Susceptibility Is New Resistance: Wheat Susceptibility Genes and Exploitation in Resistance Breeding

Abstract

Adapted pathogens and pests seriously threaten global wheat production. During pathogen and pest infections, wheat susceptibility (S) genes are exploited to support the compatibility of wheat with pathogens and pests. A plethora of wheat S genes were recently identified and revealed to regulate multiple processes, including pathogen (pre)penetration, plant immunity, pathogen sustenance, and pest feeding. The inactivation of some S genes via newly developed genome editing and TILLING techniques could reduce compatibility and confer broad-spectrum and durable resistance, which provide a new avenue for wheat resistance improvement. In this review, we summarized recent advances in the characterization of wheat S genes and highlighted their multifaceted roles in facilitating compatible interactions of wheat with adapted pathogens and pests. Current strategies, limitations, and future directions in exploiting S genes in wheat resistance breeding are discussed.

1. Introduction

As one of the most important staple crops, hexaploid bread wheat (Triticum aestivum) originated in the fertile crescent about 8500 years ago, and supplies approximately 20% of dietary calories and proteins for humans [1]. A growing population and overconsumption increased global demand for wheat grain. However, wheat yield and quality are reduced by attacks from adapted pathogens and pests (P&Ps) [2,3]. For instance, each of these eight devastating P&Ps (leaf rust, stripe rust, powdery mildew, Fusarium head blight, Septoria tritici blotch, spot blotch, tan spot, and aphid) caused wheat yield losses of more than 1% globally [2]. Therefore, breeding resistant varieties is essential for securing wheat production under P&P threats.

During the coevolution of plants with their parasites, plants acquired sophisticated immune mechanisms to cope with P&Ps infections, which provide valuable genetic resources for crop resistance breeding [4]. Typically, pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) represent two intertwined layers of induced defense systems [5]. Pattern recognition receptors (PRRs) and nucleotide-binding domain leucine-rich repeat-containing receptors (NLRs) responsible for triggering PTI and ETI are widely deployed in crop resistance breeding [6,7,8]. However, this PRR/NLR-based dominant resistance is readily overcome by P&Ps that evolved to suppress or evade PTI/ETI [6,7,8]. To establish and maintain sustained compatibility between host plants and adapted P&Ps, plant susceptibility (S) genes are extensively exploited by P&Ps [9]. Notably, modifying some S genes via genome editing and targeting induced local lesions in genomes (TILLING) could confer wheat broad-spectrum and durable resistance, which might represent a new promising strategy in wheat resistance breeding [5,10,11]. Herein, we highlight recent developments in the understanding of wheat S genes and discuss strategies, challenges, and perspectives on exploiting wheat S genes for resistance improvement.

2. Wheat S Genes Supporting Pathogen (Pre)Penetration

Successful pathogen (pre)penetration is a prerequisite for the establishment of compatibility between plants and adapted pathogens. As an adaptive innovation in land plants, lipophilic cuticle covers the plant aerial surface and contributes to plant adaptation to environmental stresses such as drought, salinity, extreme temperatures, and ultraviolet radiation [12,13]. Increasing evidence reveals that wheat surface cues from cuticle induce pre-penetration development of adapted fungal pathogens [14,15]. For instance, the silencing of TaWIN1, a regulator gene in wheat cuticle biosynthesis, via virus-induced gene silencing (VIGS), results in the attenuated biosynthesis of cuticle and reduced conidial germination of fungal pathogen powdery mildew (Blumeria graminis f. sp. tritici, Bgt) [16]. Interestingly, exogenous application of wax very-long-chain (VLC, >C20) aldehydes absent from cuticle wax of the TaWIN1-silenced plants could fully rescue the Bgt germination penalty, suggesting that wax VLC aldehydes biosynthesis positively regulated by TaWIN1 is exploited by Bgt for triggering conidial germination [16]. Consistent with this, VIGS of TaKCS6 and TaECR in bread wheat results in attenuated wax biosynthesis and decreased Bgt germination [17,18]. Bgt germination penalty on TaKCS6- or TaECR-silenced plants is restored by the application of cuticular wax extracted from wild-type wheat plants [17,18]. These studies support the idea that wheat cuticle biosynthesis genes TaWIN1, TaKCS6, and TaECR are exploited by Bgt as S genes to support its pre-penetration development.

