Genomics of interaction between the brown planthopper and rice

Genome-Wide Identification and Expression Pattern of Sugar Transporter Genes in the Brown Planthopper, Nilaparvata lugens (Stål)

Sugar transporters play important roles in controlling carbohydrate transport and are responsible for mediating the movement of sugars into cells in numerous organisms. In insects, sugar transporters not only play a role in sugar transport but may also act as receptors for virus entry and the accumulation of plant defense compounds. The brown planthopper, Nilaparvata lugens, inflicts damage on rice plants by feeding on their phloem sap, which is rich in sugars. In the present study, we identified 34 sugar transporters in N. lugens, which were classified into three subfamilies based on phylogenetic analysis. The motif numbers varied from seven to eleven, and motifs 2, 3, and 4 were identified in the functional domains of all 34 NlST proteins. Chromosome 1 was found to possess the highest number of NlST genes, harboring 15. The gut, salivary glands, fat body, and ovary were the different tissues enriched with NlST gene expression. The expression levels of NlST2, 3, 4, 7, 20, 27, 28, and 31 were higher in the gut than in the other tissues. When expressed in a Saccharomyces cerevisiae hexose transporter deletion mutant (strain EBY.VW4000), only ApST4 (previously characterized) and NlST4, 28, and 31 were found to transport glucose and fructose, resulting in functional rescue of the yeast mutant. These results provide valuable data for further studies on sugar transporters in N. lugens and lay a foundation for finding potential targets to control N. lugens.

Genome-wide association study and genomic prediction for resistance to brown planthopper in rice

The brown planthopper (BPH) is the most destructive insect pest that threatens rice production globally. Developing rice varieties incorporating BPH-resistant genes has proven to be an effective control measure against BPH. In this study, we assessed the resistance of a core collection consisting of 502 rice germplasms by evaluating resistance scores, weight gain rates and honeydew excretions. A total of 117 rice varieties (23.31%) exhibited resistance to BPH. Genome-wide association studies (GWAS) were performed on both the entire panel of 502 rice varieties and its subspecies, and 6 loci were significantly associated with resistance scores (P value < 1.0e-8). Within these loci, we identified eight candidate genes encoding receptor-like protein kinase (RLK), nucleotide-binding and leucine-rich repeat (NB-LRR), or LRR proteins. Two loci had not been detected in previous study and were entirely novel. Furthermore, we evaluated the predictive ability of genomic selection for resistance to BPH. The results revealed that the highest prediction accuracy for BPH resistance reached 0.633. As expected, the prediction accuracy increased progressively with an increasing number of SNPs, and a total of 6.7K SNPs displayed comparable accuracy to 268K SNPs. Among various statistical models tested, the random forest model exhibited superior predictive accuracy. Moreover, increasing the size of training population improved prediction accuracy; however, there was no significant difference in prediction accuracy between a training population size of 737 and 1179. Additionally, when there existed close genetic relatedness between the training and validation populations, higher prediction accuracies were observed compared to scenarios when they were genetically distant. These findings provide valuable resistance candidate genes and germplasm resources and are crucial for the application of genomic selection for breeding durable BPH-resistant rice varieties.

Combined miRNA and mRNA sequencing reveals the defensive strategies of resistant YHY15 rice against differentially virulent brown planthoppers

Introduction

The brown planthopper (BPH) poses a significant threat to rice production in Asia. The use of resistant rice varieties has been effective in managing this pest. However, the adaptability of BPH to resistant rice varieties has led to the emergence of virulent populations, such as biotype Y BPH. YHY15 rice, which carries the BPH resistance gene Bph15, exhibits notable resistance to biotype 1 BPH but is susceptible to biotype Y BPH. Limited information exists regarding how resistant rice plants defend against BPH populations with varying levels of virulence.

Methods

In this study, we integrated miRNA and mRNA expression profiling analyses to study the differential responses of YHY15 rice to both avirulent (biotype 1) and virulent (biotype Y) BPH.

Results

YHY15 rice demonstrated a rapid response to biotype Y BPH infestation, with significant transcriptional changes occurring within 6 hours. The biotype Y-responsive genes were notably enriched in photosynthetic processes. Accordingly, biotype Y BPH infestation induced more intense transcriptional responses, affecting miRNA expression, defenserelated metabolic pathways, phytohormone signaling, and multiple transcription factors. Additionally, callose deposition was enhanced in biotype Y BPH-infested rice seedlings.

Discussion

These findings provide comprehensive insights into the defense mechanisms of resistant rice plants against virulent BPH, and may potentially guide the development of insect-resistant rice varieties.

Expression Analysis Reveals Differentially Expressed Genes in BPH and WBPH Associated with Resistance in Rice RILs Derived from a Cross between RP2068 and TN1

BPH (brown planthopper) and WBPH (white backed planthopper) are significant rice pests that often co-occur as sympatric species and cause substantial yield loss. Despite their genetic similarities, different host-resistance genes confer resistance against these two hoppers. The defense mechanisms in rice against these pests are complex, and the molecular processes regulating their responses remain largely unknown. This study used specific recombinant inbred lines (RILs) derived from a cross between rice varieties RP2068-18-3-5 (BPH- and WBPH-resistant) and TN1 (BPH- and WBPH-susceptible) to investigate the mechanisms of interaction between these planthoppers and their rice hosts. WBPH and BPH were allowed to feed on specific RILs, and RNA-Seq was carried out on WBPH insects. Transcriptome profiling and qRT-PCR results revealed differential expression of genes involved in detoxification, digestion, transportation, cuticle formation, splicing, and RNA processing. A higher expression of sugar transporters was observed in both hoppers feeding on rice with resistance against either hopper. This is the first comparative analysis of gene expressions in these insects fed on genetically similar hosts but with differential resistance to BPH and WBPH. These results complement our earlier findings on the differential gene expression of the same RILs (BPH- or WBPH-infested) utilized in this study. Moreover, identifying insect genes and pathways responsible for countering host defense would augment our understanding of BPH and WBPH interaction with their rice hosts and enable us to develop lasting strategies to control these significant pests.

Large scale rice germplasm screening for identification of novel brown planthopper resistance sources

Rice (Oryza sativa L.) is a staple food crop globally. Brown planthopper (Nilaparvata lugens Stål, BPH) is the most destructive insect that threatens rice production annually. More than 40 BPH resistance genes have been identified so far, which provide valuable gene resources for marker-assisted breeding against BPH. However, it is still urgent to evaluate rice germplasms and to explore more new wide-spectrum BPH resistance genes to combat newly occurring virulent BPH populations. To this end, 560 germplasm accessions were collected from the International Rice Research Institute (IRRI), and their resistance to current BPH population of China was examined. A total of 105 highly resistant materials were identified. Molecular screening of BPH resistance genes in these rice germplasms was conducted by developing specific functional molecular markers of eight cloned resistance genes. Twenty-three resistant germplasms were found to contain none of the 8 cloned BPH resistance genes. These accessions also exhibited a variety of resistance mechanisms as indicated by an improved insect weight gain (WG) method, suggesting the existence of new resistance genes. One new BPH resistance gene, Bph44(t), was identified in rice accession IRGC 15344 and preliminarily mapped to a 0-2 Mb region on chromosome 4. This study systematically sorted out the corresponding relationships between BPH resistance genes and germplasm resources using a functional molecular marker system. Newly explored resistant germplasms will provide valualble donors for the identification of new resistance genes and BPH resistance breeding programs.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01416-x.

