Allelic diversity in an NLR gene BPH9 enables rice to combat planthopper variation

Genetics of novel brown planthopper Nilaparvata lugens (Stål) resistance genes in derived introgression lines from the interspecific cross O. sativa var. Swarna × O. nivara

The brown planthopper (BPH) Nilaparvata lugens (Stål) (Homoptera: Delphacidae) is considered a threat to rice (Oryza sativa ssp.) crop in many parts of the world including India. Among the BPH-resistance (R) genes so far reported in rice, most of them are ineffective against BPH biotype 4 predominant in the Indian sub-continent. In this study, we show the introgression line RPBio4918-230S was identified as BPH resistant after five years of rigorous screening at seedling stage and two years at tillering and reproductive stages. The inheritance of resistance indicated that two recessive genes are involved at seedling and reproductive stages. The allelic relation with known genes using linked reported markers suggested that the genes present in RPBio4918-230S are different. We report here the genetics of the two newly introgressed BPH resistance genes from O. nivara in the background of Swarna which are effective at all the important growth stages. The genes have been tentatively named as bph39(t) and bph40(t). The honeydew area (feeding rate) and days to wilt parameters observed at 30 days after sowing in BC₁F₃ indicated that newly introgressed genes have both antibiosis and tolerance mechanisms for resistance. The BPH resistance genes identified in this study would facilitate the breeding of broad spectrum and durable resistance in rice against BPH biotype 4.

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.

The Development and Characterization of Near-Isogenic and Pyramided Lines Carrying Resistance Genes to Brown Planthopper with the Genetic Background of Japonica Rice (Oryza sativa L.)

The brown planthopper (BPH: Nilaparvata lugens Stål.) is a major pest of rice, Oryza sativa, in Asia. Host plant resistance has tremendous potential to reduce the damage caused to rice by the planthopper. However, the effectiveness of resistance genes varies spatially and temporally according to BPH virulence. Understanding patterns in BPH virulence against resistance genes is necessary to efficiently and sustainably deploy resistant rice varieties. To survey BPH virulence patterns, seven near-isogenic lines (NILs), each with a single BPH resistance gene (BPH2-NIL, BPH3-NIL, BPH17-NIL, BPH20-NIL, BPH21-NIL, BPH32-NIL and BPH17-ptb-NIL) and fifteen pyramided lines (PYLs) carrying multiple resistance genes were developed with the genetic background of the japonica rice variety, Taichung 65 (T65), and assessed for resistance levels against two BPH populations (Hadano-66 and Koshi-2013 collected in Japan in 1966 and 2013, respectively). Many of the NILs and PYLs were resistant against the Hadano-66 population but were less effective against the Koshi-2013 population. Among PYLs, BPH20+BPH32-PYL and BPH2+BPH3+BPH17-PYL granted relatively high BPH resistance against Koshi-2013. The NILs and PYLs developed in this research will be useful to monitor BPH virulence prior to deploying resistant rice varieties and improve rice’s resistance to BPH in the context of regionally increasing levels of virulence.

Current understanding of the molecular players involved in resistance to rice planthoppers

Rice planthoppers are the most widespread and destructive pest of rice. Planthopper control depends greatly on the understanding of molecular players involved in resistance to planthoppers. This paper summarizes the recent progress in the understanding of some molecular players involved in resistance to planthoppers and the mechanisms involved. Recent researches showed that host-plant resistance is the most promising sustainable approach for controlling planthoppers. Planthopper-resistant varieties with a host-plant resistance gene have been released for rice products. Integrated planthopper management is a proposed strategy to prolong the durability of host-plant resistance. Bacillus spp. and their gene products or insect pathogenic fungi have great potential for application in the biological control of planthoppers. Enhancement of the activity of the natural enemies of planthoppers would be more cost-effective and environmentally friendly. Various molecular processes regulate rice-planthopper interactions. Rice encounters planthopper attacks via transcription factors, secondary metabolites, and signaling networks in which phytohormones have central roles. Maintenance of cell wall integrity and lignification act as physical barriers. Indirect defenses of rice are regulated via chemical elicitors, honeydew-associated elicitor, amendment with silicon and biochar, and salivary protein of BPH as elicitor or effector. Further research directions on planthopper control and rice defense against planthoppers are also put forward. © 2019 Society of Chemical Industry.

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.

The rice genome revolution: from an ancient grain to Green Super Rice

Rice is a staple crop for half the world's population, which is expected to grow by 3 billion over the next 30 years. It is also a key model for studying the genomics of agroecosystems. This dual role places rice at the centre of an enormous challenge facing agriculture: how to leverage genomics to produce enough food to feed an expanding global population. Scientists worldwide are investigating the genetic variation among domesticated rice species and their wild relatives with the aim of identifying loci that can be exploited to breed a new generation of sustainable crops known as Green Super Rice.

Mapping and characterization of a quantitative trait locus resistance to the brown planthopper in the rice variety IR64

Background

Rice planthoppers (main brown planthopper, Nilaparvata lugens Stål; BPH) was one of substantial threats to Asia rice production as its serious destruction and difficulties in control under field conditions. Notably, host-plant resistance was proved to be one of the effective ways to manage the pest. And stronger virulence will probably emergence when continuous use of insecticides. Therefore, more resistance genes with different resistance mechanisms were needed to be detected and then applied in the rice breeding practice.