In addition to these S genes contributing to Bgt pre-penetration development, wheat genes essential for Bgt penetration have also been identified. As an S gene initially identified in barley, mildew resistance locus O (MLO) encodes a transmembrane protein, and is essential for powdery mildew penetration in a wide range of monocots and dicots [19,20,21,22,23,24]. Knockout of TaMLO using genome editing, TILLING, or VIGS results in the enhanced wheat penetration resistance to Bgt [25,26,27,28]. At the same time, microcolony formation of Bgt is attenuated in the TaMLO mutant, indicating that TaMLO could confer additional post-penetration resistance to Bgt infection [26]. Indeed, HvMLO, a barley ortholog of TaMLO, was revealed to suppress plant defense responses such as reactive oxygen species (ROS) burst and cell death at the infection site of barley powdery mildew (Blumeria graminis f. sp. hordei, Bgh) [19]. Notably, MLO-based barley resistance against Bgh relies on vesicular trafficking and actin reorganization, but not defense-related hormones, suggesting that vesicle/membranedynamics are involved in the MLO-mediated resistance against powdery mildew [24].

3. Wheat S Genes Suppressing Plant Immunity

Upon the perception of invading adapted P&Ps, plants initiate the induced defense systems, which typically leads to transcriptome reprogramming, calcium (Ca²⁺) influx, reactive oxygen species (ROS) production, callose deposition, and even localized cell death (hypersensitive response, HR) [4,5]. In addition, the biosynthesis and signaling of defense-related phytohormones salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) are usually activated to potentiate plant immunity [29]. In the absence of P&P infections, these defense-related responses need to be suppressed to favor plant normal growth and development [30].

As byproducts of aerobic metabolisms such as photosynthesis and respiration, ROS are continuously produced in plant chloroplasts, mitochondria, and peroxisomes [31,32]. In addition, plants evolved various peroxidases and oxidases to rapidly generate ROS in response to environmental stresses [31,32]. At the same time, a plethora of ROS-scavenging enzymes and non-enzymatic antioxidants are deployed to detoxify ROS in plant cells [31,32]. As an early defense signal in plant–pathogen interactions, ROS are generated locally and systemically to induce defense gene expression and trigger cell death [31,32]. Through promoting the regeneration of ROS-scavenging antioxidant ascorbic acid (AsA), monodehydroascorbate reductases (MDHARs) regulate the ROS level in plant cells [33]. The expression of the wheat TaMDHAR4 gene is induced by ROS accumulation, and could respond to the infection of wheat stripe rust (Puccinia striiformis f. sp. tritici, Pst) [33]. The silencing of TaMDHAR4 by VIGS attenuates wheat susceptibility to Pst infection, suggesting that TaMDHAR4 contributes to Pst infection by regulating ROS levels [33]. Similarly, the expression of a wheat alkaline/neutral invertases (A/N-Invs) gene Ta-A/N-Inv1 is induced by Pst infection [34]. Notably, VIGS of Ta-A/N-Inv1 results in the wheat H₂O₂ over-accumulation and enhanced cell death, as well as reduced susceptibility to Pst infection, indicating that wheat S gene Ta-A/N-Inv1 is exploited by Pst to reduce H₂O₂ production and facilitate compatible interaction of wheat with Pst [34]. As summarized in

Table 1. Summary of wheat susceptibility (S) genes contributing to pathogen and pest infections and their application in wheat resistance breeding. Class 1: pathogen (pre)penetration. Class 2: plant immunity. Class 3: pathogen sustenance. Class 4: pest feeding.