Comprehensive identification and characterization of lncRNAs and circRNAs reveal potential brown planthopper-responsive ceRNA networks in rice

Brown planthopper (Nilaparvata lugens Stål, BPH) is one of the most destructive pests of rice. Non-coding RNA plays an important regulatory role in various biological processes. However, comprehensive identification and characterization of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in BPH-infested rice have not been performed. Here, we performed a genome-wide analysis of lncRNAs and circRNAs in BPH6-transgenic (resistant, BPH6G) and Nipponbare (susceptible, NIP) rice plants before and after BPH feeding (early and late stage) via deep RNA-sequencing. A total of 310 lncRNAs and 129 circRNAs were found to be differentially expressed. To reveal the different responses of resistant and susceptible rice to BPH herbivory, the potential functions of these lncRNAs and circRNAs as competitive endogenous RNAs (ceRNAs) were predicted and investigated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. Dual-luciferase reporter assays revealed that miR1846c and miR530 were targeted by the lncRNAs XLOC_042442 and XLOC_028297, respectively. In responsive to BPH infestation, 39 lncRNAs and 21 circRNAs were predicted to combine with 133 common miRNAs and compete for miRNA binding sites with 834 mRNAs. These mRNAs predictably participated in cell wall organization or biogenesis, developmental growth, single-organism cellular process, and the response to stress. This study comprehensively identified and characterized lncRNAs and circRNAs, and integrated their potential ceRNA functions, to reveal the rice BPH-resistance network. These results lay a foundation for further study on the functions of lncRNAs and circRNAs in the rice-BPH interaction, and enriched our understanding of the BPH-resistance response in rice.

Osa-miR162a Enhances the Resistance to the Brown Planthopper via α-Linolenic Acid Metabolism in Rice (Oryza sativa)

The brown planthopper (BPH) is the most serious pest causing yield losses in rice. MicroRNAs (miRNAs) are emerging as key modulators of plant-pest interactions. In the study, we found that osa-miR162a is induced in response to BPH attack in the seedling stage and tunes rice resistance to the BPH via the α-linolenic acid metabolism pathway as indicated by gas chromatography/liquid chromatography-mass spectrometry analysis. Overexpression of osa-miR162a inhibited the development and growth of the BPH and simultaneously reduced the release of 3-hexenal and 3-hexen-1-ol to block host recognition in the BPH. Moreover, knockdown of OsDCL1, which is targeted by osa-miR162a, inhibited α-linolenic acid metabolism to enhance the resistance to the BPH, which was similar to that in miR162a-overexpressing plants. Our study revealed a novel defense mechanism mediated by plant miRNAs developed during the long-term evolution of plant-host interaction, provided new ideas for the identification of rice resistance resources, and promoted a better understanding of pest control.

Transcriptome analysis revealed differentially expressed genes in rice functionally associated with brown planthopper defense in near isogenic lines pyramiding BPH14 and BPH15

Although rice has many pests, brown planthopper (BPH) in particular is known to cause substantial damage. The pyramiding application of BPH-resistance genes BPH14 and BPH15 has proven effective in enhancing rice defense against BPH. However, the molecular mechanisms underlying BPH14/BPH15-conferred resistance remain unexplained. In this investigation, we analyzed the transcriptomes of near isogenic lines (NILs) containing either BPH14 (B14), BPH15 (B15), or BPH14/BPH15 (B1415), as well as their recurrent parent (RP) 'Wushansimiao'. In total, we detected 14,492 differentially expressed genes (DEGs) across 12 mRNA profiles of resistant NILs and RP at different feeding stages. In the transcriptomic analysis, 531 DEGs appeared to be common among the resistant NILs compared to RP before and after BPH feeding. These common DEGs were enriched in defense response, phosphorylation, and salt stress response. In addition, 258 DEGs shared only in resistant NILs were obtained among the different feeding stages, which were enriched in oxidative stress response, karrikin response, and chloroplast organization. Considering the expression patterns and relevant research reports associated with these DEGs, 21 were chosen as BPH resistance candidates. In rice protoplasts, the candidate DEG OsPOX8.1 was confirmed to increase reactive oxygen species (ROS) accumulation by chemiluminescence measurement. Our results provide valuable information to further explore the defense mechanism of insect-resistant gene pyramiding lines and develop robust strategies for insect control.

Integrated transcriptomics and metabolomics analysis provide insight into the resistance response of rice against brown planthopper

Introduction

The brown planthopper (Nilaparvata lugens Stål, BPH) is one of the most economically significant pests of rice. The Bph30 gene has been successfully cloned and conferred rice with broad-spectrum resistance to BPH. However, the molecular mechanisms by which Bph30 enhances resistance to BPH remain poorly understood.

Methods

Here, we conducted a transcriptomic and metabolomic analysis of Bph30-transgenic (BPH30T) and BPH-susceptible Nipponbare plants to elucidate the response of Bph30 to BPH infestation.

Results

Transcriptomic analyses revealed that the pathway of plant hormone signal transduction enriched exclusively in Nipponbare, and the greatest number of differentially expressed genes (DEGs) were involved in indole 3-acetic acid (IAA) signal transduction. Analysis of differentially accumulated metabolites (DAMs) revealed that DAMs involved in the amino acids and derivatives category were down-regulated in BPH30T plants following BPH feeding, and the great majority of DAMs in flavonoids category displayed the trend of increasing in BPH30T plants; the opposite pattern was observed in Nipponbare plants. Combined transcriptomics and metabolomics analysis revealed that the pathways of amino acids biosynthesis, plant hormone signal transduction, phenylpropanoid biosynthesis and flavonoid biosynthesis were enriched. The content of IAA significantly decreased in BPH30T plants following BPH feeding, and the content of IAA remained unchanged in Nipponbare. The exogenous application of IAA weakened the BPH resistance conferred by Bph30.

Discussion

Our results indicated that Bph30 might coordinate the movement of primary and secondary metabolites and hormones in plants via the shikimate pathway to enhance the resistance of rice to BPH. Our results have important reference significance for the resistance mechanisms analysis and the efficient utilization of major BPH-resistance genes.

Advances of herbivore-secreted elicitors and effectors in plant-insect interactions

Diverse molecular processes regulate the interactions between insect herbivores and their host plants. When plants are exposed to insects, elicitors induce plant defenses, and complex physiological and biochemical processes are triggered, such as the activation of the jasmonic acid (JA) and salicylic acid (SA) pathways, Ca2+ flux, reactive oxygen species (ROS) burst, mitogen-activated protein kinase (MAPK) activation, and other responses. For better adaptation, insects secrete a large number of effectors to interfere with plant defenses on multiple levels. In plants, resistance (R) proteins have evolved to recognize effectors and trigger stronger defense responses. However, only a few effectors recognized by R proteins have been identified until now. Multi-omics approaches for high-throughput elicitor/effector identification and functional characterization have been developed. In this review, we mainly highlight the recent advances in the identification of the elicitors and effectors secreted by insects and their target proteins in plants and discuss their underlying molecular mechanisms, which will provide new inspiration for controlling these insect pests.