Results

Resistance genes in the rice variety IR64 were evaluated considering the seedling bulk test and seedling survival rate. As a result, a locus with a large LOD score of 7.23 was found between markers RM302 and YM35 on chromosome 1. The locus explained 36.9% of phenotypic variation and was tentatively denominated Bph37. Moreover, Bph1 was detected to be harbored by the markers RM28366 and RM463, and had the largest LOD score of 2.08, explaining 7.7% of phenotypic variance in the same mapping population. Finally, the preliminary-near-isogenic-lines (pre-NILs) carrying Bph37 exhibited significant tolerance to the insects. But no antibiotic or antixenotic effects were observed in the resistant plants when infested with the insects.

Conclusions

We mapped one major BPH resistance gene Bph37 in consideration of seedling survival rate and the resistance lines showed tolerance to BPH. The detected gene should be beneficial for understanding the resistance mechanism of rice to BPH and for insect-resistance rice breeding programs.

High-resolution mapping and breeding application of a novel brown planthopper resistance gene derived from wild rice (Oryza. rufipogon Griff)

BACKGROUND

The brown planthopper (Nilaparvata lugens Stål; BPH), one of the most destructive pests of rice, has proven to be a substantial threat, conferring enormous production losses in Asia and becoming a difficult challenge to manipulate and control under field conditions. The continuous use of insecticides promotes the resurgence of BPH, which results in resistant varieties adapting through the upgrading of new BPH biotypes. To overcome resistance acquired by BPH against resistance varieties, different forms of novel resistant gene fusions act as functional domains for breeding to enhance insect resistance.

RESULTS

The current study reports on the novel BPH resistance gene Bph36 derived from two introgression lines (RBPH16 and RBPH17) developed from wild rice GX2183 which was previously reported to be resistant to BPH. Using two F₂ crossing populations (Kangwenqizhan × RBPH16 and Huanghuazhan × RBPH17) in a bulked segregant analysis (BSA) for identification of resistant genes and QTL analysis, two QTLs for BPH resistance were generated on the long and short arms of chromosome 4, which was further confirmed by developing BC₁F_2:3 populations by backcrossing via marker assisted selection (MAS) approach. One BPH resistance locus on the short arm of chromosome 4 was mapped to a 38-kb interval flanked by InDel markers S13 and X48, and then was named Bph36, whereas another locus on the long arm of chromosome 4 was also detected in an interval flanked by RM16766 and RM17033, which was the same as that of Bph27. An evaluation analysis based on four parameters (BPH host selection, honeydew weight, BPH survival rate and BPH population growth rate) shows that Bph36 conferred high levels antibiosis and antixenosis to BPH. Moreover, Bph36 pyramided with Bph3, Bph27, and Bph29 through MAS into elite cultivars 9311 and MH511 (harbored Xa23), creating different background breeding lines that also exhibited strong resistance to BPH in the seedling or tillering stage.

CONCLUSION

Bph36 can be utilized in BPH resistance breeding programs to develop high resistant rice lines and the high-resolution fine mapping will facilitate further map-based cloning and marker-assisted gene pyramiding of resistant gene. MAS exploited to pyramid with Bph3, Bph27, Bph29, and Xa23 was confirmed the effectiveness for BPH resistance breeding in rice and provided insights into the molecular mechanism of defense to control this devastating insect.

A Group D MAPK Protects Plants from Autotoxicity by Suppressing Herbivore-Induced Defense Signaling

The mechanisms by which plants activate and enhance defense responses have been well studied; however, the regulatory mechanisms that allow plants to avoid excessive defense responses are poorly understood. Here, we identified a group D mitogen-activated protein kinase (MAPK) gene from rice (Oryza sativa), OsMAPK20-5, whose expression was rapidly induced by infestation of gravid female adults of a destructive rice pest, brown planthopper (BPH, Nilaparvata lugens), but not by BPH nymphs. Expression silencing of OsMAPK20-5 (irMAPK) increased the accumulation of ethylene and nitric oxide (NO) after gravid female BPH infestation, and thereby increased rice plant resistance to BPH adults and oviposited eggs. However, when exposed to high densities of gravid BPH females, irMAPK plants wilted earlier than wild-type plants, which could be attributed to the hyperaccumulation of ethylene and NO in irMAPK plants. Interestingly, when released into the field, irMAPK plants displayed broad resistance to BPH and white-backed planthopper (Sogatella furcifera), the two most destructive pests of rice, and produced higher yield. Taken together, our study shows that although OsMAPK20-5 can reduce the resistance of rice plants to planthoppers, it also enables rice plants to control excessive defense responses and thereby prevents defense-response-related autotoxicity.

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.

OsHLH61-OsbHLH96 influences rice defense to brown planthopper through regulating the pathogen-related genes

BACKGROUND

In plants, basic helix-loop-helix (bHLH) proteins form the largest transcription factor (TF) family. Among them, HLH proteins are a small group of atypical members that lack the basic domain, and form dimers with bHLH proteins. Although bHLH proteins have been proved to play important roles in plant development and physiology, the function of HLH proteins is rarely studied, not to mention in plant biotic resistance. Brown planthopper (BPH) is a kind of rice-specific insect that causes devastating yield losses each year.

RESULTS

In this study, we identified OsHLH61 gene that encodes HLH protein. OsHLH61 gene could be highly induced by BPH infestation. Furthermore, Methyl Jasmonic acid (Me-JA) and cis-12-oxo- phytodienoic acid (OPDA) induced expression of OsHLH61, while SA repressed it. We knocked down expression of OsHLH61 by RNA interference (RNAi), the transgenic plants were susceptible to BPH infestation. RNA-seq analysis revealed that some pathogen-related (PR) genes in the Salicylic acid (SA) signaling pathway that mediate plant immunity were obviously down-regulated in the OsHLH61 RNAi plants. Meanwhile, yeast two-hybrid assay and bimolecular luciferase complementation (BiLC) analysis identified bHLH096 to be an interacting factor of OsHLH61. Also, some PR genes were down-regulated in the OsbHLH96 over expressing lines. Expression of OsbHLH96 was inhibited. Besides, OsbHLH96 might interact with Jasmonate Zim-Domain3 (OsJAZ3).