Class	Wheat S Gene	S Gene Product Family	Pathogen/Pest Species	Contributions of Wheat S Genes to P&P Infections and Evidence	Application of S Genes in Resistance Breeding	Effector Targets	Reference
1	TaWIN1	AP2-EREBP-type transcription factor	Blumeria graminis f. sp. tritici (Bgt)	Silencing of TaWIN1 by VIGS results in attenuated Bgt conidial germination.	None reported	None reported	[16]
1	TaKCS6	3-Ketoacyl-CoA synthase	Bgt	Silencing of TaKCS6 by VIGS leads to reduced Bgt conidial germination.	None reported	None reported	[17]
1	TaECR	Enoyl-CoA reductase	Bgt	Silencing of TaECR by VIGS results in decreased Bgt conidial germination.	None reported	None reported	[18]
1, 2	TaMLO	Integral membrane protein	Bgt	Knockout TaMLO by TILLING enhances wheat penetration and post-penetration resistance to Bgt.	Wheat Tamlo-R32 mutant generated by genome editing confers Bgt resistance without yield penalty.	None reported	[25,26,27,28]
2	TaMDHAR4	Monodehydroascorbate reductase	Puccinia striiformis f. sp. Tritici (Pst)	Silencing of TaMDHAR4 by VIGS attenuates wheat susceptibility to Pst infection	None reported	None reported	[33]
2	Ta-A/N-Inv1	Alkaline/neutral invertase	Pst	VIGS of Ta-A/N-Inv1 results in the wheat H2O2 over- accumulation, enhanced cell death, and reduced susceptibility to Pst infection	None reported	None reported	[34]
2	TaISP	Cytochrome b6-f component	Pst	Silencing of TaISP by VIGS reduces wheat photosynthesis and susceptibility to Pst.	None reported	Pst_12806	[35]
2	TaNUDX23	Nudix hydrolase	Pst	Knocking down of TaNUDX23 expression by VIGS attenuates Pst infection.	None reported	Pst18363	[36]
2	TaBln1	Cysteine-rich peptide	Pst	Silencing of TaBln1 results in the enhanced Ca2+ influx and attenuated accessibility to Pst.	None reported	None reported	[37]
2	TaMCA1	Metacaspase	Pst	Knockdown of TaMCA1 expression by VIGS enhances wheat resistance to Pst.	None reported	None reported	[38]
2	TaBCAT1	Branched-chain amino acid (BCAA) aminotransferase	Pst	TaBCAT1-silenced wheat plants exhibit enhanced levels of BCAAs and SA, as well as attenuated susceptibility to Pst.	None reported	None reported	[39]
2	TaEDR1	Raf-like mitogen- activated protein kinase kinasekinase (MAPKKK)	Bgt	Knockout of TaEDR1 by TALENs results in attenuated wheat susceptibility to Bgt.	Wheat Taedr1 mutant generated by TALENs displays enhanced Bgt resistance without Bgt-induced cell death and obvious growth penalty.	None reported	[45]
2	TaCSN5	COP9 subunit 5-like protein	Pst	TaCSN5-silenced wheat plants exhibit reduced susceptibility to Pst.	None reported	None reported	[46]
2	TaClpS1	Caseinolytic peptidase (Clp) protease	Pst	Knockdown of TaClpS1 expression via VIGS leads to the enhanced wheat resistance to Pst.	None reported	None reported	[47]
2	TaROP10	Small GTP-binding protein	Pst	The TaRop10-silenced wheat plant exhibits enhanced resistance to Pst.	None reported	None reported	[48]
2	TaEIL1	ETHYLENE INSENSITIVE 3 (EIN3) family transcription factor	Pst	Silencing of TaEIL1 via VIGS enhances disease resistance against stripe rust.	None reported	None reported	[50]
2	TaNAC21/22/30	NAC transcription factor	Pst	Silencing of TaNAC21, TaNAC22, and TaNAC30 attenuates wheat susceptibility to stripe rust.	None reported	None reported	[51,52]
2	TaMED25	Mediator subunit	Bgt	Silencing of TaMED25 by VIGS enhances wheat resistance to Bgt.	None reported	None reported	[53]
2	TaPsIPK1	Receptor-like cytoplasmic kinase	Pst	Overexpression of TaPsIPK1 enhances wheat susceptibility to Pst infection, but the silencing of TaPsIPK1 attenuates wheat susceptibility.	Inactivation of TaPsIPK1 by genome editing confers wheat broad-spectrum resistance against Pst without yield penalty.	PsSpg1	[54]
2	TaWRKY19	WRKY transcription factor	Pst	TaWRKY19-silenced or TaWRKY19-knockout wheat plants exhibit enhanced stripe rust resistance.	None reported	None reported	[55]
2	TaHOS15	WD40-repeat protein	Bgt	Overexpression of TaHOS15 enhances wheat susceptibility to Bgt infection, but the silencing of TaHOS15 attenuates wheat susceptibility.	None reported	None reported	[59]
2	TaHDA6	RPD3-type histone deacetylase	Bgt	Overexpression of TaHDA6 attenuates wheat powdery mildew resistance, but the silencing of TaHDA6 enhances wheat resistance.	None reported	None reported	[59]
2	TaHDT701	HD2-type histone deacetylase	Bgt	Overexpression of TaHDT701 enhances wheat susceptibility to Bgt infection, but the silencing of TaHDT701 attenuates wheat susceptibility.	None reported	None reported	[60]
3	TaAMT2;3a	NH4+ transporter	Pst	Impeded Pst growth is observed in the TaAMT2;3a-silenced wheat leaves.	None reported	None reported	[61]
3	TaSTP3/6/13	Sugartransporter	Pst	Silencing of TaSTP3, TaSTP6, and TaSTP13 by VIGS reduces wheat susceptibility to Pst.	None reported	None reported	[62,63,64,65]
3	TaWRKY19/61/82	WRKY transcription factor	Pst	Pst growth is impeded in the TaWRKY19/61/82-silenced wheat leaves.	None reported	None reported	[65]
4	TaMds-1	Small heatshock protein	Hessian fly	Silencing of TaMds-1 attenuates Hessian fly infestation.	None reported	None reported	[66]
4	(1,3;1,4)-β-glucanase	Glucanase	Russian wheat aphid (RWA)	Aphid reproduction is reduced in the (1,3;1,4)-β-glucanase-silenced wheat plants.	None reported	None reported	[67]