Poaceae-specific β-1,3;1,4-d-glucans link jasmonate signalling to OsLecRK1-mediated defence response during rice-brown planthopper interactions

Brown planthopper (BPH, Nilaparvata lugens), a highly destructive insect pest, poses a serious threat to rice (Oryza sativa) production worldwide. Jasmonates are key phytohormones that regulate plant defences against BPH; however, the molecular link between jasmonates and BPH responses in rice remains largely unknown. Here, we discovered a Poaceae-specific metabolite, mixed-linkage β-1,3;1,4-d-glucan (MLG), which contributes to jasmonate-mediated BPH resistance. MLG levels in rice significantly increased upon BPH attack. Overexpressing OsCslF6, which encodes a glucan synthase that catalyses MLG biosynthesis, significantly enhanced BPH resistance and cell wall thickness in vascular bundles, whereas knockout of OsCslF6 reduced BPH resistance and vascular wall thickness. OsMYC2, a master transcription factor of jasmonate signalling, directly controlled the upregulation of OsCslF6 in response to BPH feeding. The AT-rich domain of the OsCslF6 promoter varies in rice varieties from different locations and natural variants in this domain were associated with BPH resistance. MLG-derived oligosaccharides bound to the plasma membrane-anchored LECTIN RECEPTOR KINASE1 OsLecRK1 and modulated its activity. Thus, our findings suggest that the OsMYC2-OsCslF6 module regulates pest resistance by modulating MLG production to enhance vascular wall thickness and OsLecRK1-mediated defence signalling during rice-BPH interactions.

Pest categorisation of Nilaparvata lugens

The EFSA Panel on Plant Health performed a pest categorisation of Nilaparvata lugens (Hemiptera: Delphacidae), the brown planthopper, for the European Union. N. lugens is widespread in Asia where it is native; it also occurs in Oceania where it is naturalised. N. lugens is not known to be present in the EU and is not listed in Annex II of Commission Implementing Regulation (EU) 2019/2072. It is a monophagous species and a major pest of rice (Oryza sativa). High populations of planthoppers cause leaves to initially turn orange yellow before becoming brown and dry and this is a condition called 'hopperburn' that kills the plant. N. lugens can also transmit plant viruses. It can complete 12 generations per year in tropical areas, where it resides year-round. N. lugens can undertake long-distance migration of up to 500 km from tropical areas to form transient populations in sub-tropical and temperate areas but due to low temperatures and absence of rice plants during the winter it does not establish in such areas. Entry to the EU via migration is unlikely given the distance from tropical rice growing areas. A possible but unlikely potential pathway is the import of infested rice seedlings, although we have no evidence that such trade exists. In the EU, rice is mainly planted from seed; when transplanted, it is sourced locally. N. lugens is very unlikely to survive year-round in the EU due to unsuitable climate and lack of hosts during the winter. Consequently, the pest is very unlikely to become established in the EU territory. Nevertheless, there are measures available to further reduce the likelihood of entry, establishment and spread of N. lugens within the EU. N. lugens does not satisfy the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest.

α-1,6-fucosyltransferase plays a critical role during embryogenesis of the hemimetabolous insect Nilaparvata lugens

Protein glycosylation is one of the most important post-translational modifications, modulating the properties of proteins. In insects, α-1,6-fucosyltransferase (FucT6) is an important enzyme in the glycosylation pathway, modifying the core structure of N-glycans on glycoproteins with the addition of a fucose residue. In our previous study, RNAi-mediated silencing of FucT6 in the third-instar nymphs of Nilaparvata lugens caused a failure of the ecdysis process during nymphal development, leading to high mortality. These results suggested the requirement of FucT6 during nymphal development in N. lugens. In this study, RNAi-mediated gene silencing of FucT6 in adults did not cause lethality. However, parental RNAi of FucT6 led to full failure in the hatching of eggs, and this effect was maternally mediated. Interestingly, gene expression levels of FucT6 in the eggs peaked at the katatrepsis event, where the embryo rotates 180° resulting in the head pointing towards the anterior side of the egg. Proteome analysis showed significant differences in the abundance of proteins between different embryonal developmental stages, suggesting the crucial role of FucT6 mediated core N-fucosylation in embryonal development. Therefore, correct α-1,6-fucosylation of glycoproteins is important for N. lugens during embryonic development and this study provides new insights into the role of N-glycosylation in embryogenesis in insects.

Functional Bph14 from Rathu Heenati promotes resistance to BPH at the early seedling stage of rice (Oryza sativa L.) as revealed by QTL-seq

A QTL associated with BPH resistance at the early seedling stage was identified on chromosome 3. Functional Bph14 in Rathu Heenati was associated with BPH resistance at the early seedling stage. Brown planthopper (BPH; Nilaparvata lugens Stål) is considered the most important rice pest in many Asian countries. Several BPH resistance genes have previously been identified. However, there are few reports of genes specific for BPH resistance at the early seedling stage, a crucial stage for direct-seeding cultivation. In this study, we performed a QTL-seq analysis using two bulks (20 F₂ lines in each bulk) of the F₂ population (n = 300) derived from a cross of Rathu Heenati (RH) × HCS-1 to identify QTL/genes associated with BPH resistance at the early seedling stage. An important QTL was identified on chromosome 3 and Bph14 was identified as a potential candidate gene based on the differences in gene expression and sequence variation when compared with the two parents. All plants in the resistant bulks possessed the functional Bph14 from RH and all plants in the susceptible bulk and HCS-1 contained a large deletion (2703 bp) in Bph14. The functional Bph14 gene of RH appears to be important for BPH resistance at the early seedling stage of rice and could be used in conjunction with other BPH resistance genes in rice breeding programs that confer resistance to BPH at the early and later growth stages.

Slowing virulence adaptation in Asian rice planthoppers through migration-based deployment of resistance genes

Advances in molecular biology have accelerated rice breeding for resistance to Asian planthoppers. However, experience shows that planthoppers quickly adapt to resistance in tropical overwintering areas. With only limited sources available, the large-scale deployment of resistance genes can rapidly reduce the utility of these public goods. Planthoppers that migrate from tropical to temperate Asia carry virulence against many resistance genes, but adapt more slowly to resistant rice in temperate regions. Therefore, by restricting deployment of selected genes to temperate regions, virulence-adaptation rates and the volume of migrants returning to overwintering sites could be reduced. The current open exchange of breeding materials throughout Asia urgently requires an international, multidisciplinary, stakeholder coalition to promote a more sustainable deployment of planthopper-resistant rice.