CONCLUSION

Altogether, we identified an OsHLH61-OsbHLH96 complex that might mediate defense to BPH through regulating PR genes. And OsHLH61-OsbHLH96 might be important in mediating SA and JA signaling crosstalk.

Metabolic responses of brown planthoppers to IR56 resistant rice cultivar containing multiple resistance genes

The brown planthopper (Nilaparvata lugens Stål, BPH) is one of the most destructive pests in rice production, and rice resistance is thought to be an economical and environmentally friendly strategy against BPH. Although resistant rice cultivars have been widely applied to control BPH, little is known regarding the impact of the ingestion of resistant plant phloem on the BPH physiological metabolism. In this study, the differences in the metabolic responses of BPH nymphs during the first 72 h after ingesting susceptible TN1 and resistant IR56 plant phloem were compared. The results showed that BPH nymphs feeding on IR56 plants exhibited significant decreases in honeydew excretion and body weight, and significantly lower concentrations of most of the detected sugars, vitamins and some essential amino acids but higher levels of most amides, free fatty acids and some non-essential amino acids. These findings indicate that the energy metabolism and nutrition supply of these nymphs were disturbed by the resistant rice plants. The qPCR results revealed that BPH could actively adapt to IR56 plants by upregulating the gene expression levels of some detoxification enzymes, including GST, CarE and POD, to some extent. These results provide additional information to improve our understanding of physiological mechanism underlying the loss of BPH fitness caused by resistant rice varieties.

Identification of a novel locus, BPH38(t), conferring resistance to brown planthopper (Nilaparvata lugens Stal.) using early backcross population in rice (Oryza sativa L.)

Rice is the most important staple food crop, and it feeds more than half of the world population. Brown planthopper (BPH) is a major insect pest of rice that causes 20-80% yield loss through direct and indirect damage. The identification and use of BPH resistance genes can efficiently manage BPH. A molecular marker-based genetic analysis of BPH resistance was carried out using 101 BC₁F₅ mapping population derived from a cross between a BPH-resistant indica variety Khazar and an elite BPH-susceptible line Huang-Huan-Zhan. The genetic analysis indicated the existence of Mendelian segregation for BPH resistance. A total of 702 high-quality polymorphic single nucleotide polymorphism (SNP) markers, genotypic data, and precisely estimated BPH scores were used for molecular mapping, which resulted in the identification of the BPH38(t) locus on the long arm of chromosome 1 between SNP markers 693,369 and id 10,112,165 of 496.2 kb in size with LOD of 20.53 and phenotypic variation explained of 35.91%. A total of 71 candidate genes were predicted in the detected locus. Among these candidate genes, LOC_Os01g37260 was found to belong to the FBXL class of F-box protein possessing the LRR domain, which is reported to be involved in biotic stress resistance. Furthermore, background analysis and phenotypic selection resulted in the identification of introgression lines (ILs) possessing at least 90% recurrent parent genome recovery and showing superior performance for several agro-morphological traits. The BPH resistance locus and ILs identified in the present study will be useful in marker-assisted BPH resistance breeding programs.

funRiceGenes dataset for comprehensive understanding and application of rice functional genes

Background

As a main staple food, rice is also a model plant for functional genomic studies of monocots. Decoding of every DNA element of the rice genome is essential for genetic improvement to address increasing food demands. The past 15 years have witnessed extraordinary advances in rice functional genomics. Systematic characterization and proper deposition of every rice gene are vital for both functional studies and crop genetic improvement.

Findings

We built a comprehensive and accurate dataset of ∼2800 functionally characterized rice genes and ∼5000 members of different gene families by integrating data from available databases and reviewing every publication on rice functional genomic studies. The dataset accounts for 19.2% of the 39 045 annotated protein-coding rice genes, which provides the most exhaustive archive for investigating the functions of rice genes. We also constructed 214 gene interaction networks based on 1841 connections between 1310 genes. The largest network with 762 genes indicated that pleiotropic genes linked different biological pathways. Increasing degree of conservation of the flowering pathway was observed among more closely related plants, implying substantial value of rice genes for future dissection of flowering regulation in other crops. All data are deposited in the funRiceGenes database (https://funricegenes.github.io/). Functionality for advanced search and continuous updating of the database are provided by a Shiny application (http://funricegenes.ncpgr.cn/).

Conclusions

The funRiceGenes dataset would enable further exploring of the crosslink between gene functions and natural variations in rice, which can also facilitate breeding design to improve target agronomic traits of rice.

Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species

The African wild rice species Oryza longistaminata has several beneficial traits compared to cultivated rice species, such as resistance to biotic stresses, clonal propagation via rhizomes, and increased biomass production. To facilitate breeding efforts and functional genomics studies, we de-novo assembled a high-quality, haploid-phased genome. Here, we present our assembly, with a total length of 351 Mb, of which 92.2% was anchored onto 12 chromosomes. We detected 34,389 genes and 38.1% of the genome consisted of repetitive content. We validated our assembly by a comparative linkage analysis and by examining well-characterized gene families. This genome assembly will be a useful resource to exploit beneficial alleles found in O. longistaminata. Our results also show that it is possible to generate a high-quality, functionally complete rice genome assembly from moderate SMRT read coverage by exploiting synteny in a closely related Oryza species.