and Figure 1, wheat cytochrome b6-f component gene TaISP and Nudix hydrolase gene TaNUDX23 are also harnessed by Pst to suppress ROS accumulation and contribute to compatibility between wheat and Pst [35,36].

Regulators of Ca²⁺ influx, cell death, and SA production were identified as wheat S genes contributing to the compatible interaction of wheat with Pst and Bgt [37,38,39,40,41,42,43]. The expression of wheat gene Blufensin1 (TaBln1) is induced by Pst infection, and the wheat cysteine-rich peptide TaBln1 could interact with calmodulin TaCaM3 at the plasma membrane [37]. The silencing of wheat TaBln1 results in the enhanced Ca²⁺ influx and attenuated accessibility to Pst, whereas VIGS of wheat TaCaM3 decreases the Ca²⁺ influx and reduces wheat resistance to Pst [37]. These results implythat the wheat susceptibility factor TaBln1 impairs Ca²⁺ influx by interaction with TaCaM3, leading to the suppression of wheat defense and contributing to the compatibility between wheat and Pst [37]. Another wheat S gene TaMCA1 encodes a metacaspase ortholog and could inhibit Bax-induced cell death when expressed in tobacco and wheat leaves [38]. Silencing of TaMCA1 by VIGS enhances wheat resistance to Pst, implying that the wheat S gene TaMCA1 facilitates compatibility between wheat and Pst by suppressing cell death [38]. In addition, the expression of wheat branched-chain amino acid (BCAA) aminotransferase gene TaBCAT1 is potentiated during stripe rust development [39]. TaBCAT1-silenced wheat plants exhibit enhanced levels of BCAAs and SA, as well as attenuated susceptibility to Pst, suggesting that the S gene TaBCAT1 promotes wheat accessibility to Pst via modulating BCAAs metabolisms and SA production [39].

Enhanced Disease Resistance 1 (EDR1) is initially identified from Arabidopsis and encodes a Raf-like mitogen-activated protein kinase kinasekinase (MAPKKK) [40]. The Arabidopsisedr1 mutant exhibits mildew-induced mesophyll cell death and SA-dependent powdery mildew resistance [41,42]. Further studies reveal that AtEDR1 negatively regulates AtMPK3, AtMPK6, and AtATL1, positive regulators in plant defense signaling and cell death, thereby suppressing plant immunity in Arabidopsis [43,44]. Notably, wheat Taedr1 mutant generated by genome editing displays enhanced powdery mildew resistance without mildew-induced cell death and obvious growth penalty, suggesting that the wheat S gene mutant Taedr1 might be a valuable resource in resistance breeding [45].