Identification of two QTLs, BPH41 and BPH42, and their respective gene candidates for brown planthopper resistance in rice

The brown planthopper (BPH) is the leading cause of insect damage to rice plants and BPH infestations have caused profound losses in rice production since the 1970's. There is an urgent need to discover new BPH resistance genes to ensure the successful production of rice. Here, a new BPH resistance source provided by SeedWorks International Pvt. Ltd., SWD10, was used for this purpose. QTL mapping using 232 F2 progenies and 216 polymorphic markers revealed two dominant BPH resistance QTLs, BPH41 and BPH42, located on chromosome 4. BPH resistance mechanism test revealed that antibiosis and antixenosis mechanisms both play a role in BPH resistance conferred by these two QTLs. The QTLs were delimited between markers SWRm_01617 and SWRm_01522 for BPH41, and SWRm_01695 and SWRm_00328 for BPH42. Additionally, using RNA-seq data of lines containing the resistant QTLs, we shortlisted four and three gene candidates for BPH41 and BPH42, respectively. Differential gene expression analysis of lines containing the QTLs suggested that SWD10 BPH resistance is contributed by the plant's innate immunity and the candidate genes may be part of the rice innate immunity pathway. Currently, the newly identified QTLs are being utilized for breeding BPH resistant rice varieties and hybrids.

Genome-wide identification of long non-coding (lncRNA) in Nilaparvata lugens's adaptability to resistant rice

Background

The brown planthopper (BPH), Nilaparvata lugens (Stål), is a very destructive pest that poses a major threat to rice plants worldwide. BPH and rice have developed complex feeding and defense strategies in the long-term co-evolution.

Methods

To explore the molecular mechanism of BPH's adaptation to resistant rice varieties, the lncRNA expression profiles of two virulent BPH populations were analyzed. The RNA-seq method was used to obtain the lncRNA expression data in TN1 and YHY15.

Results

In total, 3,112 highly reliable lncRNAs in TN1 and YHY15 were identified. Compared to the expression profiles between TN1 and YHY15, 157 differentially expressed lncRNAs, and 675 differentially expressed mRNAs were identified. Further analysis of the possible regulation relationships between differentially expressed lncRNAs and differentially expressed mRNAs, identified three pair antisense targets, nine pair cis-regulation targets, and 3,972 pair co-expressed targets. Function enriched found arginine and proline metabolism, glutathione metabolism, and carbon metabolism categories may significantly affect the adaptability in BPH when it is exposed to susceptible and resistant rice varieties. Altogether, it provided scientific data for the study of lncRNA regulation of brown planthopper resistance to rice. These results are helpful in the development of new control strategies for host defense against BPH and breeding rice for high yield.

Bulked Segregant RNA Sequencing Revealed Difference Between Virulent and Avirulent Brown Planthoppers

The brown planthopper (Nilaparvata lugens Stål, BPH) is one of the most devastating insect pests of rice (Oryza sativa L.), but BPH populations have varying degrees of virulence to rice varieties carrying different resistance genes. To help efforts to characterize these variations we applied bulked segregant RNA sequencing (BSR-seq) to identify differentially expressed genes (DEGs) and genetic loci associated with BPH virulence to YHY15 rice plants carrying the resistance gene Bph15. BPHs that are highly virulent or avirulent to these plants were selected from an F2 population to form two contrasting bulks, and BSR-seq identified 751 DEGs between the bulks. Genes associated with carbohydrate, amino acid and nucleotide metabolism, the endocrine system, and signal transduction were upregulated in the avirulent insects when they fed on these plants. The results also indicated that shifts in lipid metabolism and digestive system pathways were crucial for the virulent BPHs' adaptation to the resistant rice. We identified 24 single-nucleotide polymorphisms (SNPs) in 21 genes linked with BPH virulence. Possible roles of genes apparently linked to BPH virulence are discussed. Our results provide potentially valuable information for further studies of BPH virulence mechanisms and development of robust control strategies.

Twenty years of rice genomics research: From sequencing and functional genomics to quantitative genomics

Since the completion of the rice genome sequencing project in 2005, we have entered the era of rice genomics, which is still in its ascendancy. Rice genomics studies can be classified into three stages: structural genomics, functional genomics, and quantitative genomics. Structural genomics refers primarily to genome sequencing for the construction of a complete map of rice genome sequence. This is fundamental for rice genetics and molecular biology research. Functional genomics aims to decode the functions of rice genes. Quantitative genomics is large-scale sequence- and statistics-based research to define the quantitative traits and genetic features of rice populations. Rice genomics has been a transformative influence on rice biological research and contributes significantly to rice breeding, making rice a good model plant for studying crop sciences.

Salivary protein 7 of the brown planthopper functions as an effector for mediating tricin metabolism in rice plants

The brown planthopper (BPH), Nilaparvata lugens, is an important pest that affects rice (Oryza sativa) production in Asia. The flavone tricin (5,7,4'-trihydroxy-3',5'-dimethoxy flavone) is a valuable secondary metabolite commonly found in rice plants that can defend rice plants against infestation by BPH. BPH damage can reduce the metabolic level of tricin in rice. Our preliminary transcriptome research results showed that BPH salivary protein 7 (NlSP7), is highly responsive to tricin stimuli. However, the function of NlSP7 in mediating the interaction between the rice plant and the BPH is unknown. In this study, we cloned the NlSP7 gene in N. lugens and found that its mRNA level was greater in the presence of high tricin content than low tricin content, regardless of whether the BPHs were fed a rice plant diet or an artificial diet containing 100 mg/L tricin. Knocking down NlSP7 resulted in BPH individuals spending more time in the non-penetration and pathway phase, and less time feeding on the phloem of rice plants. These changes decreased BPH food intake, feeding behavior, and fitness, as well as the tricin content of the rice plants. These findings demonstrate that the salivary protein 7 of BPH functions as an effector for tricin metabolism in rice.

Bio-Efficacy of Chrysoeriol7, a Natural Chemical and Repellent, against Brown Planthopper in Rice

Brown planthopper (BPH, Nilaparvata lugens Stal.) is the most damaging rice pest affecting stable rice yields worldwide. Currently, methods for controlling BPH include breeding a BPH-resistant cultivar and using synthetic pesticides. Nevertheless, the continuous cultivation of resistant cultivars allows for the emergence of various resistant races, and the use of synthetic pesticides can induce environmental pollution as well as the emergence of unpredictable new pest species. As plants cannot migrate to other locations on their own to combat various stresses, the production of secondary metabolites allows plants to protect themselves from stress and tolerate their reproduction. Pesticides using natural products are currently being developed to prevent environmental pollution and ecosystem disturbance caused by synthetic pesticides. In this study, after BPH infection in rice, chrysoeriol7 (C7), a secondary metabolite that induces resistance against BPH, was assessed. After C7 treatment and BPH infection, relative expression levels of the flavonoid-related genes were elevated, suggesting that in plants subjected to BPH, compounds related to flavonoids, among the secondary metabolites, play an important role in inducing resistance. The plant-derived natural compound chrysoeriol7 can potentially thus be used to develop environmentally friendly pesticides. The suggested control of BPH can be effectively used to alleviate concerns regarding environmental pollution and to construct a relatively safe rice breeding environment.

Genetic and molecular understanding of host rice resistance and Nilaparvata lugens adaptation

The variability of brown planthopper (BPH) populations and diversity of the host rice germplasm provide an ideal model for exploring the genetic and molecular basis of insect-plant interactions. During the long-term evolutionary arms race, complicated feeding and defense strategies have developed in BPH and rice. Nine major BPH resistance genes have been cloned and the exploration of BPH resistance genes medicated mechanism against BPH shed a light on the molecular basis of the rice-BPH interaction. This short review provides an update on our current understanding of the genetic and molecular mechanism for rice resistance and BPH adaptation. Understanding the interactions between BPH and rice will provide novel insights for sustainable control of this pest.

