Bph32, a novel gene encoding an unknown SCR domain-containing protein, confers resistance against the brown planthopper in rice

Revealing Genomic Traits and Evolutionary Insights of Oryza officinalis from Southern China Through Genome Assembly and Transcriptome Analysis

Wild rice, as the ancestor of cultivated rice, has accumulated a wide range of beneficial traits through prolonged natural selection and evolution. Oryza officinalis, belonging to the CC genome, differs significantly from the AA genome. In this study, we utilized second- and third-generation sequencing, along with Hi-C technology, to assemble the genome of MT10 (O. officinalis). The assembled genome is 552.58 Mb, with contigs and scaffold N50 values of 40.04 and 44.48 Mb, respectively, and 96.73% of the sequences anchored to 12 chromosomes. A total of 33,813 genes were annotated, and repetitive sequences account for 54.24% of the MT10 genome. The number of unique genes in MT10 exceeds that in the O. officinalis genome from Thailand, and their divergence time is estimated at 1.6 million years ago. The MT10 genome exhibits fewer expanded gene families compared to contracted ones, with the expanded families predominantly associated with disease and pest resistance. Comparative genomic analysis of MT10 and Nipponbare reveals sequence variations in biotic and abiotic resistance-related genes. In particular, the presence of R genes and cystatin gene families in MT10 may contribute to its unique insect resistance. Transcriptome analyses indicate that flavonoid biosynthesis and MAPK-related genes are expressed in response to brown planthopper infestation. This study represents the first chromosome-level genome assembly of MT10, providing a reference sequence for the efficient cloning of beneficial genes from O. officinalis, which holds significant potential for the genetic improvement of cultivated rice.

Insight into Rice Resistance to the Brown Planthopper: Gene Cloning, Functional Analysis, and Breeding Applications

This review provides a comprehensive overview of the current understanding of rice resistance to the brown planthopper (BPH), a major pest that poses significant threats to rice production through direct feeding damage and by transmitting viruses such as Rice grassy stunt virus (RGSV) and Rice ragged stunt virus (RRSV). We highlight the emergence of various BPH biotypes that have overcome specific resistance genes in rice. Advances in genetic mapping and cloning have identified 17 BPH resistance genes, classified into typical R genes encoding nucleotide-binding leucine-rich repeat (NLR) proteins and atypical R genes such as lectin receptor kinases and proteins affecting cell wall composition. The molecular mechanisms of these genes involve the activation of plant defense pathways mediated by phytohormones like jasmonic acid (JA), salicylic acid (SA), and ethylene, as well as the production of defensive metabolites. We also examine the complex interactions between BPH salivary proteins and rice defense responses, noting how salivary effectors can both suppress and trigger plant immunity. The development and improvement of BPH-resistant rice varieties through conventional breeding and molecular marker-assisted selection are discussed, including strategies like gene pyramiding to enhance resistance durability. Finally, we outline the challenges and future directions in breeding for durable BPH resistance, emphasizing the need for continued research on resistance mechanisms and the development of rice varieties with broad-spectrum and long-lasting resistance.

Recent Advances in Gene Mining and Hormonal Mechanism for Brown Planthopper Resistance in Rice

Rice (Oryza sativa L.) feeds half the world's population and serves as one of the most vital staple food crops globally. The brown planthopper (BPH, Nilaparvata lugens Stål), a major piercing-sucking herbivore specific to rice, accounts for large yield losses annually in rice-growing areas. Developing rice varieties with host resistance has been acknowledged as the most effective and economical approach for BPH control. Accordingly, the foremost step is to identify BPH resistance genes and elucidate the resistance mechanism of rice. More than 70 BPH resistance genes/QTLs with wide distributions on nine chromosomes have been identified from rice and wild relatives. Among them, 17 BPH resistance genes were successfully cloned and principally encoded coiled-coil nucleotide-binding leucine-rich repeat (CC-NB-LRR) protein and lectin receptor kinase (LecRK), as well as proteins containing a B3 DNA-binding domain, leucine-rich repeat domain (LRD) and short consensus repeat (SCR) domain. Multiple mechanisms contribute to rice resistance against BPH attack, including transcription factors, physical barriers, phytohormones, defense metabolites and exocytosis pathways. Plant hormones, including jasmonic acid (JA), salicylic acid (SA), ethylene (ET), abscisic acid (ABA), gibberellins (GAs), cytokinins (CKs), brassinosteroids (BRs) and indoleacetic-3-acid (IAA), play crucial roles in coordinating rice defense responses to the BPH. Here, we summarize some recent advances in the genetic mapping, cloning and biochemical mechanisms of BPH resistance genes. We also review the latest studies on our understanding of the function and crosstalk of phytohormones in the rice immune network against BPHs. Further directions for rice BPH resistance studies and management are also proposed.

TMT-based quantitative proteomics analysis of defense responses induced by the Bph3 gene following brown planthopper infection in rice

BACKGROUND

The brown planthopper (BPH) is an economically significant pest of rice. Bph3 is a key BPH resistance gene. However, the proteomic response of rice to BPH infestation, both in the presence and absence of Bph3, remains largely unexplored.

RESULTS

In this study, we employed tandem mass tag labeling in conjunction with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis to identify differentially expressed proteins (DEPs) in rice samples. We detected 265 and 125 DEPs via comparison of samples infected with BPH for 2 and 4 days with untreated samples of the BPH-sensitive line R582. For the Bph3 introgression line R373, we identified 29 and 94 DEPs in the same comparisons. Bioinformatic analysis revealed that Bph3 significantly influences the abundance of proteins associated with metabolic pathways, secondary metabolite biosynthesis, microbial metabolism in diverse environments, and phenylpropanoid biosynthesis. Moreover, Bph3 regulates the activity of proteins involved in the calcium signaling pathway, mitogen-activated protein kinase (MAPK) signaling pathway, and plant hormone signal transduction.

CONCLUSIONS

Our results indicate that Bph3 enhances the resistance of rice to BPH mainly by inhibiting the down-regulation of proteins associated with metabolic pathways; calcium signaling, the MAPK signaling pathway, and plant hormone signal transduction might also be involved in BPH resistance induced by Bph3.

Breeding for brown plant hopper resistance in rice: recent updates and future perspectives

Rice yield is often threatened by various stresses caused by biotic and abiotic agents. Many biotic stress factors are known to cause crop growth and yield from seedling to maturity. The brown plant hopper (BPH) can potentially reduce the rice yield to an extent of up to 80%. Intensive research efforts in 1972 led to a better understanding of pathogens/insect and host-plant resistance. This resulted in the identification of about 70 BPH-resistant genes and quantitative trait loci (QTLs) from diversified sources including wild germplasm. However, the BPH-resistant improved varieties with a single resistant gene lose the effectiveness of the gene because of the evolution of new biotypes. This review inferred that the level of resistance durable when incorporating multiple 'R' gene combinations when compared to a single gene. Breeding tools like wide hybridization, biparental crosses, marker-assisted introgression, pyramiding, and genetic engineering have been widely employed to breed rice varieties with single or combination of 'R' genes conferring durable resistance to BPH. Many other genes like receptor-like kinase genes, transcriptional factors, etc., were also found to be involved in the resistant mechanisms of 'R' genes. Due to this, the durability of the resistance can be improved and the level of resistance of the 'R' genes can be increased by adopting newer breeding tools like genome editing which hold promise to develop rice varieties with stable resistance.