Stefan Reuscher et al. assembled the genome of an African wild rice species to facilitate breeding efforts and functional genomic studies. They used SMRT sequencing, chromosomal synteny between rice species, and a linkage map to assemble the 351 Mb genome into 12 chromosomes.

Identification and fine mapping of Bph33, a new brown planthopper resistance gene in rice (Oryza sativa L.)

BACKGROUND

Host-plant resistance is the most desirable and economic way to overcome BPH damage to rice. As single-gene resistance is easily lost due to the evolution of new BPH biotypes, it is urgent to explore and identify new BPH resistance genes.

RESULTS

In this study, using F_2:3 populations and near-isogenic lines (NILs) derived from crosses between two BPH-resistant Sri Lankan rice cultivars (KOLAYAL and POLIYAL) and a BPH-susceptible cultivar 9311, a new resistance gene Bph33 was fine mapped to a 60-kb region ranging 0.91-0.97 Mb on the short arm of chromosome 4 (4S), which was at least 4 Mb distant from those genes/QTLs (Bph12, Bph15, Bph3, Bph20, QBph4 and QBph4.2) reported before. Seven genes were predicted in this region. Based on sequence and expression analyses, a Leucine Rich Repeat (LRR) family gene (LOC_Os04g02520) was identified as the most possible candidate of Bph33. The gene exhibited continuous and stable resistance from seedling stage to tillering stage, showing both antixenosis and antibiosis effects on BPH.

CONCLUSION

The results of this study will facilitate map-based cloning and marker-assisted selection of the gene.

Silencing of miR156 confers enhanced resistance to brown planthopper in rice

Silencing of miR156 in rice confers enhanced resistance to brown planthopper through reducing JA and JA-Ile biosynthesis. Rice brown planthopper (BPH, Nilaparvata lugens Stål) threatens the sustainability of rice production and global food security. Due to the rapid adaptation of BPH to current germplasms in rice, development of novel types of resistant germplasms becomes increasingly important. Plant ontogenetic defense against pathogen and herbivores offers a broad spectrum and durable resistance, and has been experimentally tested in many plants; however, the underlying molecular mechanism remains unclear. miR156 is the master regulator of ontogeny in plants; modulation of miR156 is, therefore, expected to cause corresponding changes in BPH resistance. To test this hypothesis, we silenced miR156 using a target mimicry method in rice, and analyzed the resistance of miR156-silenced plants (MIM156) to BPH. MIM156 plants exhibited enhanced resistance to BPH based on analyses of honeydew excretion, nymph survival, fecundity of BPH, and the survival ratio of rice plants after BPH infestation. Molecular analysis indicated that the expression of MPK3, MPK6, and WRKY70, three genes involved in BPH resistance and jasmonic acid (JA) signaling, was altered in MIM156 plants. The JA and bioactive jasmonoyl-isoleucine levels and the expression of genes involved in JA biosynthesis were significantly reduced in MIM156 plants. Restoration of JA level by exogenous application increased the number of BPH feeding on MIM156 plants and reduced its resistance to BPH. Our findings suggest that miR156 negatively regulates BPH resistance by increasing JA level in rice; therefore, modulation of miR156-SPLs' pathway may offer a promising way to breed rice varieties with enhanced resistance against BPH and elite agronomically important traits.

Monosomic alien addition lines (MAALs) of Oryza rhizomatis in Oryza sativa: production, cytology, alien trait introgression, molecular analysis and breeding application

Key message Development of MAALs and disomic introgression lines derived from the cross between O. sativa and O. rhizomatis to exploit and utilize the valuable traits for rice improvement. The CC genome wild species, Oryza rhizomatis, possesses valuable traits for rice improvement. Unlike other CC genome wild rice, O. rhizomatis is less studied and none of the research has focused on the utilization of this resource in rice breeding. The transfer of novel genes governing the valuable traits from O. rhizomatis is difficult due to high genome incompatibility with O. sativa. Here we report the development of backcross progenies and complete sets of monosomic alien addition lines (MAALs) for the first time from O. rhizomatis in O. sativa line IR31917-45-3-2. Autotetraploid IR31917-45-3-2 (4x = AAAA) was used to generate allotriploid F₁, and the F₁ plant was backcrossed to IR31917-45-3-2 (2x). Forty-seven BC₁F₁ and 73 BC₂F₁ plants were produced with chromosome numbers ranging from 24 to 33 (2x + 9) and 24 to 27 (2x + 3), respectively. A complete set of MAALs were identified by morphological, cytological and marker-based analysis. A total of 116 CC genome-specific InDel markers across the 12 chromosome of rice were used to detect O. rhizomatis chromosome segments in F₁, BC₁F₁, BC₂F₂, MAALs and disomic introgression lines (DILs). Expressions of major phenotypic traits inherited from O. rhizomatis were observed in MAAL-derived DILs. Small chromosomal segments of O. rhizomatis for chromosomes 1, 2, 4, 5, 6, 7, 10 and 12 were detected in DILs, and some of the introgression lines showed insect resistance against brown planthopper and green leafhopper. These newly developed MAALs and DILs will be useful for gene mining and more precise faster transfer of favorable genes to improve rice cultivars.

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.