Transcriptomic and proteomic responses to brown plant hopper (Nilaparvata lugens) in cultivated and Bt-transgenic rice (Oryza sativa) and wild rice (O. rufipogon)

Strategies are still employed to reduce insect damage in crop production, including conventional breeding with wild germplasm resources and transgenic technology with foreign genes' insertion. Cultivated and Bt-transgenic rice (Oryza sativa) and two ecotypes of wild rice (O. rufipogon) were treated by a 72 h feeding of brown plant hopper (Nilaparvata lugens). Under the feeding of N. lugens, compared with the cultivated rice (568 and 4), more differentially expressed genes (DEGs) and differentially accumulated proteins (DAPs) were identified in transgenic rice (2098 and 11) and two wild ecotypes (1990, 39 and 1932, 25, respectively). The iTRAQ analysis showed 79 DAPs and confirmed the results of RNA-seq, which showed the least GO terms and KEGG pathways responding to herbivory in the cultivated rice. DAPs significantly enriched two GO terms that are related with Bph14 and Bph33 genes in rice. Most of DEGs and DAPs were related to plant biological processes of plant-pathogen interaction and plant hormone signal transduction, and hormone signaling and transcription factors regulate the immune response of rice to BPH. Our results demonstrated the similarity in the wild rice and Bt-transgenic rice for their transcriptomic and proteomic response to herbivory, while cultivated rice lacked enough pathways in response to herbivory. STATEMENT OF SIGNIFICANCE OF THE STUDY: The iTRAQ analysis and RNA-seq were employed 39 to identify differentially expressed genes (DEGs) and differentially accumulated proteins (DAPs) in seedlings of cultivated, Bt-transgenic and two wild rice ecotypes under feeding of brown plant hopper. Wild rice showed DEGs and DAPs related to biochemical pathways of plant pathogen interactions and plant hormone signal transductions, while cultivated rice lacked enough pathways in response to herbivory. Crop domestication weakened the response of plants to herbivory, while the insertion of Bt gene might promote the response of plants to herbivory. Growing environment plays an important role in regulating gene networks of plant response to herbivory. Our results highlighted the importance of conservation of crop wild species. SIGNIFICANCE: Insect damage is one of main factors in reducing agricultural production, and technologies and methods were employed to control insect pests in agricultural systems. Transgenic technology is developed to produce insect-resistant crops, but receive concerns on biosafety risks. Alternatively, crop wild species are important genetic resource in crop breeding to produce trait-specific varieties. Here, we investigated the molecular mechanisms of plant response to herbivory in wild, Bt-transgenic and cultivated rice, and found crop domestication weakened the response of plants to herbivory. The insertion of foreign Bt gene may promote the expression of other genes. In addition, our results showed growing environment plays an important role in regulating gene networks of plant response to herbivory. These results highlight the importance of wild species conservation, with the strategy of in situ conservation.

The control of the brown planthopper by the rice Bph14 gene is affected by nitrogen

BACKGROUND

Brown rice planthopper (BPH) is a devastating rice pest in Asia. Bph14 is the first cloned BPH-resistance gene in rice, inducing callose deposition while impeding BPH feeding. Nitrogen application affects plant growth and resistance. However, there is little evidence on the influence of nitrogen on the callose content or regulation of rice BPH resistance. In this study, Luoyou9348 (containing Bph14 and highly resistant to BPH) and Yangliangyou6 (without Bph14 and susceptible to BPH) were planted under varying nitrogen regimes (0 , 90, 180 kg ha^-1 ) to determine their effects on the resistance levels of rice to BPH feeding. The experiments involved BPH performance, plant volatile profiling and BPH preferences in laboratory and field experiments.

RESULTS

We found that BPH egg hatching rate, total number of eggs laid and BPH preference increased with increasing nitrogen application in both rice varieties. However, the expression of Bph14, callose content and BPH feeding significantly declined with an increase in nitrogen fertilization in Luoyou9348, compared with Yangliangyou6. Also, the emission of volatile terpene compounds increased with increasing nitrogen application, which resulted in an increase in BPH numbers on both varieties. Two-way analysis of variance indicated a significant interaction between rice variety and nitrogen in BPH feeding behavior.

CONCLUSION

Our findings provide an insight for addressing problems involved in the incorporation of insecticidal genes into crop plants. The effects of nitrogen on insecticidal gene expression in rice plant defense are discussed. © 2020 Society of Chemical Industry.

A, Chakraborty A, Thirunavukkarasu N. Multiple Genome Wide Association Mapping Models Identify Quantitative Trait Nucleotides for Brown Planthopper (Nilaparvata lugens) Resistance in MAGIC Indica Population of Rice

Brown planthopper (BPH), one of the most important pests of the rice (Oryza sativa) crop, becomes catastrophic under severe infestations and causes up to 60% yield loss. The highly disastrous BPH biotype in the Indian sub-continent is Biotype 4, which also known as the South Asian Biotype. Though many resistance genes were mapped until now, the utility of the resistance genes in the breeding programs is limited due to the breakdown of resistance and emergence of new biotypes. Hence, to identify the resistance genes for this economically important pest, we have used a multi-parent advanced generation intercross (MAGIC) panel consisting of 391 lines developed from eight indica founder parents. The panel was phenotyped at the controlled conditions for two consecutive years. A set of 27,041 cured polymorphic single nucleotide polymorphism (SNPs) and across-year phenotypic data were used for the identification of marker–trait associations. Genome-wide association analysis was performed to find out consistent associations by employing four single and two multi-locus models. Sixty-one SNPs were consistently detected by all six models. A set of 190 significant marker-associations identified by fixed and random model circulating probability unification (FarmCPU) were considered for searching resistance candidate genes. The highest number of annotated genes were found in chromosome 6 followed by 5 and 1. Ninety-two annotated genes identified across chromosomes of which 13 genes are associated BPH resistance including NB-ARC (nucleotide binding in APAF-1, R gene products, and CED-4) domain-containing protein, NHL repeat-containing protein, LRR containing protein, and WRKY70. The significant SNPs and resistant lines identified from our study could be used for an accelerated breeding program to develop new BPH resistant cultivars.

A combined microRNA and transcriptome analyses illuminates the resistance response of rice against brown planthopper

Background

The brown planthopper (BPH, Nilaparvata lugens Stål) is a kind of phloem-feeding pest that adversely affects rice yield. Recently, the BPH-resistance gene, BPH6, was cloned and applied in rice breeding to effectively control BPH. However, the molecular mechanisms underlying BPH6 are poorly understood.