ACL1-ROC4/5 complex reveals a common mechanism in rice response to brown planthopper infestation and drought

Brown planthopper (BPH) is the most destructive insect pest of rice. Drought is the most detrimental environmental stress. BPH infestation causes adaxial leaf-rolling and bulliform cells (BCs) shrinkage similar to drought. The BC-related abaxially curled leaf1 (ACL1) gene negatively regulates BPH resistance and drought tolerance, with decreased cuticular wax in the gain-of-function mutant ACL1-D. ACL1 shows an epidermis-specific expression. The TurboID system and multiple biochemical assays reveal that ACL1 interacts with the epidermal-characteristic rice outermost cell-specific (ROC) proteins. ROC4 and ROC5 positively regulate BPH resistance and drought tolerance through modulating cuticular wax and BCs, respectively. Overexpression of ROC4 and ROC5 both rescue ACL1-D mutant in various related phenotypes. ACL1 competes with ROC4/ROC5 in homo-dimer and hetero-dimer formation, and interacts with the repressive TOPLESS-related proteins. Altogether, we illustrate that ACL1-ROC4/5 complexes synergistically mediate drought tolerance and BPH resistance through regulating cuticular wax content and BC development in rice, a mechanism that might facilitate BPH-resistant breeding.

Virulence Adaptation by Rice Planthoppers and Leafhoppers to Resistance Genes and Loci: A Review

In recent decades, research on developing and deploying resistant rice has accelerated due to the availability of modern molecular tools and, in particular, advances in marker-assisted selection. However, progress in understanding virulence adaptation has been relatively slow. This review tracks patterns in virulence adaptation to resistance genes (particularly Bph1, bph2, Bph3, and bph4) and examines the nature of virulence based on selection experiments, responses by virulent populations to differential rice varieties (i.e., varieties with different resistance genes), and breeding experiments that interpret the genetic mechanisms underlying adaptation. The review proposes that varietal resistance is best regarded as a combination of minor and major resistance traits against which planthoppers develop partial or complete virulence through heritable improvements that are reversable or through evolutionary adaptation, respectively. Agronomic practices, deployment patterns, and herbivore population pressures determine the rates of adaptation, and there is growing evidence that pesticide detoxification mechanisms can accelerate virulence adaptation. Research to delay adaptation has mainly focused on gene pyramiding (i.e., including ≥ two major genes in a variety) and multilines (i.e., including ≥ two resistant varieties in a field or landscape); however, these strategies have not been adequately tested and, if not managed properly, could inadvertently accelerate adaptation compared to sequential deployment. Several research gaps remain and considerable improvements in research methods are required to better understand and manage virulence adaptation.

Identification and candidate analysis of a new brown planthopper resistance locus in an Indian landrace of rice, paedai kalibungga

The brown planthopper (Nilaparvata lugens Stål, BPH) is the most destructive pest of rice (Oryza sativa L.). Utilizing resistant rice cultivars that harbor resistance gene/s is an effective strategy for integrated pest management. Due to the co-evolution of BPH and rice, a single resistance gene may fail because of changes in the virulent BPH population. Thus, it is urgent to explore and map novel BPH resistance genes in rice germplasm. Previously, an indica landrace from India, Paedai kalibungga (PK), demonstrated high resistance to BPH in both in Wuhan and Fuzhou, China. To map BPH resistance genes from PK, a BC1F2:3 population derived from crosses of PK and a susceptible parent, Zhenshan 97 (ZS97), was developed and evaluated for BPH resistance. A novel BPH resistance locus, BPH39, was mapped on the short arm of rice chromosome 6 using next-generation sequencing-based bulked segregant analysis (BSA-seq). BPH39 was validated using flanking markers within the locus. Furthermore, near-isogenic lines carrying BPH39 (NIL-BPH39) were developed in the ZS97 background. NIL-BPH39 exhibited the physiological mechanisms of antibiosis and preference toward BPH. BPH39 was finally delimited to an interval of 84 Kb ranging from 1.07 to 1.15 Mb. Six candidate genes were identified in this region. Two of them (LOC_Os06g02930 and LOC_Os06g03030) encode proteins with a similar short consensus repeat (SCR) domain, which displayed many variations leading to amino acid substitutions and showed higher expression levels in NIL-BPH39. Thus, these two genes are considered reliable candidate genes for BPH39. Additionally, transcriptome sequencing, DEGs analysis, and gene RT-qPCR verification preliminary revealed that BPH39 may be involved in the jasmonic acid (JA) signaling pathway, thus mediating the molecular mechanism of BPH resistance. This work will facilitate map-based cloning and marker-assisted selection for the locus in breeding programs targeting BPH resistance.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01485-6.

Substitution mapping and characterization of brown planthopper resistance genes from traditional rice cultivar 'Rathu Heenati' (Oryza sativa L.)

The brown planthopper (BPH; Nilaparvata lugens Stål) is a devastating pest that causes severe rice yield losses in Asia. Introducing multiple BPH resistance genes into rice cultivars is an effective and sustainable way to mitigate yield losses. A traditional rice cultivar, 'Rathu Heenati', has durable BPH resistance due to multiple resistance genes (including BPH3 and BPH17) and quantitative trait loci (QTLs). However, these genes have not been used in Japanese rice breeding owing to limited genetic information. To identify markers tightly linked to BPH3 and BPH17 introgressed into the 'Sagabiyori' (susceptible) genetic background, we performed substitution mapping. BPH3 was delimited between RM3132 and RM589 on chromosome 6, and BPH17 between RM16493 and RM16531 on chromosome 4. We also performed QTL analysis to identify additional BPH resistance genes from 'Rathu Heenati' and detected a QTL, denoted as qBPH3.1, on chromosome 3. The effect of pyramiding BPH3 and BPH17 was significantly greater against virulent BPH populations than that of either gene alone. The combination of BPH3, BPH17 and qBPH3.1 from 'Rathu Heenati' might be facilitated to improve commercial Japanese cultivars with more robust BPH resistance.

Fine mapping and breeding application of two brown planthopper resistance genes derived from landrace rice

The Brown planthopper (Nilaparvata lugens Stål; BPH) is known to cause significant damage to rice crops in Asia, and the use of host-resistant varieties is an effective and environmentally friendly approach for controlling BPH. However, genes limited resistance genes that are used in insect-resistant rice breeding programs, and landrace rice varieties are materials resources that carry rich and versatile genes for BPH resistance. Two landrace indica rice accessions, CL45 and CL48, are highly resistant to BPH and show obvious antibiosis against BPH. A novel resistance locus linked to markers 12M16.983 and 12M19.042 was identified, mapped to chromosome 12 in CL45, and designated Bph46. It was finely mapped to an interval of 480 kb and Gene 3 may be the resistance gene. Another resistance locus linked to markers RM26567 and 11MA104 was identified and mapped to chromosome 11 in CL48 and designated qBph11.3 according to the nominating rule. It was finely mapped to an interval of 145 kb, and LOC_Os11g29090 and LOC_Os11g29110 may be the resistance genes. Moreover, two markers, 12M16.983 and 11MA104, were developed for CL45 and CL48, respectively, using marker-assisted selection (MAS) and were confirmed by backcrossing individuals and phenotypic detection. Interestingly, we found that the black glume color is closely linked to the BPH resistance gene in CL48 and can effectively assist in the identification of positive individuals for breeding. Finally, several near-isogenic lines with a 9311 or KW genetic background, as well as pyramid lines with two resistance parents, were developed using MAS and exhibited significantly high resistance against BPHs.

Pyramiding BPH genes in rice maintains resistance against the brown planthopper under climate change

BACKGROUND

Nilaparvata lugens (brown planthopper; BPH) is a significant rice pest in Asia, causing substantial yield losses. Pyramiding BPH resistance genes with diverse resistance traits into rice cultivars is an effective strategy for pest management. However, the response of pyramiding combinations to environmental changes remains unclear. To address this knowledge gap, we investigated three pyramiding rice lines (BPH2 + 32, BPH9 + 32, and BPH18 + 32) in the context of varying climate change conditions, ensuring sufficient N. lugens-rice interactions. Thus, we set three environmental conditions [30/25 °C (day/night) with 500 ppm CO2 concentration, 32/27 °C (day/night) with 600 ppm CO2 concentration, and 35/30 °C (day/night) with 1000 ppm CO2 concentration].

