25_TD$IF][80] (Figure 3). TBF1 is an important TF for the growth-to-defense switch upon immune induction [49]. The researchers used the ‘TBF1 cassette’ containing the immune-inducible promoter and two pathogen-responsive upstream open reading frames (uORFs) of the TBF1 gene to drive the NLR snc1 (suppressor of npr1) gene in arabidopsis and the AtNPR1 gene in rice. Surprisingly, the translational control of the two genes mediated by the TBF1 uORFs resulted in broad-spectrum disease resistance without compromising plant fitness. Because the uORF sequences are conserved in many plants, this strategy has opened a new avenue to engineering crop plants with broad-spectrum resistance and with minimal adverse effects on plant growth and development. Although this approach is effective for biotrophic and hemibiotrophic pathogens, further research should be conducted to determine the effect of uORF-mediated resistance to necrotrophic pathogens that can extract nutrients from dead or dying cells during infection.
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Figure 3. Translational Control of the Immunity Regulator AtNPR1 to Balance Immunity and Yield in Rice. (A) AtNPR1 is the master immune regulatory gene in arabidopsis. When ectopically expressed in rice under the control of the 35S promoter and the mutated TBF1 50 leader, AtNPR1 is transcribed and translated. High levels of AtNPR1 proteins lead to the induction of PR gene expression and then to enhanced immunity. However, the strong immunity to pathogens is associated with a yield penalty. (B) When AtNPR1 is expressed under the control of the TBF1 promoter and its 50 leader with uORF1 and uORF2, both AtNPR1 transcription and translation are tightly controlled. In the absence of pathogen infection, the translational repression of AtNPR1 by uORF1 and uORF2 is turned on, and the synthesis and degradation of AtNPR1 reach a balance, which has a minimal effect on crop yield. When a pathogen infects rice plants, the translational repression of AtNPR1 by uORF1 and uORF2 is alleviated. The accumulation of higher levels of AtNPR1 activates PR gene expression to enhance broad-spectrum immunity against different pathogens. PR, pathogenesis related; uORF, upstream open reading frame.
Concluding Remarks and Future Perspectives Much progress has been made in the last decade in the use of the model plant arabidopsis to understand the trade-offs between immunity and plant growth. Although much less is known in crop plants, our understanding of the cost of resistance on yield has improved in recent years. For the foreseeable future, plant breeders will continue to use R genes to combat plant diseases because they are effective against pathogen infection in the field and because molecular markers linked to the R genes are available. Given the yield penalty associated with some R genes, breeders must select genotypes closest to the Pareto front that have minimal yield penalties [253_TD$IF][63]. Although Deng et al. [68], Hu et al. [76], Xu et al. [80], and others have provided new knowledge and novel strategies to minimize fitness costs in arabidopsis and rice, developing new crop cultivars that have strong, durable disease resistance and that lack a yield penalty in the field remains difficult. The following research themes may emerge from these studies. First, researchers should determine which R genes currently used in crop production carry a yield penalty. Second, natural genotypes in the crop germplasm that suffer from
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autoimmunity and reduced growth but that carry pleiotropic broad-spectrum resistance against a wide range of pathogens might be useful for crop breeding and should be identified. Third, researchers should determine whether there are any susceptible NLR alleles, like PigmS, that have the opposite effect of R genes on yield. Fourth, the influence of genetic background and environment should be investigated for R genes with fitness costs. Fifth, identification of uORF-like sequences, or other mechanisms that can provide fine control of translation in crop plants, can be useful for engineering cultivars with broad-spectrum resistance. Finally, future advances that increase our understanding of the trade-offs between immunity and yield (see Outstanding Questions) will provide plant breeders with novel strategies to rapidly and efficiently select highly resistant cultivars without yield penalties to feed the increasing world population.
Outstanding Questions
Acknowledgments
Are there other genes like TBF1 that control the expression of defense genes at the translational level for genetic engineering of broad-spectrum resistance without a yield penalty in crop plants?
We thank the National Natural Science Foundation [256_TD$IF]of China (31571944 and 31422045), the National Key Research and Development Program [257_TD$IF]of China (2016YFD0100600), and the Young Elite Scientist Sponsorship of China Association for Science and Technology (2015QNRC001) for providing funding. In addition, the authors would like to apologize to those authors whose work could not be cited because of space limitations.
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