Brassinosteroids mediate susceptibility to brown planthopper by integrating with the salicylic acid and jasmonic acid pathways in rice

Improved knowledge of the interactions between plants and insects will facilitate better insect control in crops. Brassinosteroids (BRs) play a vital role in plant growth, developmental processes, and responses to pathogen infection, but the role of BRs in interactions between plants and insects remain largely unknown. In this study, we characterized a negative role of BRs in rice defense against brown planthopper (BPH, Nilaparvata lugens) and examined its underlying mechanisms. We found that BPH infestation suppressed the BR pathway while successively activating the salicylic acid (SA) and jasmonic acid (JA) pathways. In addition, BR-overproducing mutants and plants treated with 24-epibrassinolide (BL) showed increased susceptibility to BPH, whereas BR-deficient mutants were more resistant than the wild-type. BRs down-regulated the expression of genes related to the SA pathway and reduced SA content while genes related to the JA pathway were up-regulated and JA content increased after BPH infestation. Furthermore, BR-mediated suppression of the SA pathway was impaired both in JA-deficient and JA-insensitive mutants. Our results demonstrate that BRs promote the susceptibility of rice plants to BPH by modulating the SA and JA pathways.

Current understanding of maize and rice defense against insect herbivores

Plants have sophisticated defense systems to fend off insect herbivores. How plants defend against herbivores in dicotyledonous plants, such as Arabidopsis and tobacco, have been relatively well studied, yet little is known about the defense responses in monocotyledons. Here, we review the current understanding of rice (Oryza sativa) and maize (Zea mays) defense against insects. In rice and maize, elicitors derived from insect herbivore oral secretions or oviposition fluids activate phytohormone signaling, and transcriptomic changes mediated mainly by transcription factors lead to accumulation of defense-related secondary metabolites. Direct defenses, such as trypsin protein inhibitors in rice and benzoxazinoids in maize, have anti-digestive or toxic effects on insect herbivores. Herbivory-induced plant volatiles, such as terpenes, are indirect defenses, which attract the natural enemies of herbivores. R gene-mediated defenses against herbivores are also discussed.

Why Do Herbivorous Mites Suppress Plant Defenses?

Plants have evolved numerous defensive traits that enable them to resist herbivores. In turn, this resistance has selected for herbivores that can cope with defenses by either avoiding, resisting or suppressing them. Several species of herbivorous mites, such as the spider mites Tetranychus urticae and Tetranychus evansi, were found to maximize their performance by suppressing inducible plant defenses. At first glimpse it seems obvious why such a trait will be favored by natural selection. However, defense suppression appeared to readily backfire since mites that do so also make their host plant more suitable for competitors and their offspring more attractive for natural enemies. This, together with the fact that spider mites are infamous for their ability to resist (plant) toxins directly, justifies the question as to why traits that allow mites to suppress defenses nonetheless seem to be relatively common? We argue that this trait may facilitate generalist herbivores, like T. urticae, to colonize new host species. While specific detoxification mechanisms may, on average, be suitable only on a narrow range of similar hosts, defense suppression may be more broadly effective, provided it operates by targeting conserved plant signaling components. If so, resistance and suppression may be under frequency-dependent selection and be maintained as a polymorphism in generalist mite populations. In that case, the defense suppression trait may be under rapid positive selection in subpopulations that have recently colonized a new host but may erode in relatively isolated populations in which host-specific detoxification mechanisms emerge. Although there is empirical evidence to support these scenarios, it contradicts the observation that several of the mite species found to suppress plant defenses actually are relatively specialized. We argue that in these cases buffering traits may enable such mites to mitigate the negative side effects of suppression in natural communities and thus shield this trait from natural selection.

Genome-Wide Analysis of Genetic Variations and the Detection of Rich Variants of NBS-LRR Encoding Genes in Common Wild Rice Lines

Common wild rice (Oryza rufipogon Griff.) is invaluable genetic resource for rice resistance breeding. Whole-genome re-sequencing was conducted to systematically analyze the variations in two new inbred lines (Huaye 3 and Huaye 4) developed from a common wild rice. A total of 4,841,127 SNPs, 1,170,479 InDels, 24,080 structural variations (SVs), and 298 copy number variations (CNVs) were identified in three materials. Approximately 16.24 and 5.64% of the total SNPs and InDels of Huaye 3 and Huaye 4 were located in genic regions, respectively. Together, 12,486 and 15,925 large-effect SNPs, and 12,417 and 14,513 large-effect InDels, which affect the integrity of the encoded protein, were identified in Huaye 3 and Huaye 4, respectively. The distribution map of 194 and 245 NBS-LRR encoding homologs was constructed across 12 rice chromosomes. Further, GO enrichment analysis of the homologs with identical genotype variations in Huaye 3 and Huaye 4 revealed 67, 82, and 58 homologs involved in cell death, response to stress, and both terms, respectively. Comparative analysis displayed that 550 out of 652 SNPs and 129 out of 147 InDels were present in a widely used blast-susceptible rice variety (LTH). Protein-protein interaction analysis revealed a strong interaction between NBS-LRR candidates and several known R genes. One homolog of disease resistance protein (RPM1) was involved in the plant-pathogen interaction pathway. Artificial inoculation of disease/insect displayed resistance phenotypes against rice blast and brown planthopper in two lines. The results will provide allele-specific markers for rice molecular breeding.

Resistance of rice to insect pests mediated by suppression of serotonin biosynthesis

Rice is one of the world's most important foods, but its production suffers from insect pests, causing losses of billions of dollars, and extensive use of environmentally damaging pesticides for their control^1,2. However, the molecular mechanisms of insect resistance remain elusive. Although a few resistance genes for planthopper have been cloned, no rice germplasm is resistant to stem borers. Here, we report that biosynthesis of serotonin, a neurotransmitter in mammals³, is induced by insect infestation in rice, and its suppression confers resistance to planthoppers and stem borers, the two most destructive pests of rice². Serotonin and salicylic acid derive from chorismate⁴. In rice, the cytochrome P450 gene CYP71A1 encodes tryptamine 5-hydroxylase, which catalyses conversion of tryptamine to serotonin⁵. In susceptible wild-type rice, planthopper feeding induces biosynthesis of serotonin and salicylic acid, whereas in mutants with an inactivated CYP71A1 gene, no serotonin is produced, salicylic acid levels are higher and plants are more insect resistant. The addition of serotonin to the resistant rice mutant and other brown planthopper-resistant genotypes results in a loss of insect resistance. Similarly, serotonin supplementation in artificial diet enhances the performance of both insects. These insights demonstrate that regulation of serotonin biosynthesis plays an important role in defence, and may prove valuable for breeding insect-resistant cultivars of rice and other cereal crops.