RESULTS

All three pyramiding rice lines maintained the insect resistant ability under the three environmental settings. In particular, the BPH18 + 32 rice line exhibited stronger antibiotic and antixenosis effects against N. lugens. In addition, BPH18 + 32 rice line had better shoot resilience under N. lugens infestation, whereas the performance of the other two selected pyramiding rice lines varied. Thus, although BPH2, BPH9, and BPH18 represent three alleles at the same locus, their resistance levels against N. lugens may vary under distinct climate change scenarios, as evidenced by the performance of N. lugens on the three pyramiding rice lines.

CONCLUSION

Our findings indicate that all three tested pyramiding rice lines maintained their insect resistance in the face of diverse climate change scenarios. However, these lines exhibited varied repellent responses and resilience capacities in response to climate change. Thus, the combination of pyramiding genes needs to be considered for future breeding programs. © 2023 Society of Chemical Industry.

OsmiR319-OsPCF5 modulate resistance to brown planthopper in rice through association with MYB proteins

BACKGROUND

The brown planthopper (BPH) is a kind of piercing-sucking insect specific to rice, with the damage tops the list of pathogens and insects in recent years. microRNAs (miRNAs) are pivotal regulators of plant-environment interactions, while the mechanism underlying their function against insects is largely unknown.

RESULTS

Here, we confirmed that OsmiR319, an ancient and conserved miRNA, negatively regulated resistance to BPHs, with overexpression of OsmiR319 susceptible to BPH, while suppression of OsmiR319 resistant to BPH in comparison with wild type. Meanwhile, we identified several targets of OsmiR319 that may mediate BPH resistance. Among them, OsPCF5 was the most obviously induced by BPH feeding, and over expression of OsPCF5 was resistance to BPH. In addition, various biochemical assays verified that OsPCF5 interacted with several MYB proteins, such as OsMYB22, OsMYB30, and OsMYB30C.Genetically, we revealed that both OsMYB22 and OsMYB30C positively regulated BPH resistance. Genetic interaction analyses confirmed that OsMYB22 and OsMYB30C both function in the same genetic pathway with OsmiR319b to mediate BPH resistance.

CONCLUSIONS

Altogether, we revealed that OsPCF5 regulates BPH resistance via association with several MYB proteins downstream of OsmiR319, these MYB proteins might function as regulators of BPH resistance through regulating the phenylpropane synthesis.

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.

Defense Regulatory Network Associated with circRNA in Rice in Response to Brown Planthopper Infestation

The brown planthopper (BPH), Nilaparvata lugens (Stål), a rice-specific pest, has risen to the top of the list of significant pathogens and insects in recent years. Host plant-mediated resistance is an efficient strategy for BPH control. Nonetheless, BPH resistance in rice cultivars has succumbed to the emergence of distinct virulent BPH populations. Circular RNAs (circRNAs) play a pivotal role in regulating plant-environment interactions; however, the mechanisms underlying their insect-resistant functions remain largely unexplored. In this study, we conducted an extensive genome-wide analysis using high-throughput sequencing to explore the response of rice circRNAs to BPH infestations. We identified a total of 186 circRNAs in IR56 rice across two distinct virulence groups: IR-IR56-BPH (referring to IR rice infested by IR56-BPH) and IR-TN1-BPH, along with a control group (IR-CK) without BPH infestation. Among them, 39 circRNAs were upregulated, and 43 circRNAs were downregulated in the comparison between IR-IR56-BPH and IR-CK. Furthermore, in comparison with IR-CK, 42 circRNAs exhibited upregulation in IR-TN1-BPH, while 42 circRNAs showed downregulation. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that the targets of differentially expressed circRNAs were considerably enriched in a multitude of biological processes closely linked to the response to BPH infestations. Furthermore, we assessed a total of 20 randomly selected circRNAs along with their corresponding expression levels. Moreover, we validated the regulatory impact of circRNAs on miRNAs and mRNAs. These findings have led us to construct a conceptual model that circRNA is associated with the defense regulatory network in rice, which is likely facilitated by the mediation of their parental genes and competing endogenous RNA (ceRNA) networks. This model contributes to the understanding of several extensively studied processes in rice-BPH interactions.

Recent Advances in the Genetic and Biochemical Mechanisms of Rice Resistance to Brown Planthoppers (Nilaparvata lugens Stål)

Rice (Oryza sativa L.) is the staple food of more than half of Earth's population. Brown planthopper (Nilaparvata lugens Stål, BPH) is a host-specific pest of rice responsible for inducing major losses in rice production. Utilizing host resistance to control N. lugens is considered to be the most cost-effective method. Therefore, the exploration of resistance genes and resistance mechanisms has become the focus of breeders' attention. During the long-term co-evolution process, rice has evolved multiple mechanisms to defend against BPH infection, and BPHs have evolved various mechanisms to overcome the defenses of rice plants. More than 49 BPH-resistance genes/QTLs have been reported to date, and the responses of rice to BPH feeding activity involve various processes, including MAPK activation, plant hormone production, Ca2+ flux, etc. Several secretory proteins of BPHs have been identified and are involved in activating or suppressing a series of defense responses in rice. Here, we review some recent advances in our understanding of rice-BPH interactions. We also discuss research progress in controlling methods of brown planthoppers, including cultural management, trap cropping, and biological control. These studies contribute to the establishment of green integrated management systems for brown planthoppers.

Available cloned genes and markers for genetic improvement of biotic stress resistance in rice

Biotic stress is one of the major threats to stable rice production. Climate change affects the shifting of pest outbreaks in time and space. Genetic improvement of biotic stress resistance in rice is a cost-effective and environment-friendly way to control diseases and pests compared to other methods such as chemical spraying. Fast deployment of the available and suitable genes/alleles in local elite varieties through marker-assisted selection (MAS) is crucial for stable high-yield rice production. In this review, we focused on consolidating all the available cloned genes/alleles conferring resistance against rice pathogens (virus, bacteria, and fungus) and insect pests, the corresponding donor materials, and the DNA markers linked to the identified genes. To date, 48 genes (independent loci) have been cloned for only major biotic stresses: seven genes for brown planthopper (BPH), 23 for blast, 13 for bacterial blight, and five for viruses. Physical locations of the 48 genes were graphically mapped on the 12 rice chromosomes so that breeders can easily find the locations of the target genes and distances among all the biotic stress resistance genes and any other target trait genes. For efficient use of the cloned genes, we collected all the publically available DNA markers (~500 markers) linked to the identified genes. In case of no available cloned genes yet for the other biotic stresses, we provided brief information such as donor germplasm, quantitative trait loci (QTLs), and the related papers. All the information described in this review can contribute to the fast genetic improvement of biotic stress resistance in rice for stable high-yield rice production.

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.