Components in protein degradation and Rho-of-Plant (ROPs) signaling pathways were identified as suppressors of wheat disease resistance [46,47,48]. The highly conserved constitutive photomorphogenesis 9 (COP9) signalosome (CSN) complex is involved in protein degradation via the ubiquitin–proteasome pathway [46]. Wheat COP9 subunit 5-like gene TaCSN5 is induced during Pst infection, and TaCSN5-silenced wheat plants exhibit reduced susceptibility to Pst [46]. Another wheat S gene, TaClpS1, encodes a caseinolytic peptidase (Clp) protease, an adaptor mediating protein degradation, and is induced during stripe rust development [47]. Knockdown of TaClpS1 expression via VIGS leads to the enhanced wheat resistance to Pst, whereas exogenous expression of TaClpS1 in Nicotiana benthamiana promotes the infection of the oomycete pathogen Phytophthora parasitica [47]. These studies suggest that wheat protein degradation pathways involving TaCSN5 and TaClpS1 are exploited by Pst to suppress plant defense and promote compatible interactions of wheat with Pst [46,47]. As small GTP-binding proteins, plant ROPs are widely involved in the signaling processes in plant development and stress response [48]. The TaRop10-silenced wheat plant exhibits enhanced resistance to Pst, suggesting that the wheat ROP signaling pathway might be harnessed by Pst for promoting wheat accessibility to Pst [48].

As an integral part of plant immunity, the expression of defense genes is induced by P&P infections [49]. A plethora of wheat transcriptional and epigenetic regulators suppressing plant defense gene expression have been identified [49]. For instance, the silencing of wheat transcription factor genes TaEIL1 and TaNAC21/22/30 via VIGS potentiates defense gene expression and enhances disease resistance against stripe rust [50,51,52]. Wheat susceptibility factor TaMED25, a mediator subunit, interacts with TaEIL1 to activate TaERF1 expression, and negatively regulates powdery mildew resistance, indicating the involvement of wheat mediator genes in the establishment of compatible interactions between wheat and Bgt [53]. The wheat receptor-like cytoplasmic kinase TaPsIPK1 was recently demonstrated to phosphorylate the transcription factor TaCBF1d for the transcriptional switch to defense suppression [54]. Interestingly, wheat transcription factor TaWRKY19 was shown to directly bind to promoter regions of TaNOX10, a NADPH oxidase gene involved in ROS production, and represses TaNOX10 expression [55]. Expression of TaWRKY19 is induced upon Pst infection, whereas TaWRKY19-silenced or TaWRKY19-knockout wheat plants exhibit both enhanced ROS accumulation and increased stripe rust resistance [55]. This evidence supports the idea that wheat susceptibility factor TaWRKY19 negatively regulates ROS production and Pst resistance via transcriptional suppression of TaNOX10.

As an important epigenetic mechanism, histone (de)acetylation plays an important role in the regulation of plant direct defense response and immune memory [56,57,58]. Generally, histone acetylation catalyzed by histone acetyltransferase contributes to gene activation, whereas histone deacetylation mediated by histone deacetylases is associated with gene suppression [56,57]. Wheat S genes TaHDA6 and TaHDT701 encode histone deacetylases and are induced during powdery mildew development [59,60]. TaHDA6 and TaHDT701 are shown to interact with WD40-repeat protein TaHOS15 and bind to promoter regions of defense genes such as TaPR1, TaPR2, TaPR5, and TaWRKY45 [59,60]. The silencing of TaHDA6, TaHOS15, and TaHDT701 potentiates histone acetylation in defense genes, leading to the enhanced expression of defense genes and potentiated powdery mildew resistance [59,60]. These studies suggest that wheat susceptibility factors TaHDA6, TaHOS15, and TaHDT701 repress plant resistance to Bgt via epigenetic suppression of defense genes.