High-resolution genetic mapping of a novel brown planthopper resistance locus, Bph34 in Oryza sativa L. X Oryza nivara (Sharma & Shastry) derived interspecific F2 population

A BPH-resistant locus designated as Bph34 identified in Oryza nivara acc. IRGC104646 on long arm of chromosome 4 using high-resolution mapping with 50 K SNP chip. BPH resistance contributed by locus showed dominant inheritance in F₂ and F₃. The Bph34 locus is 91 kb in size and contains 11 candidate genes. In addition to SNP markers, SSR markers, RM16994 and RM17007 co-segregated with the BPH resistance. These two SSR markers can facilitate marker-assisted transfer of the Bph34 locus into elite rice cultivars in all labs. Brown planthopper (BPH, Nilaparvata lugen Stål) is one of the most destructive insects of rice (Oryza sativa L.) causing significant yield losses annually. Exploiting host plant resistance to BPH and incorporating resistant genes in susceptible commercial cultivars is economical and environmentally friendly approach to manage this pest. Here, we report high-resolution mapping of a novel genetic locus for resistance to BPH, designated as Bph34 on long arm of rice chromosome 4. The locus was mapped using an interspecific F₂ population derived from a cross between susceptible indica cultivar PR122 and BPH-resistant wild species, O. nivara acc. IRGC104646. Inheritance studies performed using F₂ and F_2:3 populations revealed the presence of single dominant gene. Construction of high-density linkage map using 50 K SNP chip (OsSNPnks) followed by QTL mapping identified single major locus at 28.8 LOD score between SNP markers, AX-95952039 and AX-95921548. The major locus contributing resistance to BPH designated as Bph34 and explained 68.3% of total phenotypic variance. The Bph34 locus is 91 Kb in size on Nipponbare reference genome-IRGSP-1.0 and contains 11 candidate genes. In addition to associated SNP markers, two SSR markers, RM16994 and RM17007, also co-segregated with the Bph34 which can be used efficiently for markers assisted transfer into elite rice cultivars across the labs.

Evaluation and breeding application of six brown planthopper resistance genes in rice maintainer line Jin 23B

BACKGROUND

The brown planthopper (BPH), an insect species that feeds on rice plants (Oryza sativa L.), is one of the most destructive insect pests of rice. BPH can be controlled with chemical pesticides, but they are expensive in terms of the cost and environmental hazards. Hence, utilization of resistance genes in resistant varieties is considered as a more economical and eco-friendly effective method for control.

RESULTS

In this study, six dominant BPH-resistance genes (Bph3, Bph14, Bph15, Bph18, Bph20 and Bph21) were introduced into an elite indica rice cultivar Jin 23B using the marker-assisted selection (MAS) method of breeding. One line combining Bph14 and Bph15 and six single gene introgression lines were used to evaluate the gene effects based on three parameters: seedling and tillering resistance of the rice genotypes, honeydew weight, and BPH survival rate. Among all improved lines, combination of Bph14 and Bph15 had the largest effect in conferring resistance to BPH. Bioassays showed that the order of the gene effects was Bph14/Bph15 > Bph15 ≥ Bph14 ≥ Bph20 ≥ Bph21 ≥ Bph3 > Bph18 > none at the rice seedling stage. The pyramided or single-gene introgression lines showed enhanced resistance relative to the control. Furthermore, field trial data demonstrated that yields of improved Jin 23B lines were similar to the control under BPH-free field conditions.

CONCLUSIONS

Each of the BPH resistance genes reduced BPH growth and development, and was effective at both the seedling and tillering growth stages. These lines can be used in rice hybrid and production in China.

Thai Hom Mali Rice: Origin and Breeding for Subsistence Rainfed Lowland Rice System

The world-renowned Thai Hom Mali Rice has been the most important aromatic rice originating in Thailand. The aromatic variety was collected from Chachoengsao, a central province, and after pure-line selection, it was officially named as Khao Dawk Mali 105, (KDML105). Because of its superb fragrance and cooking quality, KDML105 has been a model variety for studying genes controlling grain quality and aroma. The aromatic gene was cloned in KDML105, as an amino aldehyde dehydrogenase (AMADH) or better known as BADH2 located on chromosome 8. Later on, all other aromatic rice genes were discovered as allelic to the AMADH. As a selection of local landrace variety found in rainfed areas, the Thai Jasmine rice showed adaptive advantages over improved irrigated rice in less fertile lowland rainfed conditions. Because KDML105 was susceptible to most diseases and insect pests, marker-assisted backcross selection (MABC) was used for the genetic improvement since 2000. After nearly 17 years of MABC for integrating new traits into KDML105, a new generation of KDML105, designated HM84, was developed which maintains the cooking quality and fragrance, and has gained advantages during flash flooding, disease, and insect outbreak.