Development and characterization of near-isogenic lines for brown planthopper resistance genes in the genetic background of japonica rice 'Sagabiyori'

The brown planthopper (BPH: Nilaparvata lugens Stål) is one of the most destructive insects in rice production. The use of host plant resistance has potential to reduce damage caused by BPH. The heat tolerance japonica rice 'Sagabiyori', with superior grain quality and high soluble starch in the stem, is highly susceptible to damage by BPH. Here, to enhance its BPH resistance, we developed seven near-isogenic lines (NILs) carrying BPH2, BPH17-ptb, BPH32, BPH3, BPH17, BPH20, and BPH21 through marker-assisted selection and evaluated resistance to two BPH populations. Most lines were more resistant to the Hadano-1966 BPH population than Sagabiyori but were less effective against the highly virulent Koshi-2013 population. Nevertheless, in antixenosis tests, Koshi-2013 settled less on all NILs than on Sagabiyori. In addition, adult mortality and the percentage of fresh weight loss of lines carrying BPH17 and BPH3 indicated that these lines have higher resistance to Koshi-2013 than Sagabiyori. Current study revealed that BPH resistance of Sagabiyori became stronger by transferring BPH3 and BPH17 genes. Thus, BPH3 and BPH17 might be valuable for breeding programs to enhance BPH resistance of high grain quality rice varieties with heat tolerance.

SET Domain Group 703 Regulates Planthopper Resistance by Suppressing the Expression of Defense-Related Genes

Plant defense responses against insect pests are intricately regulated by highly complex regulatory networks. Post-translational modifications (PTMs) of histones modulate the expression of genes involved in various biological processes. However, the role of PTMs in conferring insect resistance remains unclear. Through the screening of a T-DNA insertion activation-tagged mutant collection in rice, we identified the mutant planthopper susceptible 1 (phs1), which exhibits heightened expression of SET domain group 703 (SDG703). This overexpression is associated with increased susceptibility to the small brown planthopper (SBPH), an economically significant insect pest affecting rice crops. SDG703 is constitutively expressed in multiple tissues and shows substantial upregulation in response to SBPH feeding. SDG703 demonstrates the activity of histone H3K9 methyltransferase. Transcriptomic analysis revealed the downregulation of genes involved in effector-triggered immunity (ETI) and pattern-triggered immunity (PTI) in plants overexpressing SDG703. Among the downregulated genes, the overexpression of SDG703 in plants resulted in a higher level of histone H3K9 methylation compared to control plants. Collectively, these findings indicate that SDG703 suppresses the expression of defense-related genes through the promotion of histone methylation, consequently leading to reduced resistance against SBPH. The defense-related genes regulated by histone methylation present valuable targets for developing effective pest management strategies in future studies. Furthermore, our study provides novel insight into the epigenetic regulation involved in plant-insect resistance.

Recent Advances in Molecular Mechanism and Breeding Utilization of Brown Planthopper Resistance Genes in Rice: An Integrated Review

Over half of the world's population relies on rice as their staple food. The brown planthopper (Nilaparvata lugens Stål, BPH) is a significant insect pest that leads to global reductions in rice yields. Breeding rice varieties that are resistant to BPH has been acknowledged as the most cost-effective and efficient strategy to mitigate BPH infestation. Consequently, the exploration of BPH-resistant genes in rice and the development of resistant rice varieties have become focal points of interest and research for breeders. In this review, we summarized the latest advancements in the localization, cloning, molecular mechanisms, and breeding of BPH-resistant rice. Currently, a total of 70 BPH-resistant gene loci have been identified in rice, 64 out of 70 genes/QTLs were mapped on chromosomes 1, 2, 3, 4, 6, 8, 10, 11, and 12, respectively, with 17 of them successfully cloned. These genes primarily encode five types of proteins: lectin receptor kinase (LecRK), coiled-coil-nucleotide-binding-leucine-rich repeat (CC-NB-LRR), B3-DNA binding domain, leucine-rich repeat domain (LRD), and short consensus repeat (SCR). Through mediating plant hormone signaling, calcium ion signaling, protein kinase cascade activation of cell proliferation, transcription factors, and miRNA signaling pathways, these genes induce the deposition of callose and cell wall thickening in rice tissues, ultimately leading to the inhibition of BPH feeding and the formation of resistance mechanisms against BPH damage. Furthermore, we discussed the applications of these resistance genes in the genetic improvement and breeding of rice. Functional studies of these insect-resistant genes and the elucidation of their network mechanisms establish a strong theoretical foundation for investigating the interaction between rice and BPH. Furthermore, they provide ample genetic resources and technical support for achieving sustainable BPH control and developing innovative insect resistance strategies.

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.

Near-isogenic lines for resistance to brown planthopper with the genetic background of Indica Group elite rice (Oryza sativa L.) variety 'IR64'

The brown planthopper (BPH), Nilaparvata lugens Stål, is an insect pest that severely damages rice (Oryza sativa L.) in Asia, causing huge yield loss. Use of resistant variety is a cost-effective and eco-friendly strategy for maintaining BPH populations below the economic injury level. However, current BPH populations have been changed to virulence against resistant varieties. In this study, to estimate effective combinations among eight BPH resistance genes (BPH32, BPH17-ptb, BPH20, BPH17, BPH3, BPH25, BPH26 and qBPH6), eight near-isogenic lines with the genetic background of an Indica Group rice variety 'IR64' (IR64-NIL) were developed using marker-assisted selection. The genome recoveries of these NILs ranged from 89.3% to 98.8% and agronomic traits of them were similar to those of 'IR64'. In modified seed box screening test, resistance level of IR64-NILs was higher than that of 'IR64'. In antibiosis test, high adult mortalities of BPH (from 56.0% to 97.0%) were observed among NILs, in comparison with that of 'IR64'. Among IR64-NILs, the line carrying BPH17 showed the highest resistance level at all tests. Thus, these IR64-NILs with multiple BPH resistance genes could be valuable breeding lines for enhancing resistance levels by gene pyramiding and multiline variety.

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.

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.

Molecular mechanisms, genetic mapping, and genome editing for insect pest resistance in field crops

Improving crop resistance against insect pests is crucial for ensuring future food security. Integrating genomics with modern breeding methods holds enormous potential in dissecting the genetic architecture of this complex trait and accelerating crop improvement. Insect resistance in crops has been a major research objective in several crop improvement programs. However, the use of conventional breeding methods to develop high-yielding cultivars with sustainable and durable insect pest resistance has been largely unsuccessful. The use of molecular markers for identification and deployment of insect resistance quantitative trait loci (QTLs) can fastrack traditional breeding methods. Till date, several QTLs for insect pest resistance have been identified in field-grown crops, and a few of them have been cloned by positional cloning approaches. Genome editing technologies, such as CRISPR/Cas9, are paving the way to tailor insect pest resistance loci for designing crops for the future. Here, we provide an overview of diverse defense mechanisms exerted by plants in response to insect pest attack, and review recent advances in genomics research and genetic improvements for insect pest resistance in major field crops. Finally, we discuss the scope for genomic breeding strategies to develop more durable insect pest resistant crops.

Transcriptome and metabolome analyses reveal the responses of brown planthoppers to RH resistant rice cultivar

The brown planthopper (BPH) Nilaparvata lugens (Stål) (Hemiptera: Delphacidae) is one of the most destructive rice pests in Asia. The application of insect-resistant rice cultivars is currently one of the principal means of controlling BPH. Understanding the physiological response mechanisms of BPH feeding on insect-resistant rice is the key for maintaining rice yield. Here, we measured the ecological fitness and analyzed the whole-body transcriptome and metabolome of BPH reared on susceptible cultivar Taichung Native 1 (TN1) and resistant cultivar Rathu Heenati (RH). Our results showed that RH significantly decreased the survival rate, female adult weight, honeydew secretion, the number of eggs laid per female and fat content of BPH. We identified 333 upregulated and 486 downregulated genes in BPH feeding on RH. These genes were mainly involved in energy metabolism, amino acid metabolism, hormone synthesis and vitamin metabolism pathways. We also detected 145 differentially accumulated metabolites in BPH reared on RH plants compared to BPH reared on TN1 plants, including multiple carbohydrates, amino acids, lipids, and some nucleosides. Combined analyses of transcriptome and metabolome showed that five pathways, including starch, sucrose, and galactose metabolism, were altered. The network for these pathways was subsequently visualized. Our results provide insights into the mechanisms of metabolite accumulation in BPH feeding on the RH rice variety. The results could help us better understand how insect-resistant rice cultivars combat BPH infestation, which is important for the comprehensive management of BPH.