4. Wheat S Genes Facilitating Pathogen Sustenance and Pest Feeding

Once the compatible interactions of wheat with adapted pathogens were established, pathogens acquired nutrients from wheat cells for growth and proliferation. There is increasing evidence that wheat nutrient transporter genes are widely exploited by pathogens for nutrient uptake and sustained compatibility [61,62,63,64,65]. Plant ammonium (NH₄⁺) transporters are involved in the NH₄⁺ uptake from soil and are responsible for maintaining nitrogen (N) status in plant cells [61]. It is reported that Pst infection leads to decreased NH₄⁺ concentration and induces expression of the NH₄⁺ transporter gene TaAMT2;3a in wheat leaves [61]. Interestingly, NH₄⁺ concentration is enhanced by Pst infection in the TaAMT2;3a-silenced wheat leaves, which is accompanied by impeded Pst growth [61]. This evidence supports the idea that the NH₄⁺ transporter gene TaAMT2;3a is exploited by Pst to facilitate NH₄⁺ uptake from wheat cells and promotes pathogen infection and growth.

Sugar derived from wheat hosts serves as the major carbon (C) source taken upby phytopathogens. Increasing evidence reveals that adapted pathogens, especially biotrophic fungal pathogens, employ wheat sugar transporter genes for carbon uptake [62,63,64,65]. For instance, the wheat sugar transporter genes TaSTP3, TaSTP6, and TaSTP13 are upregulated by Pst infection [63,64,65]. The wheat leaf rust (Lr) resistance gene Lr67 was identified to encode an inactive mutant of TaSTP13 [62]. Through heterodimerization with functional TaSTP13, LR67 exerts a dominant–negative effect to reduce wheat hexose accumulation for pathogen acquisition, and confers wheat partial resistance to all three rust pathogen species and powdery mildew [62]. Consistent with this, the silencing of TaSTP3, TaSTP6, and TaSTP13 by VIGS reduces wheat susceptibility to Pst, whereas overexpression of these wheat sugar transporter genes in Arabidopsis thaliana leads to increased glucose accumulation and enhances susceptibility to powdery mildew (Golovinomyces cichoracearum) [63,64,65]. Notably, transcription factors TaWRKY19, TaWRKY61, and TaWRKY82 are demonstrated to activate the expression of TaSTP3 induced by Pst infection, suggesting that the transcriptional activation of TaSTP3 mediated by TaWRKY19/61/82 is exploited for the sugar acquisition of adapted fungal pathogens [65].

During an infestation, insect pests such as Hessian fly and Russian wheat aphid (RWA) harness wheat S genes for resource acquisition from host plants [66,67]. Wheat S gene TaMds-1 (Mayetiola destructor susceptibility-1) encodes a small heatshock protein and is induced by the Hessian fly. Ectopic expression and heat induction of TaMds-1 in resistant wheat variety confers susceptibility to Hessian fly [66]. In contrast, silencing of TaMds-1 inhibits Hessian-fly-induced nutritive cell formation at the feeding site of host plants and attenuates Hessian fly infestation, suggesting wheat S gene TaMds-1 isexploited for inducing wheat metabolic changes and nutritive cells formation, thereby contributing to nutrition acquisition and infestation of Hessian fly [66]. Another wheat S gene (1,3;1,4)-β-glucanase is highly upregulated during RWA infestation [67]. Aphid reproduction and plant symptom severity are reduced in the (1,3;1,4)-β-glucanase-silenced wheat plants, suggesting that wheat S gene (1,3;1,4)-β-glucanase contributes to aphid infestation [67].