Rice Functional Genomics Research: Past Decade and Future

Rice (Oryza sativa) is a major staple food crop for more than 3.5 billion people worldwide. Understanding the regulatory mechanisms of complex agronomic traits in rice is critical for global food security. Rice is also a model plant for genomics research of monocotyledons. Thanks to the rapid development of functional genomic technologies, over 2000 genes controlling important agronomic traits have been cloned, and their molecular biological mechanisms have also been partially characterized. Here, we briefly review the advances in rice functional genomics research during the past 10 years, including a summary of functional genomics platforms, genes and molecular regulatory networks that regulate important agronomic traits, and newly developed tools for gene identification. These achievements made in functional genomics research will greatly facilitate the development of green super rice. We also discuss future challenges and prospects of rice functional genomics research.

Bph6 encodes an exocyst-localized protein and confers broad resistance to planthoppers in rice

The brown planthopper (BPH) and white-backed planthopper (WBPH) are the most destructive insect pests of rice, and they pose serious threats to rice production throughout Asia. Thus, there are urgent needs to identify resistance-conferring genes and to breed planthopper-resistant rice varieties. Here we report the map-based cloning and functional analysis of Bph6, a gene that confers resistance to planthoppers in rice. Bph6 encodes a previously uncharacterized protein that localizes to exocysts and interacts with the exocyst subunit OsEXO70E1. Bph6 expression increases exocytosis and participates in cell wall maintenance and reinforcement. A coordinated cytokinin, salicylic acid and jasmonic acid signaling pathway is activated in Bph6-carrying plants, which display broad resistance to all tested BPH biotypes and to WBPH without sacrificing yield, as these plants were found to maintain a high level of performance in a field that was heavily infested with BPH. Our results suggest that a superior resistance gene that evolved long ago in a region where planthoppers are found year round could be very valuable for controlling agricultural insect pests.

A Mucin-Like Protein of Planthopper Is Required for Feeding and Induces Immunity Response in Plants

The brown planthopper, Nilaparvata lugens, is a pest that threatens rice (Oryza sativa) production worldwide. While feeding on rice plants, planthoppers secrete saliva, which plays crucial roles in nutrient ingestion and modulating plant defense responses, although the specific functions of salivary proteins remain largely unknown. We identified an N. lugens-secreted mucin-like protein (NlMLP) by transcriptome and proteome analyses and characterized its function, both in brown planthopper and in plants. NlMLP is highly expressed in salivary glands and is secreted into rice during feeding. Inhibition of NlMLP expression in planthoppers disturbs the formation of salivary sheaths, thereby reducing their performance. In plants, NlMLP induces cell death, the expression of defense-related genes, and callose deposition. These defense responses are related to Ca2+ mobilization and the MEK2 MAP kinase and jasmonic acid signaling pathways. The active region of NlMLP that elicits plant responses is located in its carboxyl terminus. Our work provides a detailed characterization of a salivary protein from a piercing-sucking insect other than aphids. Our finding that the protein functions in plant immune responses offers new insights into the mechanism underlying interactions between plants and herbivorous insects.

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.

The Coiled-Coil and Nucleotide Binding Domains of BROWN PLANTHOPPER RESISTANCE14 Function in Signaling and Resistance against Planthopper in Rice

BROWN PLANTHOPPER RESISTANCE14 (BPH14), the first planthopper resistance gene isolated via map-based cloning in rice (Oryza sativa), encodes a coiled-coil, nucleotide binding site, leucine-rich repeat (CC-NB-LRR) protein. Several planthopper and aphid resistance genes encoding proteins with similar structures have recently been identified. Here, we analyzed the functions of the domains of BPH14 to identify molecular mechanisms underpinning BPH14-mediated planthopper resistance. The CC or NB domains alone or in combination (CC-NB [CN]) conferred a similar level of brown planthopper resistance to that of full-length (FL) BPH14. Both domains activated the salicylic acid signaling pathway and defense gene expression. In rice protoplasts and Nicotiana benthamiana leaves, these domains increased reactive oxygen species levels without triggering cell death. Additionally, the resistance domains and FL BPH14 protein formed homocomplexes that interacted with transcription factors WRKY46 and WRKY72. In rice protoplasts, the expression of FL BPH14 or its CC, NB, and CN domains increased the accumulation of WRKY46 and WRKY72 as well as WRKY46- and WRKY72-dependent transactivation activity. WRKY46 and WRKY72 bind to the promoters of the receptor-like cytoplasmic kinase gene RLCK281 and the callose synthase gene LOC_Os01g67364.1, whose transactivation activity is dependent on WRKY46 or WRKY72. These findings shed light on this important insect resistance mechanism.

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.

Development of 25 near-isogenic lines (NILs) with ten BPH resistance genes in rice (Oryza sativa L.): production, resistance spectrum, and molecular analysis

A first set of 25 NILs carrying ten BPH resistance genes and their pyramids was developed in the background of indica variety IR24 for insect resistance breeding in rice. Brown planthopper (Nilaparvata lugens Stal.) is one of the most destructive insect pests in rice. Development of near-isogenic lines (NILs) is an important strategy for genetic analysis of brown planthopper (BPH) resistance (R) genes and their deployment against diverse BPH populations. A set of 25 NILs with 9 single R genes and 16 multiple R gene combinations consisting of 11 two-gene pyramids and 5 three-gene pyramids in the genetic background of the susceptible indica rice cultivar IR24 was developed through marker-assisted selection. The linked DNA markers for each of the R genes were used for foreground selection and confirming the introgressed regions of the BPH R genes. Modified seed box screening and feeding rate of BPH were used to evaluate the spectrum of resistance. BPH reaction of each of the NILs carrying different single genes was variable at the antibiosis level with the four BPH populations of the Philippines. The NILs with two- to three-pyramided genes showed a stronger level of antibiosis (49.3-99.0%) against BPH populations compared with NILs with a single R gene NILs (42.0-83.5%) and IR24 (10.0%). Background genotyping by high-density SNPs markers revealed that most of the chromosome regions of the NILs (BC₃F₅) had IR24 genome recovery of 82.0-94.2%. Six major agronomic data of the NILs showed a phenotypically comparable agronomic performance with IR24. These newly developed NILs will be useful as new genetic resources for BPH resistance breeding and are valuable sources of genes in monitoring against the emerging BPH biotypes in different rice-growing countries.