Identification and Functional Analysis of the Caffeic Acid O-Methyltransferase (COMT) Gene Family in Rice (Oryza sativa L.)

Caffeic acid O-methyltransferase (COMT) is one of the core enzymes involved in lignin synthesis. However, there is no systematic study on the rice COMT gene family. We identified 33 COMT genes containing the methyltransferase-2 domain in the rice genome using bioinformatic methods and divided them into Group I (a and b) and Group II. Motifs, conserved domains, gene structure and SNPs density are related to the classification of OsCOMTs. The tandem phenomenon plays a key role in the expansion of OsCOMTs. The expression levels of fourteen and thirteen OsCOMTs increased or decreased under salt stress and drought stress, respectively. OsCOMTs showed higher expression levels in the stem. The lignin content of rice was measured in five stages; combined with the expression analysis of OsCOMTs and multiple sequence alignment, we found that OsCOMT8, OsCOMT9 and OsCOMT15 play a key role in the synthesis of lignin. Targeted miRNAs and gene ontology annotation revealed that OsCOMTs were involved in abiotic stress responses. Our study contributes to the analysis of the biological function of OsCOMTs, which may provide information for future rice breeding and editing of the rice genome.

Identification of Novel Candidate of Brown Planthopper Resistance Gene Bph44 in Rice (Oryza sativa Lin)

Brown Planthopper (BPH) still consider a major threat to rice farmers. Exploring novel resistance genes that relate to the BPH population in the targeted rice-growing area might be a suitable solution. We identified and mapped the gene locus using 175 lines of F2:3 populations derived from Balamawee x PD601. Genomic analysis was then used to identify the candidate gene governing the resistance toward BPH. We discovered a novel genetic locus for BPH resistance in the long arm of chromosome 4 linked to markers Q31 and RM17007 at 4.76 and 5.42 cM, respectively, with total phenotypic variation reaching 52.21 % at LOD 29.68. The tolerance mechanism influences the nature of this resistance, as shown by the Functional Plant Loss Index. Resistance level, mechanism of resistance, and physical mapping reveal that the resistance genes in this study differ from the previous study, therefore we propose this novel gene as Bph44.

Development and Validation of Diagnostic KASP Markers for Brown Planthopper Resistance in Rice

Rice (Oryza sativa L.) is an important source of nutrition for the world's burgeoning population that often faces yield loss due to infestation by the brown planthopper (BPH, Nilaparvata lugens (Stål)). The development of rice cultivars with BPH resistance is one of the crucial precedences in rice breeding programs. Recent progress in high-throughput SNP-based genotyping technology has made it possible to develop markers linked to the BPH more quickly than ever before. With this view, a genome-wide association study was undertaken for deriving marker-trait associations with BPH damage scores and SNPs from genotyping-by-sequencing data of 391 multi-parent advanced generation inter-cross (MAGIC) lines. A total of 23 significant SNPs involved in stress resistance pathways were selected from a general linear model along with 31 SNPs reported from a FarmCPU model in previous studies. Of these 54 SNPs, 20 were selected in such a way to cover 13 stress-related genes. Kompetitive allele-specific PCR (KASP) assays were designed for the 20 selected SNPs and were subsequently used in validating the genotypes that were identified, six SNPs, viz, snpOS00912, snpOS00915, snpOS00922, snpOS00923, snpOS00927, and snpOS00929 as efficient in distinguishing the genotypes into BPH-resistant and susceptible clusters. Bph17 and Bph32 genes that are highly effective against the biotype 4 of the BPH have been validated by gene specific SNPs with favorable alleles in M201, M272, M344, RathuHeenati, and RathuHeenati accession. These identified genotypes could be useful as donors for transferring BPH resistance into popular varieties with marker-assisted selection using these diagnostic SNPs. The resistant lines and the significant SNPs unearthed from our study can be useful in developing BPH-resistant varieties after validating them in biparental populations with the potential usefulness of SNPs as causal markers.

Combined Effects of Soil Silicon and Host Plant Resistance on Planthoppers, Blast and Bacterial Blight in Tropical Rice

Simple Summary

Rice is often attacked by several herbivores and plant pathogens at the same time. Public research has mainly focused on enhancing rice resistance against these biotic stresses by selecting rice lines with resistance genes during breeding programs. However, rice resistance to biotic stresses is also affected by soil nutrients, including available nitrogen and silicon. Nitrogen tends to reduce resistance, but silicon can increase resistance. We assessed the effects of combining soil silicon with host plant resistance against rice planthoppers, blast disease, and bacterial blight disease. We used pure silicon (SiO₂) to avoid the confounding effects of nutrients associated with silicates. We also assessed the effects of nitrogenous fertilizer on silicon-augmented resistance to planthoppers. We found that high nitrogen diminishes the capacity of soil silicon and host resistance to reduce planthopper fitness (i.e., nitrogen was antagonistic); but that silicon counters nitrogen-related reductions in rice antixenosis defenses (e.g., repellency) against gravid female planthoppers (i.e., an additive effect of silicon and resistance). Silicon augmented resistance against blast and bacterial blight, but the effects were most apparent on susceptible varieties. Plants infected with bacterial blight generally grew larger in silicon amended soils. We discuss how silicon improves seedling quality by augmenting broad-spectrum resistance.

Abstract

Soil silicon enhances rice defenses against a range of biotic stresses. However, the magnitude of these effects can depend on the nature of the rice variety. We conducted a series of greenhouse experiments to examine the effects of silicon on planthoppers (Nilaparvata lugens [BPH] and Sogatella furcifera [WBPH]), a leafhopper (Nephotettix virescens [GLH]), blast disease (Magnaporthe grisea) and bacterial blight (Xanthomonas oryzae) in susceptible and resistant rice. We added powdered silica gel (SiO₂) to paddy soil at equivalent to 0.25, 1.0, and 4.0 t ha⁻¹. Added silicon reduced BPH nymph settling, but the effect was negligible under high nitrogen. In a choice experiment, BPH egg-laying was lower than untreated controls under all silicon treatments regardless of nitrogen or variety, whereas, in a no-choice experiment, silicon reduced egg-laying on the susceptible but not the resistant (BPH32 gene) variety. Stronger effects in choice experiments suggest that silicon mainly enhanced antixenosis defenses. We found no effects of silicon on WBPH or GLH. Silicon reduced blast damage to susceptible and resistant (Piz, Piz-5 and Pi9 genes) rice. Silicon reduced damage from a virulent strain of bacterial blight but had little effect on a less virulent strain in susceptible and resistant (Xa4, Xa7 and Xa4 + Xa7 genes) varieties. When combined with resistance, silicon had an additive effect in reducing biomass losses to plants infested with bacterial blight (resistance up to 50%; silicon 20%). We discuss how silicon-containing soil amendments can be combined with host resistance to reduce biotic stresses in rice.

Effect of nitrogen fertilizer on the resistance of rice near-isogenic lines with BPH resistance genes

BACKGROUND

Nitrogen is an essential macronutrient for plant growth and development. Crops with a high nitrogen input usually have high yields. However, outbreaks of brown planthoppers (Nilaparvata lugens; BPH) frequently occur on rice farms with excessive nitrogen inputs. Rice plants carrying BPH resistance genes are used for integrated pest management. Thus, the impact of nitrogen on the resistance of rice near-isogenic lines (NILs) with BPH resistance genes was investigated.