5. Pathogen Effectors Targeting Wheat S Genes

To colonize and infect host plants, adapted P&Ps evolved effectors to manipulate plant immunity and metabolism [68,69]. Accumulating studies support the idea that pathogen effectors could target wheat S genes to facilitate infection [35,36,54]. Expression of Pst effector gene Pst_12806 is induced during infection, and silencing of Pst_12806 by host-induced gene silencing (HIGS) attenuates Pst infection [35]. Further studies reveal that Pst_12806 accumulates in wheat chloroplasts and interacts with TaISP, a subunit of the cytochrome b6-f complex [35]. Significantly, the silencing of TaISP by VIGS reduces wheat photosynthesis and susceptibility to Pst, whereas overexpression of Pst_12806 in N. benthamiana attenuates photosynthesis, ROS production, and BAX-induced cell death [35]. This evidence suggests that effector protein Pst_12806 inhibits the production of photosynthesis-derived ROS by interfering with the chloroplast protein TaISP, thereby attenuating plant immunity and contributing to Pst infection. Another effector gene Pst18363 is also upregulated during Pst infection, and the knockdown of Pst18363 by HIGS compromises Pst infection [36]. Pst18363 is found to bind and stabilize wheat Nudix hydrolase TaNUDX23, a negative regulator of ROS production, implicating that the effector protein Pst18363 suppresses ROS production to facilitate Pst infection by stabilizing TaNUDX23 [36]. Another Pst effector protein PsSpg1 was recently demonstrated to interact with the wheat susceptibility factor TaPsIPK1, a receptor-like cytoplasmic kinase, to potentiate its kinase activity and nuclear localization, thereby enhancing the wheat susceptibility to Pst [54]. Interestingly, knockout of TaPsIPK1 could induce defense priming and confer broad-spectrum resistance to strip rust without yield penalty in the field, suggesting that the wheat S gene TaPsIPK1 targeted by Pst effector PsSpg1 has great potential in resistance breeding [54].

6. Strategies and Challenges on Exploiting Wheat S Genes in Resistance Breeding

Wheat yield and grain quality are substantially reduced by P&P infections [2]. Breeding resistant varieties with durable and broad-spectrum resistance is one of the most effective strategies for controlling P&Ps and securing wheat production [70,71,72]. Resistance (R) genes mediating race-specific resistance and quantitative trait loci (QTLs) conferring partial resistance are widely employed in wheat resistance breeding. Single R/QTL-mediated resistance could readily be overcome by new pathogen races, which limits their application in crop breeding [6,7,8]. Stacking multiple R genes, combining R genes with QTLs, and engineering NLRs for expanded recognition specificity represent new promising strategies for crop resistance improvement [6,7,8]. As an alternative direction, the inactivation of S genes could effectively reverse susceptibility and confer crop resistance [70,71,72].

Advanced genome editing systems transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)–Cas (CRISPR–associated) are employed for engineering crop genomes and create new opportunities for the inactivation of wheat S genes [73,74,75,76,77,78]. Indeed, targeted knockout of S genes TaWRKY19 and TaPsIPK1 in wheat using CRISPR–Cas9 systems confers resistance to Pst [54,55]. Notably, the Tapsipk1 mutant exhibits broad-spectrum resistance against Pst without yield penalty in field tests, suggesting that the Tapsipk1 mutant is a valuable genetic resource for future wheat resistance breeding [54]. Genome editing of wheat S genes TaMLO and TaEDR1 by TALENs enhances powdery mildew resistance [27,45]. Interestingly, wheat mutant Tamlo-R32 generated by CRISPR–Cas9 systems confers robust powdery mildew resistance without yield penalty [28]. Further studies reveal that a 304-kilobase pair-targeted deletion in Tamlo-R32 mutant causes changes in local chromatin structure and results in the activation of Tonoplast monosaccharide transporter 3 (TaTMT3B), which could rescue the growth and yield penalties associated with MLO resistance [28]. This evidence supports the idea that genome editing of wheat S genes could effectively generate resistant varieties.

Conventional genome editing requires plant genetic transformation and regeneration, which hinders its use in recalcitrant crops like hexaploid bread wheat [75,76,77,78]. Wang et al. recently reported that the overexpression of the wheat gene TaWOX5, a regeneration-related gene of WUSCHEL family, could overcome genotype dependency and greatly enhance wheat transformation efficiency [79]. Debernardi et al. demonstrate that the expression of a chimeric protein harboring the wheat GROWTH-REGULATING FACTOR 4 (GRF4) and its cofactor GRF-INTERACTING FACTOR 1 (GIF1) improves the regeneration efficiency of transgenic wheat plants. These emerging techniques in wheat transformation and regeneration enhance the capacity for the inactivation of wheat S genes by conventional genome editing [80]. Through engineering a Barley stripe mosaic virus-based sgRNA delivery vector (BSMV-sg), Li et al. recently performed a heritable genome editing in Cas9 transgenic wheat plants via virus infection. Genome-edited progenies were obtained at frequencies of 12.9–100%, and most of the mutants are virus free [81]. This convenient and tissue culture-free approach for genome editing paves a new path for the manipulation of S genes and resistance breeding in bread wheat [81].