Results

Here, an integrated miRNA and mRNA expression profiling analysis was performed on BPH6-transgenic (BPH6G) and Nipponbare (wild type, WT) plants after BPH infestation, and a total of 217 differentially expressed miRNAs (DEMs) and 7874 differentially expressed mRNAs (DEGs) were identified. 29 miRNAs, including members of miR160, miR166 and miR169 family were opposite expressed during early or late feeding stages between the two varieties, whilst 9 miRNAs were specifically expressed in BPH6G plants, suggesting involvement of these miRNAs in BPH6-mediated resistance to BPH. In the transcriptome analysis, 949 DEGs were opposite expressed during early or late feeding stages of the two genotypes, which were enriched in metabolic processes, cellular development, cell wall organization, cellular component movement and hormone transport, and certain primary and secondary metabolite synthesis. 24 genes were further selected as candidates for BPH resistance. Integrated analysis of the DEMs and DEGs showed that 34 miRNAs corresponding to 42 target genes were candidate miRNA-mRNA pairs for BPH resistance, 18 pairs were verified by qRT-PCR, and two pairs were confirmed by in vivo analysis.

Conclusions

For the first time, we reported integrated small RNA and transcriptome sequencing to illustrate resistance mechanisms against BPH in rice. Our results provide a valuable resource to ascertain changes in BPH-induced miRNA and mRNA expression profiles and enable to comprehend plant-insect interactions and find a way for efficient insect control.

Herbivore-induced rice resistance against rice blast mediated by salicylic acid

In agro-ecosystems, plants are important mediators of interactions between their associated herbivorous insects and microbes, and any change in plants induced by one species may lead to cascading effects on interactions with other species. Often, such effects are regulated by phytohormones such as jasmonic acid (JA) and salicylic acid (SA). Here, we investigated the tripartite interactions among rice plants, three insect herbivores (Chilo suppressalis, Cnaphalocrocis medinalis or Nilaparvata lugens), and the causal agent of rice blast disease, the fungus Magnaporthe oryzae. We found that pre-infestation of rice by C. suppressalis or N. lugens but not by C. medinalis conferred resistance to M. oryzae. For C. suppressalis and N. lugens, insect infestation without fungal inoculation induced the accumulation of both JA and SA in rice leaves. In contrast, infestation by C. medinalis increased JA levels but reduced SA levels. The exogenous application of SA but not of JA conferred resistance against M. oryzae. These results suggest that pre-infestation by C. suppressalis or N. lugens conferred resistance against M. oryzae by increasing SA accumulation. These findings enhance our understanding of the interactions among rice plant, insects and pathogens, and provide valuable information for developing an ecologically sound strategy for controlling rice blast.

Novel crosstalk between ethylene- and jasmonic acid-pathway responses to a piercing-sucking insect in rice

Ethylene (ET) and jasmonic acid (JA) play important roles in plant defenses against biotic stresses. Crosstalk between JA and ET has been well studied in mediating pathogen resistance, but its roles in piercing-sucking insect resistance are unclear. The brown planthopper (BPH; Nilaparvata lugens) is the most notorious piercing-sucking insect specific to rice (Oryza sativa) that severely affects yield. A genetic analysis revealed that OsEBF1 and OsEIL1, which are in the ET signaling pathway, positively and negatively regulated BPH resistance, respectively. Molecular and biochemical analyses revealed direct interactions between OsEBF1 and OsEIL1. OsEBF1, an E3 ligase, mediated the degradation of OsEIL1 through the ubiquitination pathway, indicating the negative regulation of the ET-signaling pathway in response to BPH infestation. An RNA sequencing analysis revealed that a JA biosynthetic pathway-related gene, OsLOX9, was downregulated significantly in the oseil1 mutant. Biochemical analyses, including yeast one-hybrid, dual luciferase, and electrophoretic mobility shift assay, confirmed the direct regulation of OsLOX9 by OsEIL1. This study revealed the synergistic and negative regulation of JA and ET pathways in response to piercing-sucking insect attack. The synergistic mechanism was realized by transcriptional regulation of OsEIL1 on OsLOX9. OsEIL1-OsLOX9 is a novel crosstalk site in these two phytohormone signaling pathways.

Challenging battles of plants with phloem-feeding insects and prokaryotic pathogens

For the past 4 decades, intensive molecular studies of mostly leaf mesophyll cell-infecting pathogens and chewing insects have led to compelling models of plant-pathogen and plant-insect interactions. Yet, some of the most devastating pathogens and insect pests live in or feed on the phloem, a systemic tissue belonging to the plant vascular system. Phloem tissues are difficult to study, and phloem-inhabiting pathogens are often impossible to culture, thus limiting our understanding of phloem-insect/pathogen interactions at a molecular level. In this Perspective, we highlight recent literature that reports significant advances in the understanding of phloem interactions with insects and prokaryotic pathogens and attempt to identify critical questions that need attention for future research. It is clear that study of phloem-insect/pathogen interactions represents an exciting frontier of plant science, and influx of new scientific expertise and funding is crucial to achieve faster progress in this important area of research that is integral to global food security.

Combining next-generation sequencing and single-molecule sequencing to explore brown plant hopper responses to contrasting genotypes of japonica rice

BACKGROUND

The brown plant hopper (BPH), Nilaparvata lugens, is one of the major pest of rice (Oryza sativa). Plant defenses against insect herbivores have been extensively studied, but our understanding of insect responses to host plants' resistance mechanisms is still limited. The purpose of this study is to characterize transcripts of BPH and reveal the responses of BPH insects to resistant rice at transcription level by using the advanced molecular techniques, the next-generation sequencing (NGS) and the single-molecule, real-time (SMRT) sequencing.

RESULTS

The current study obtained 24,891 collapsed isoforms of full-length transcripts, and 20,662 were mapped to known annotated genes, including 17,175 novel transcripts. The current study also identified 915 fusion genes, 1794 novel genes, 2435 long non-coding RNAs (lncRNAs), and 20,356 alternative splicing events. Moreover, analysis of differentially expressed genes (DEGs) revealed that genes involved in metabolic and cell proliferation processes were significantly enriched in up-regulated and down-regulated sets, respectively, in BPH fed on resistant rice relative to BPH fed on susceptible wild type rice. Furthermore, the FoxO signaling pathway was involved and genes related to BPH starvation response (Nlbmm), apoptosis and autophagy (caspase 8, ATG13, BNIP3 and IAP), active oxygen elimination (catalase, MSR, ferritin) and detoxification (GST, CarE) were up-regulated in BPH responses to resistant rice.

CONCLUSIONS

The current study provides the first demonstrations of the full diversity and complexity of the BPH transcriptome, and indicates that BPH responses to rice resistance, might be related to starvation stress responses, nutrient transformation, oxidative decomposition, and detoxification. The current result findings will facilitate further exploration of molecular mechanisms of interaction between BPH insects and host rice.