RESULTS

We tested these NILs using a standard seedbox screening test and a modified bulk seedling test under different nitrogen treatments. The amount of nitrogen applied had an impact on the resistance of some lines with BPH resistance genes. In addition, three NILs (NIL-BPH9, NIL-BPH17, and NIL-BPH32) were further examined for antibiosis and antixenosis under varying nitrogen regimes. The N. lugens nymph population growth rate, honeydew excretion, female fecundity, and nymph survival rate on the three NILs were not affected by different nitrogen treatments except the nymph survival rate on NIL-BPH9 and the nymph population growth rate on NIL-BPH17. Furthermore, in the settlement preference test, the preference of N. lugens nymphs for IR24 over NIL-BPH9 or NIL-BPH17 increased under the high-nitrogen regime, whereas the preference of N. lugens nymphs for IR24 over NIL-BPH32 was not affected by the nitrogen treatments.

CONCLUSIONS

Our results indicated that the resistance of three tested NILs did not respond to different nitrogen regimes and that NIL-BPH17 exerted the most substantial inhibitory effect on N. lugens growth and development.

Genomic insights on the contribution of introgressions from Xian/Indica to the genetic improvement of Geng/Japonica rice cultivars

Hybridization between Xian/indica (XI) and Geng/japonica (GJ) rice combined with utilization of plant ideotypes has greatly contributed to yield improvements in modern GJ rice in China over the past 50 years. To explore the genomic basis of improved yield and disease resistance in GJ rice, we conducted a large-scale genomic landscape analysis of 816 elite GJ cultivars representing multiple eras of germplasm from China. We detected consistently increasing introgressions from three XI subpopulations into GJ cultivars since the 1980s and found that the XI genome introgressions significantly increased the grain number per panicle (GN) and decreased the panicle number per plant. This contributed to the improvement of plant type during modern breeding, changing multi-tiller plants to moderate tiller plants with a large panicle size and increasing the blast resistance. Notably, we found that key gene haplotypes controlling plant architecture, yield components, and pest and disease resistance, including IPA1, SMG1, DEP3, Pib, Pi-d2, and Bph3, were introduced from XI rice by introgression. By GWAS analysis, we detected a GN-related gene Gnd5, which had been consistently introgressed from XI into GJ cultivars since the 1980s. Gnd5 is a GRAS transcription factor gene, and Gnd5 knockout mutants showed a significant reduction in GN. The estimated genetic effects of genes varied among different breeding locations, which explained the distinct introgression levels of XI gene haplotypes, including Gnd5, DEP3, etc., to these GJ breeding pedigrees. These findings reveal the genomic contributions of introgressions from XI to the trait improvements of GJ rice cultivars and provide new insights for future rice genomic breeding.

Plant elicitor peptide signalling confers rice resistance to piercing-sucking insect herbivores and pathogens

Rice is a staple food crop worldwide, and its production is severely threatened by phloem-feeding insect herbivores, particularly the brown planthopper (BPH, Nilaparvata lugens), and destructive pathogens. Despite the identification of many BPH resistance genes, the molecular basis of rice resistance to BPH remains largely unclear. Here, we report that the plant elicitor peptide (Pep) signalling confers rice resistance to BPH. Both rice PEP RECEPTORs (PEPRs) and PRECURSORs of PEP (PROPEPs), particularly OsPROPEP3, were transcriptionally induced in leaf sheaths upon BPH infestation. Knockout of OsPEPRs impaired rice resistance to BPH, whereas exogenous application of OsPep3 improved the resistance. Hormone measurement and co-profiling of transcriptomics and metabolomics in OsPep3-treated rice leaf sheaths suggested potential contributions of jasmonic acid biosynthesis, lipid metabolism and phenylpropanoid metabolism to OsPep3-induced rice immunity. Moreover, OsPep3 elicitation also strengthened rice resistance to the fungal pathogen Magnaporthe oryzae and bacterial pathogen Xanthamonas oryzae pv. oryzae and provoked immune responses in wheat. Collectively, this work demonstrates a previously unappreciated importance of the Pep signalling in plants for combating piercing-sucking insect herbivores and promises exogenous application of OsPep3 as an eco-friendly immune stimulator in agriculture for crop protection against a broad spectrum of insect pests and pathogens.

Metabolite profiles of brown planthopper-susceptible and resistant rice (Oryza sativa) varieties associated with infestation and mechanical stimuli

Understanding brown planthopper (BPH) resistance mechanism will expedite selective breeding of better BPH resistant lines of rice (Oryza sativa). Metabolic responses during BPH infestation derived from wound stress imposed by insect feeding, comparing with mechanical piercing will provide an insight into resistance mechanism in rice. Therefore, this study aimed to compare the metabolic responses of needle piercing treatment and BPH feeding treatment in BPH-susceptible (KD) and BPH-resistant (RH) varieties at four different time points (0, 6, 24 and 96 h) using liquid chromatography-high resolution mass spectrometry (LC-HRMS). Phenotypes of RH were not different among the treatments, whereas KD exhibited hopperburn symptom at 96 h post-BPH infestation. Principal component and cluster analyses revealed that metabolite profiles between KD and RH were different in response to both insect and mechanical stimuli. Metabolite profiles of RH under BPH and mechanical treatments at 24 and 96 h were different from the untreated, whereas metabolite profiles of KD after BPH infestation at 24 and 96 h were distinct from needle piercing and no treatment, suggesting that the resistant variety has an ability to adapt and defend both mechanical and insect stimuli. Metabolomics result showed that BPH infestation perturbed purine salvage biosynthesis (e.g., inosine, hypoxanthine) in both varieties, amino acid biosynthesis (e.g., phenylalanine, tryptophan) in KD, while the infestation perturbed lysine metabolism (pipecolic acid) and phenylpropanoid pathway (2-anisic acid) only in RH. BPH and mechanical stimuli perturbed phenylamide only in RH, but not in KD. These findings revealed that different rice varieties utilize different metabolites in response to insect and mechanical stimuli, resulting in different degrees of resistance.

From Green Super Rice to green agriculture: Reaping the promise of functional genomics research

Producing sufficient food with finite resources to feed the growing global population while having a smaller impact on the environment has always been a great challenge. Here, we review the concept and practices of Green Super Rice (GSR) that have led to a paradigm shift in goals for crop genetic improvement and models of food production for promoting sustainable agriculture. The momentous achievements and global deliveries of GSR have been fueled by the integration of abundant genetic resources, functional gene discoveries, and innovative breeding techniques with precise gene and whole-genome selection and efficient agronomic management to promote resource-saving, environmentally friendly crop production systems. We also provide perspectives on new horizons in genomic breeding technologies geared toward delivering green and nutritious crop varieties to further enhance the development of green agriculture and better nourish the world population.

Rice functional genomics: decades' efforts and roads ahead

Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.

Rice functional genomics: decades' efforts and roads ahead

Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.

Substitution mapping and characterization of brown planthopper resistance genes from indica rice variety, 'PTB33' (Oryza sativa L.)