TILLING utilizes chemical mutagenesis and high-throughput screening approaches to generate the single-nucleotide mutations in targeted genome regions such as S genes of interest [82]. Through introducing saturated mutagenesis, TILLING could be applied in hexaploid bread wheat [83]. Acevedo-Garcia et al. crossed TaMLO mutant lines identified in the TILLING screen and successfully created triple homozygous TaMLO lines that display enhanced Bgt resistance [26]. Since TILLING-derived crop varieties are accepted as non-transgenic, the targeted mutagenesis of wheat S genes by TILLING might provide a great opportunity for commercial resistance breeding [84]. In addition, S gene mutations generated by genome editing and TILLING could be introduced into elite wheat cultivars through cross-breeding, which is facilitated by advanced genomic breeding (GB) methods such as marker-assisted selection (MAS) and marker-assisted backcrossing (MABC) [85,86,87].

Although the past decades have seen substantial progress in identifying wheat S genes, we still have a long way to go towards fully uncovering the mechanism of wheat S genes facilitating P&P infections. For instance, most the characterized wheat S genes are revealed to facilitate infection of biotrophic fungal pathogens such as Pst and Bgt, while S genes promoting wheat accessibility to other P&Ps, especially insect pests [88] and necrotrophic pathogens, are poorly understood. Furthermore, the rice S gene OsPIP1;3 and citrus S gene CsLOB1 contribute to effector translocation and symptom development, respectively, but the wheat S gene controlling these processes remains to be identified [89,90,91,92]. Moreover, temperature changes could affect the stability and durability of disease resistance conferred by some R/QTLs [93,94]. It is vital to analyze the temperature sensitivity of inactive S gene-based resistance, and identify temperature-insensitive inactive S genes to secure the wheat’s durable resistance under a changing climate. In addition, S genes regulate many processes in plant development and stress adaptation, and the understanding of plant genetic pathways/networks involving S genes would facilitate their proper application in wheat breeding.

7. Concluding Remarks and Perspectives

In this review, we summarized recent progress in characterizing wheat S genes and their functions in regulating pathogen (pre)penetration, plant immunity, pathogen sustenance, and pest feeding, and highlighted effector proteins manipulating wheat S genes (Table 1). Strategies and challenges in exploiting wheat S genes for resistance improvement were discussed. As depicted in Figure 1, multiple breeding strategies such as genome editing, TILLING, and cross-breeding could be deployed to modulate S gene for improving wheat resistance. Although the inactivation of S genes could attenuate wheat susceptibility to some P&P infections, many challenges need to be addressed regarding the exploitation of S genes in wheat resistance breeding. For instance, fitness cost is usually associated with resistance conferred by the inactive S gene. Identifying new S genes whose mutation confers enhanced resistance without negative effects on wheat growth and yield would contribute to the germplasm innovation for future resistance breeding. Furthermore, evaluation of the resistance spectrum of inactive S genes is crucial for the design of broad-spectrum resistance via stacking multiple inactive S genes and/or combining inactive S genes with R/QTLs. This broad-spectrum resistance could effectively protect wheat plants from multi-virulent pathogen populations common in the field. Moreover, different parasites usually employ distinct strategies for infection. It is, therefore, vital for wheat breeders to identify new S genes conferring wheat broad-spectrum susceptibility to a wide range of P&Ps. In addition, the release of crop varieties generated by genome editing is unacceptable in some countries/regions. Therefore, the regulatory framework on genome editing needs to be modified in these countries/regions before the release of wheat varieties with edited S genes. With the progress in the understanding of wheat S gene and advances in biotechnologies, modulating S genes would greatly promote wheat resistance improvement.