The OsmiR396-OsGRF8-OsF3H-flavonoid pathway mediates resistance to the brown planthopper in rice (Oryza sativa)

Multi-functional microRNAs (miRNAs) are emerging as key modulators of plant-pathogen interactions. Although the involvement of some miRNAs in plant-insect interactions has been revealed, the underlying mechanisms are still elusive. The brown planthopper (BPH) is the most notorious rice (Oryza sativa)-specific insect that causes severe yield losses each year and requires urgent biological control. To reveal the miRNAs involved in rice-BPH interactions, we performed miRNA sequencing and identified BPH-responsive OsmiR396. Sequestering OsmiR396 by overexpressing target mimicry (MIM396) in three genetic backgrounds indicated that OsmiR396 negatively regulated BPH resistance. Overexpression of one BPH-responsive target gene of OsmiR396, growth regulating factor 8 (OsGRF8), showed resistance to BPH. Furthermore, the flavonoid contents increased in both the OsmiR396-sequestered and the OsGRF8 overexpressing plants. By analysing 39 natural rice varieties, the elevated flavonoid contents were found to correlate with enhanced BPH resistance. Artificial applications of flavonoids to wild type (WT) plants also increased resistance to BPH. A BPH-responsive flavanone 3-hydroxylase (OsF3H) gene in the flavonoid biosynthetic pathway was proved to be directly regulated by OsGRF8. A genetic functional analysis of OsF3H revealed its positive role in mediating both the flavonoid contents and BPH resistance. And analysis of the genetic correlation between OsmiR396 and OsF3H showed that down-regulation of OsF3H complemented the BPH resistance characteristic and simultaneously decreased the flavonoid contents of the MIM396 plants. Thus, we revealed a new BPH resistance mechanism mediated by the OsmiR396-OsGRF8-OsF3H-flavonoid pathway. Our study suggests potential applications of miRNAs in BPH resistance breeding.

Identification of spontaneous mutation for broad-spectrum brown planthopper resistance in a large, long-term fast neutron mutagenized rice population

BACKGROUND

The development of rice varieties with broad-spectrum resistance to insect pests is the most promising approach for controlling a fast evolving insect pest such as the brown planthopper (BPH). To cope with rapid evolution, discovering new sources of broad-spectrum resistance genes is the ultimate goal.

RESULTS

We used a forward genetics approach to identify BPH resistance genes in rice (Oryza sativa L.) using double digest restriction site-associated DNA sequencing (ddRADseq) for quantitative trait loci (QTL)-seq of the backcross inbred lines (BILs) derived from a cross between the BPH-susceptible cultivar KDML105 and BPH-resistant cultivar Rathu Heenati (RH). Two major genomic regions, located between 5.78-7.78 Mb (QBPH4.1) and 15.22-17.22 Mb (QBPH4.2) on rice chromosome 4, showed association with BPH resistance in both pooled BILs and individual highly resistant and susceptible BILs. The two most significant candidate resistance genes located within the QBPH4.1 and QBPH4.2 windows were lectin receptor kinase 3 (OsLecRK3) and sesquiterpene synthase 2 (OsSTPS2), respectively. Functional markers identified in these two genes were used for reverse screening 9323 lines of the fast neutron (FN)-mutagenized population developed from the BPH-susceptible, purple-pigmented, indica cultivar Jao Hom Nin (JHN). Nineteen FN-mutagenized lines (0.24%) carried mutations in the OsLecRK3 and/or OsSTPS2 gene. Among these mutant lines, only one highly resistant line (JHN4) and three moderately resistant lines (JHN09962, JHN12005, and JHN19525) were identified using three active, local BPH populations. The 19 mutant lines together with three randomly selected mutant lines, which did not harbor mutations in the two target genes, were screened further for mutations in six known BPH resistance genes including BPH9, BPH14, BPH18, BPH26, BPH29, and BPH32. Multiple single nucleotide polymorphisms (SNPs) and insertion-deletion (Indel) mutations were identified, which formed gene-specific haplotype patterns (HPs) essential for broad-spectrum resistance to BPH in both BILs and JHN mutant populations.

CONCLUSION

On the one hand, HPs of OsLekRK2-3, OsSTPS2, and BPH32 determined broad-spectrum resistance to BPH among RH-derived BILs. On the other hand, in the JHN mutant population, BPH9 together with seven significant genes on chromosome 4 played a crucial role in BPH resistance.

Overexpression of Arabidopsis Nucleotide-Binding and Leucine-Rich Repeat Genes RPS2 and RPM1(D505V) Confers Broad-Spectrum Disease Resistance in Rice

The nucleotide-binding domain leucine-rich repeat (NLR) immune receptors play important roles in innate plant immunity. The activation of NLRs is specifically induced by their cognate effectors released from pathogens. Autoactive NLRs are expected to confer broad-spectrum resistance because they do not need cognate effectors to activate their immune responses. In this study, we demonstrated that the NLR genes RPS2 and RPM1(D505V) from Arabidopsis were autoactive in Oryza sativa and conferred broad-spectrum resistance to fungal pathogen Magnaporthe oryzae, bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo), and pest brown planthopper (BPH, Nilaparvata lugens Stål). These results revealed that interfamily transfer of dicot NLRs to monocot species could be functional. The transgenic plants displayed early and strong induction of reactive oxygen species (ROS), callose deposition, and expression of defense-related genes after challenged with M. oryzae. The transcriptome analysis showed that the expressions of some defense-related genes were primed to adapt the transformed autoactive NLRs in the transgenic plants. This study indicates that autoactive NLRs are a promising resource for breeding crops with broad-spectrum resistance and provides new insights for engineering disease resistance.

Lipid profiles reveal different responses to brown planthopper infestation for pest susceptible and resistant rice plants

INTRODUCTION

Brown planthopper (BPH) is the most destructive insect pest for rice, causing major reductions in rice yield and large economic losses. More than 31 BPH-resistance genes have been located, and several of them have been isolated. Nevertheless, the metabolic mechanism related to BPH-resistance genes remain uncharacterized.

OBJECTIVES

To elucidate the resistance mechanism of the BPH-resistance gene Bph6 at the metabolic level, a Bph6-transgenic line R6 (BPH-resistant) and the wild-type Nipponbare (BPH-susceptible) were used to investigate their lipid profiles under control and BPH treatments.

METHODS

In conjunction with multivariate statistical analysis and quantitative real-time PCR, BPH-induced lipid changes in leaf blade and leaf sheath were investigated by GC-MS-based lipidomics.

RESULTS

Forty-five lipids were identified in leaf sheath extracts. Leaf sheath lipidomics analysis results show that BPH infestation induces significant differences in the lipid profiles of Nipponbare and R6. The levels of hexadecanoic acid, methyl ester, linoleic acid, methyl ester, linolenic acid, methyl ester, glycidyl palmitate, eicosanoic acid, methyl ester, docosanoic acid, methyl ester, beta-monolinolein, campesterol, beta-sitosterol, cycloartenol, phytol and phytyl acetate had undergone enormous changes after BPH feeding. These results illustrate that BPH feeding enhances sterol biosynthetic pathway in Nipponbare plants, and strengthens wax biosynthesis and phytol metabolism in R6 plants. The results of quantitative real-time PCR of 5 relevant genes were consistent with the changes in metabolic level. Forty-five lipids were identified in the leaf blade extracts. BPH infestation induces distinct changes in the lipid profiles of the leaf blade samples of Nipponbare and R6. Although the lipid changes in Nipponbare are more drastic, the changes within the two varieties are similar. Lipid profiles in leaf sheath brought out significant differences than in leaf blade within Nipponbare and R6. We propose that Bph6 mainly affects the levels of lipids in leaf sheath, and mediates resistance by deploying metabolic re-programming during BPH feeding.

CONCLUSION

The results indicate that wax biosynthesis, sterol biosynthetic pathway and phytol metabolism play vital roles in rice response to BPH infestation. This finding demonstrated that the combination of lipidomics and quantitative real-time PCR is an effective approach to elucidating the interactions between brown planthopper and rice mediated by resistance genes.