Rice (Oryza sativa L.) yield is severely reduced by the brown planthopper (BPH), Nilaparvata lugens Stål, in Asian countries. Increasing resistance in rice against BPH can mitigate yield loss. Previous reports indicated the presence of three BPH resistance genes, BPH2, BPH17-ptb, and BPH32, in durable resistant indica rice cultivar 'PTB33'. However, several important questions remain unclear; the genetic locations of BPH resistance genes on rice chromosomes and how these genes confer resistance, especially with relationship to three major categories of resistance mechanisms; antibiosis, antixenosis or tolerance. In this study, locations of BPH2, BPH17-ptb, and BPH32 were delimited using chromosome segment substitution lines derived from crosses between 'Taichung 65' and near-isogenic lines for BPH2 (BPH2-NIL), BPH17-ptb (BPH17-ptb-NIL), and BPH32 (BPH32-NIL). BPH2 was delimited as approximately 247.5 kbp between RM28449 and ID-161-2 on chromosome 12. BPH17-ptb and BPH32 were located between RM1305 and RM6156 on chromosome 4 and RM508 and RM19341 on chromosome 6, respectively. The antibiosis, antixenosis, and tolerance were estimated by several tests using BPH2-NIL, BPH17-ptb-NIL, and BPH32-NIL. BPH2 and BPH17-ptb showed resistance to antibiosis and antixenosis, while BPH17-ptb and BPH32 showed tolerance. These results contribute to the development of durable BPH resistance lines using three resistance genes from 'PTB33'.

Nitrogenous Fertilizer Reduces Resistance but Enhances Tolerance to the Brown Planthopper in Fast-Growing, Moderately Resistant Rice

The brown planthopper, Nilaparvata lugens (Stål), is a key challenge to rice production in Asia. Outbreaks of planthoppers are associated with excessive fertilizer applications; consequently, we examined planthopper interactions with susceptible, tolerant and resistant varieties of rice under varying levels of soil nitrogen in a greenhouse experiment. We compared planthopper fitness (survival × reproduction) and plant tolerance (functional plant loss index) for 16 varieties at 0, 80 and 150 Kg added nitrogen ha^-1. The planthoppers grew larger, developed more quickly and laid more eggs on susceptible varieties, compared with the resistant and tolerant varieties. Moreover, soil nitrogen generally increased planthopper fitness on resistant varieties, but relative resistance was maintained. Functional plant loss was highest among the susceptible varieties, but weight and growth rate reductions per mg of planthopper were often highest in the tolerant varieties. Tolerance was associated with large, fast-growing plants, with at least moderate resistance to the planthopper. Susceptibility was associated with a small size and/or an absence of resistance genes. Our results suggested that early-tillering rice plants can be both resistant and tolerant to the brown planthopper, but cannot be both susceptible and tolerant of planthoppers at high densities. This indicates that at least moderate resistance is required for tolerance against this herbivore. Furthermore, although dwarf varieties had a low tolerance of planthoppers, they could express resistance through functioning resistance genes.

Balancing selection and wild gene pool contribute to resistance in global rice germplasm against planthopper

Interactions and co-evolution between plants and herbivorous insects are critically important in agriculture. Brown planthopper (BPH) is the most severe insect of rice, and the biotypes adapt to feed on different rice genotypes. Here, we present genomics analyses on 1,520 global rice germplasms for resistance to three BPH biotypes. Genome-wide association studies identified 3,502 single nucleotide polymorphisms (SNPs) and 59 loci associated with BPH resistance in rice. We cloned a previously unidentified gene Bph37 that confers resistance to BPH. The associated loci showed high nucleotide diversity. Genome-wide scans for trans-species polymorphisms revealed ancient balancing selection at the loci. The secondarily evolved insect biotypes II and III exhibited significantly higher virulence and overcame more rice varieties than the primary biotype I. In response, more SNPs and loci evolved in rice for resistance to biotypes II and III. Notably, three exceptional large regions with high SNP density and resistance-associated loci on chromosomes 4 and 6 appear distinct between the resistant and susceptible rice varieties. Surprisingly, these regions in resistant rice might have been retained from wild species Oryza nivara. Our findings expand the understanding of long-term interactions between rice and BPH and provide resistance genes and germplasm resources for breeding durable BPH-resistant rice varieties.

Genome-Wide Association Study Reveals a New Quantitative Trait Locus in Rice Related to Resistance to Brown Planthopper Nilaparvata lugens (Stål)

Simple Summary

The brown planthopper Nilaparvata lugens (Stål) (BPH) is one of the main rice pests in Asian areas. The development of rice varieties harboring resistance genes is the most economical and effective method of managing BPH. In this study, 123 rice germplasms were identified for resistance and durable resistance by using the rice planthopper resistance identification system. Forty-two of the 123 rice varieties were classified as resistant to brown planthopper, and among them, twelve rice varieties had a long, durable resistance period. One potential durable resistance to brown planthopper locus on chromosome 2 was found by a genome-wide association study (GWAS). There are 13 candidate genes at this locus, and several of them are related to disease and pest resistance. Our study found a potential durable resistance locus to BPH, which has guiding significance for subsequent resistance breeding.

Abstract

The brown planthopper (BPH) is one of the main pests endangering rice yields. The development of rice varieties harboring resistance genes is the most economical and effective method of managing BPH. To identify new BPH resistance-related genes, a total of 123 rice varieties were assessed for resistance and durable resistance. Three varieties were immune, and nine were highly resistant to BPH. After whole-genome resequencing of all 123 varieties, 1,897,845 single nucleotide polymorphisms (SNPs) were identified. Linkage disequilibrium (LD) decay analysis showed that the average LD of the SNPs at 20 kb was 0.30 (r²) and attenuated to half value (~0.30) at a distance of about 233 kb. A genome-wide association study (GWAS) of durable resistance to BPH was conducted using the Fast-MLM model. One quantitative trait locus, identified on chromosome 2, included 13 candidate genes. Two candidate genes contained a leucine-rich repeat and CC-NBS-LRR or NB-ARC domains, which might confer resistance to pests or diseases. Interestingly, LOC_Os02g27540 was highly expressed and was induced by BPH; GWAS identified potential rice genes coding for durable resistance to BPH. This study helps to elucidate the mechanism of durable resistance to BPH in rice and provides essential genetic information for breeding and functional verification of resistant varieties.

Impact of Climate Change on Health and Well-Being of People in Hindu Kush Himalayan Region: A Narrative Review

Climate change and variability affect virtually everyone and every region of the world but the effects are nowhere more prominent than in mountain regions and people living therein. The Hindu Kush Himalayan (HKH) region is a vast expanse encompassing 18% of the world’s mountainous area. Sprawling over 4.3 million km², the HKH region occupies areas of eight countries namely Nepal, Bhutan, Afghanistan, Bangladesh, China, India, Myanmar, and Pakistan. The HKH region is warming at a rate higher than the global average and precipitation has also increased significantly over the last 6 decades along with increased frequency and intensity of some extreme events. Changes in temperature and precipitation have affected and will like to affect the climate-dependent sectors such as hydrology, agriculture, biodiversity, and human health. This paper aims to document how climate change has impacted and will impact, health and well-being of the people in the HKH region and offers adaptation and mitigation measures to reduce the impacts of climate change on health and well-being of the people. In the HKH region, climate change boosts infectious diseases, non-communicable diseases (NCDs), malnutrition, and injuries. Hence, climate change adaptation and mitigation measures are needed urgently to safeguard vulnerable populations residing in the HKH region.

The Impact of Climate Change on the Resistance of Rice Near-Isogenic Lines with Resistance Genes Against Brown Planthopper

BACKGROUND

The impact of climate change on insect resistance genes is elusive. Hence, we investigated the responses of rice near-isogenic lines (NILs) that carry resistance genes against brown planthopper (BPH) under different environmental conditions.

RESULTS

We tested these NILs under three environmental settings (the atmospheric temperature with corresponding carbon dioxide at the ambient, year 2050 and year 2100) based on the Intergovernmental Panel on Climate Change prediction. Comparing between different environments, two of nine NILs that carried a single BPH-resistant gene maintained their resistance under the environmental changes, whereas two of three NILs showed gene pyramiding with two maintained BPH resistance genes despite the environmental changes. In addition, two NILs (NIL-BPH17 and NIL-BPH20) were examined in their antibiosis and antixenosis effects under these environmental changes. BPH showed different responses to these two NILs, where the inhibitory effect of NIL-BPH17 on the BPH growth and development was unaffected, while NIL-BPH20 may have lost its resistance during the environmental changes.