Identification and fine mapping of a new gene, BPH31 conferring resistance to brown planthopper biotype 4 of India to improve rice, Oryza sativa L

BACKGROUND

Rice (Oryza sativa L.) is the staple food for more than 3.5 billion people, mainly in Asia. Brown planthopper (BPH) is one of the most destructive insect pests of rice that limits rice production. Host-plant resistance is one of the most efficient ways to overcome BPH damage to the rice crop.

RESULTS

BPH bioassay studies from 2009 to 2015 conducted in India and at the International Rice Research Institute (IRRI), Philippines, revealed that the cultivar CR2711-76 developed at the National Rice Research Institute (NRRI), Cuttack, India, showed stable and broad-spectrum resistance to several BPH populations of the Philippines and BPH biotype 4 of India. Genetic analysis and fine mapping confirmed the presence of a single dominant gene, BPH31, in CR2711-76 conferring BPH resistance. The BPH31 gene was located on the long arm of chromosome 3 within an interval of 475 kb between the markers PA26 and RM2334. Bioassay analysis of the BPH31 gene in CR2711-76 was carried out against BPH populations of the Philippines. The results from bioassay revealed that CR2711-76 possesses three different mechanisms of resistance: antibiosis, antixenosis, and tolerance. The effectiveness of flanking markers was tested in a segregating population and the InDel type markers PA26 and RM2334 showed high co-segregation with the resistance phenotype. Foreground and background analysis by tightly linked markers as well as using the Infinium 6 K SNP chip respectively were applied for transferring the BPH31 gene into an indica variety, Jaya. The improved BPH31-derived Jaya lines showed strong resistance to BPH biotypes of India and the Philippines.

CONCLUSION

The new BPH31 gene can be used in BPH resistance breeding programs on the Indian subcontinent. The tightly linked DNA markers identified in the study have proved their effectiveness and can be utilized in BPH resistance breeding in 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.

Genomics of interaction between the brown planthopper and rice

Rice (Oryza sativa L.) and the brown planthopper (Nilaparvata lugens (Stål)) form a model system for dissection of the mechanism of interaction between insect pest and crop. In this review, we focus on the genomics of BPH-rice interaction. On the side of rice, a number of BPH-resistance genes have been identified genetically. Thirteen of these genes have been cloned which shed a light on the molecular basis of the interaction. On the aspect of BPH, a lot of salivary proteins have been identified using transcriptome and proteome techniques. The genetic loci of virulence were mapped in BPH genome based on the linkage map. The understanding of interaction between BPH and rice will provide novel insights into efficient control of this pest.

Development of Elite BPH-Resistant Wide-Spectrum Restorer Lines for Three and Two Line Hybrid Rice

Hybrid rice has contributed significantly to the world food security. Breeding of elite high-yield, strong-resistant broad-spectrum restorer line is an important strategy for hybrid rice in commercial breeding programs. Here, we developed three elite brown planthopper (BPH)-resistant wide-spectrum restorer lines by pyramiding big-panicle gene Gn8.1, BPH-resistant genes Bph6 and Bph9, fertility restorer genes Rf3, Rf4, Rf5, and Rf6 through molecular marker assisted selection. Resistance analysis revealed that the newly developed restorer lines showed stronger BPH-resistance than any of the single-gene donor parent Luoyang-6 and Luoyang-9. Moreover, the three new restorer lines had broad spectrum recovery capabilities for Honglian CMS, Wild abortive CMS and two-line GMS sterile lines, and higher grain yields than that of the recurrent parent 9,311 under nature field conditions. Importantly, the hybrid crosses also showed good performance for grain yield and BPH-resistance. Thus, the development of elite BPH-resistant wide-spectrum restorer lines has a promising future for breeding of broad spectrum BPH-resistant high-yield varieties.

Overexpression of OsRRK1 Changes Leaf Morphology and Defense to Insect in Rice

It has been reported that the receptor-like cytoplasmic kinases (RLCKs) regulate many biological processes in plants, but only a few members have been functionally characterized. Here, we isolated a rice gene encoding AtRRK1 homology protein kinase, OsRRK1, which belongs to the RLCK VI subfamily. OsRRK1 transcript accumulated in many tissues at low to moderate levels and at high levels in leaves. Overexpression of OsRRK1 (OE-OsRRK1) caused adaxial rolling and erect morphology of rice leaves. In the rolled leaves of OE-OsRRK1 plants, both the number and the size of the bulliform cells are decreased compared to the wild-type (WT) plants. Moreover, the height, tiller number, and seed setting rate were reduced in OE-OsRRK1 plants. In addition, the brown planthopper (BPH), a devastating pest of rice, preferred to settle on WT plants than on the OE-OsRRK1 plants in a two-host choice test, indicating that OE-OsRRK1 conferred an antixenosis resistance to BPH. The analysis of transcriptome sequencing demonstrated that several receptor kinases and transcription factors were differentially expressed in OE-OsRRK1 plants and WT plants. These results indicated that OsRRK1 may play multiple roles in the development and defense of rice, which may facilitate the breeding of novel rice varieties.