Expression Profile of Defense Genes in Rice Lines Pyramided with Resistance Genes Against Bacterial Blight, Fungal Blast and Insect Gall Midge

BACKGROUND

Rice, a major food crop of the world, endures many major biotic stresses like bacterial blight (BB), fungal blast (BL) and the insect Asian rice gall midge (GM) that cause significant yield losses. Progress in tagging, mapping and cloning of several resistance (R) genes against aforesaid stresses has led to marker assisted multigene introgression into elite cultivars for multiple and durable resistance. However, no detailed study has been made on possible interactions among these genes when expressed simultaneously under combined stresses.

RESULTS

Our studies monitored expression profiles of 14 defense related genes in 11 rice breeding lines derived from an elite cultivar with different combination of R genes against BB, BL and GM under single and multiple challenge. Four of the genes found implicated earlier under combined GM and BB stress were confirmed to be induced (≥ 2 fold) in stem tissue following GM infestation; while one of these, cytochrome P450 family protein, was also induced in leaf in plants challenged by either BB or BL but not together. Three of the genes highlighted earlier in plants challenged by both BB and BL were also found induced in stem under GM challenge. Pi54 the target R gene against BL was also found induced when challenged by GM. Though expression of some genes was noted to be inhibited under combined pest challenge, such effects did not result in compromise in resistance against any of the target pests.

CONCLUSION

While R genes generally tended to respond to specific pest challenge, several of the downstream defense genes responded to multiple pest challenge either single, sequential or simultaneous, without any distinct antagonism in expression of resistance to the target pests in two of the pyramided lines RPNF05 and RPNF08.

A Gene Family Coding for Salivary Proteins (SHOT) of the Polyphagous Spider Mite Tetranychus urticae Exhibits Fast Host-Dependent Transcriptional Plasticity

The salivary protein repertoire released by the herbivorous pest Tetranychus urticae is assumed to hold keys to its success on diverse crops. We report on a spider mite-specific protein family that is expanded in T. urticae. The encoding genes have an expression pattern restricted to the anterior podocephalic glands, while peptide fragments were found in the T. urticae secretome, supporting the salivary nature of these proteins. As peptide fragments were identified in a host-dependent manner, we designated this family as the SHOT (secreted host-responsive protein of Tetranychidae) family. The proteins were divided in three groups based on sequence similarity. Unlike TuSHOT3 genes, TuSHOT1 and TuSHOT2 genes were highly expressed when feeding on a subset of family Fabaceae, while expression was depleted on other hosts. TuSHOT1 and TuSHOT2 expression was induced within 24 h after certain host transfers, pointing toward transcriptional plasticity rather than selection as the cause. Transfer from an 'inducer' to a 'noninducer' plant was associated with slow yet strong downregulation of TuSHOT1 and TuSHOT2, occurring over generations rather than hours. This asymmetric on and off regulation points toward host-specific effects of SHOT proteins, which is further supported by the diversity of SHOT genes identified in Tetranychidae with a distinct host repertoire.

Marker assisted pyramiding of Bph6 and Bph9 into elite restorer line 93-11 and development of functional marker for Bph9

BACKGROUND

The brown planthopper (BPH) has become the most destructive and a serious threat to the rice production in Asia. Breeding the resistant varieties with improved host resistance is the most effective and ecosystem-friendly strategy of BPH biological management. As host resistance was always broken down by the presence of the upgrading BPH biotype, the more resistant varieties with novel resistance genes or pyramiding known identified BPH resistance genes would be needed urgently for higher resistant level and more durability of resistance.

RESULTS

Here, we developed near isogenic lines of Bph9 (NIL-Bph9) by backcrossing elite cultivar 93-11 with Pokkali (harboring Bph9) using marker-assisted selection (MAS). Subsequently, we pyramided Bph6 and Bph9 in 93-11 genetic background through MAS. The resulting Bph6 and Bph9 pyramided line LuoYang69 had stronger antixenotic and antibiosis effects on BPH and exhibited significantly enhanced resistance to BPH than near isogenic lines NIL-Bph6 and NIL-Bph9. LuoYang69 derived hybrids, harboring heterozygous Bph6 and Bph9 genes, also conferred high level of resistance to BPH. Furthermore, LuoYang69 did not affect the elite agronomic traits and rice grain quality of 93-11. The current study also developed functional markers for Bph9. Using functional dominant marker, we screened and evaluated worldwide accessions of rice germplasm. Of the 673 varieties tested, 8 cultivars were identified to harbor functional Bph9 gene.

CONCLUSION

The development of Bph6 and Bph9 pyramided line LuoYang69 provides valuable resource to develop hybrid rice with highly and durable BPH resistance. The development of functional markers will promote MAS of Bph9. The identified Bph9 containing cultivars can be used as new sources for BPH resistance breeding programs.

Functional Study of Cytochrome P450 Enzymes from the Brown Planthopper (Nilaparvata lugens Stål) to Analyze Its Adaptation to BPH-Resistant Rice

Plant-insect interactions constitute a complex of system, whereby plants synthesize toxic compounds as the main defense strategy to combat herbivore assault, and insects deploy detoxification systems to cope with toxic plant compounds. Cytochrom P450s are among the main detoxification enzymes employed by insects to combat the chemical defenses of host plants. In this study, we used Nilaparvata lugens (BPH) to constitute an ideal system for studying plant-insect interactions. By feeding BPHs with artificial diets containing ethanol extracts, we show that biotype Y BPHs have a greater ability to metabolize exogenous substrates than biotype 1 BPHs. NlCPR knockdown inhibited the ability of BPHs to feed on YHY15. qRT-PCR was used to screen genes in the P450 family, and upregulation of CYP4C61, CYP6AX1, and CYP6AY1 induced by YHY15 was investigated. When the three P450 genes were knocked down, only CYP4C61 dsRNA treatment was inhibited the ability of BPHs to feed on YHY15. These results indicate that BPH P450 enzymes are a key factor in the physiological functions of BPH when feeding on BPH-resistant rice.

Identification and analysis of brown planthopper-responsive microRNAs in resistant and susceptible rice plants

The brown planthopper (BPH) is the most devastating insect pest of rice. The rice gene BPH15 confers resistance to BPH. MicroRNAs (miRNAs) regulate a spectrum of development and defense response processes in plants. In this study, we analyzed six miRNA profiles of a BPH15 introgression line (P15) and a susceptible recipient line (PC) at three time points (0 h, 6 h and 48 h) after BPH attack, and identified 464 known miRNAs and 183 potential novel miRNAs. Before the BPH feeding, we identified 23 miRNAs differentially expressed in P15 and PC. We speculated that the resistant plant is in a priming state by the regulation of miRNAs. After the BPH feeding, 104 miRNAs were found to be expressed differentially in P15 (68 in P15-6/P15-0, 36 in P15-48/P15-0), and 80 miRNAs were found expressed differentially in PC (32 in PC-6/PC-0, 48 in PC-48/PC-0), which illustrated that miRNA expression is activated upon attack. These miRNAs regulate different pathways that contribute to the basal defense and specific resistance of rice to the BPH. Our study provides additional data for scientists to further explore the mechanism of plant defense against insect attack and to find a way for efficient insect control.