CONCLUSION

Our results indicate that BPH resistance genes could be affected by climate change. NIL-BPH17 has a strong inhibitory effect on BPH feeding on phloem and would be unaffected by environmental changes, while NIL-BPH20 would lose its ability during the environmental changes.

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.

Rice Sesquiterpene Plays Important Roles in Antixenosis against Brown Planthopper in Rice

The rice sesquiterpene synthase II gene (OsSTPS2, LOC_Os04g27430), which is involved in the antixenosis defense mechanism of rice against brown planthopper (BPH) infestation, was identified in the BPH-resistant rice variety Rathu Heenati (RH). In contrast, the gene was not functional in the BPH-susceptible rice variety KDML105 (KD). Single-nucleotide polymorphisms (SNPs) in the promoter region and in exon 5 of the gene and a seven amino acid deletion in the deduced protein sequence are suggested as factors that negatively regulate the function of the gene. Sequence analysis of the promoter region and expression analysis of the OsSTPS2 gene in several rice genotypes revealed the correlation of SNPs of the ATHB-1, SBE1, and P-factor with the expression of the gene. Genomic and complementary DNA (cDNA) sequence analysis at exon 5 of the gene showed that the 21 bp deletion naturally occurred in several rice genotypes. The antixenosis of the BPH feeding preference (AFP) of rice varieties differed in the seven amino acid deletion lesion of the gene, suggesting that the seven amino acid deletion negatively controls the antixenosis mechanism during BPH infestation. Analysis of the plant volatile compounds released after BPH infestation suggested that E-β-farnesene (EBF) is the major product of the OsSTPS2 gene.

Development of 'multiresistance rice' by an assembly of herbicide, insect and disease resistance genes with a transgene stacking system

BACKGROUND

Weeds, diseases and pests pose serious threats to rice production and cause significant economic losses. Cultivation of rice varieties with resistance to herbicides, diseases and pests is believed to be the most economical and environmentally friendly method to deal with these problems.

RESULTS

In this study, a highly efficient transgene stacking system was used to assembly the synthetic glyphosate-tolerance gene (I. variabilis-EPSPS*), lepidopteran pest resistance gene (Cry1C*), brown planthopper resistance genes (Bph14* and OsLecRK1*), bacterial blight resistance gene (Xa23*) and rice blast resistance gene (Pi9*) onto a transformable artificial chromosome vector. The construct was transferred into ZH11 (a widely used japonica rice cultivar Zhonghua 11) via Agrobacterium-mediated transformation and 'multiresistance rice' (MRR) with desirable agronomic traits was obtained. The results showed that MRR had significantly improved resistance to glyphosate, borers, brown planthopper, bacterial blight and rice blast relative to the recipient cultivar ZH11. Besides, under the natural occurrence of pests and diseases in the field, the yield of MRR was significantly higher than that of ZH11.

CONCLUSION

A multigene transformation strategy was employed to successfully develop rice lines with multiresistance to glyphosate, borers, brown planthopper, bacterial blight and rice blast, and the obtained MRR is expected to have great application potential. © 2020 Society of Chemical Industry.

Genomics-assisted breeding for successful development of multiple-stress-tolerant, climate-smart rice for southern and southeastern Asia

Rice (Oryza sativa L.) in rainfed marginal environments is prone to multiple abiotic and biotic stresses, which can occur in combination in a single cropping season and adversely affect rice growth and yield. The present study was undertaken to develop high-yielding, climate-resilient rice that can provide tolerance to multiple biotic and abiotic stresses. An assembled first-crossing scheme was employed to transfer 15 quantitative trait loci (QTL) and genes-qDTY_1.1 , qDTY_2.1 , qDTY_3.1 , qDTY_12.1 (drought), Sub1 (submergence), Gm4 (gall midge), Pi9, Pita2 (blast), Bph3, Bph17 (brown plant hoppers), Xa4, xa5, xa13, Xa21, and Xa23 (bacterial leaf blight)-from eight different parents using genomics-assisted breeding. A funnel mating design was employed to assemble all the targeted QTL and genes into a high-yielding breeding line IR 91648-B-1-B-3-1. Gene-based linked markers were used in each generation from intercrossing to the F₆ generation for tracking the presence of desirable alleles of targeted QTL and genes. Single-plant selections were performed from F₂ onwards to select desirable recombinants possessing alleles of interest with suitable phenotypes. Phenotyping of 95 homozygous F₆ lines carrying six to 10 QTL and genes was performed for nonstress, reproductive-stage (RS) drought, blast, bacterial leaf blight (BLB), gall midge (GM), and for grain quality parameters such as chalkiness, amylose content (AC), gelatinization temperature (GT), and head rice recovery (HRR). Finally, 56 F₇ homozygous lines were found promising for multiple-location evaluation for grain yield (GY) and other traits. These multiple-stress-tolerant lines with the desired grain quality profiling can be targeted for varietal release in southern and southeastern Asia through national release systems.

Elevated temperatures diminish the effects of a highly resistant rice variety on the brown planthopper

This study compares the effects of temperature (constant at 15, 20, 25, 30 and 35 °C) on adult longevity, oviposition, and nymph development of the brown planthopper, Nilaparvata lugens, on susceptible and resistant rice varieties. The resistant variety contained the BPH32 gene. In our experiments, nymphs failed to develop to adults at 15, 20 and 35 °C on either variety. Host resistance had its greatest effect in reducing adult survival at 20–25 °C and its greatest effect in reducing nymph weight gain at 25 °C. This corresponded with optimal temperatures for adult survival (20–25 °C) and nymph development (25–30 °C). At 25 and 30 °C, adult females achieved up to three oviposition cycles on the susceptible variety, but only one cycle on the resistant variety. Maximum egg-laying occurred at 30 °C due to larger numbers of egg batches produced during the first oviposition cycle on both the susceptible and resistant varieties, and larger batches during the second and third oviposition cycles on the susceptible variety; however, resistance had its greatest effect in reducing fecundity at 25 °C. This revealed a mismatch between the optimal temperatures for resistance and for egg production in immigrating females. Increasing global temperatures could reduce the effectiveness of anti-herbivore resistance in rice and other crops where such mismatches occur.

Deficiency of mitochondrial outer membrane protein 64 confers rice resistance to both piercing-sucking and chewing insects in rice

The brown planthopper (BPH) and striped stem borer (SSB) are the most devastating insect pests in rice (Oryza sativa) producing areas. Screening for endogenous resistant genes is the most practical strategy for rice insect-resistance breeding. Forty-five mutants showing high resistance against BPH were identified in a rice T-DNA insertion population (11,000 putative homozygous lines) after 4 years of large-scale field BPH-resistance phenotype screening. Detailed analysis showed that deficiency of rice mitochondrial outer membrane protein 64 (OM64) gene resulted in increased resistance to BPH. Mitochondrial outer membrane protein 64 protein is located in the outer mitochondrial membrane by subcellular localization and its deficiency constitutively activated hydrogen peroxide (H₂ O₂ ) signaling, which stimulated antibiosis and tolerance to BPH. The om64 mutant also showed enhanced resistance to SSB, a chewing insect, which was due to promotion of Jasmonic acid biosynthesis and related responses. Importantly, om64 plants presented no significant changes in rice yield-related characters. This study confirmed OM64 as a negative regulator of rice herbivore resistance through regulating H₂ O₂ production. Mitochondrial outer membrane protein 64 is a potentially efficient candidate to improve BPH and SSB resistance through gene deletion. Why the om64 mutant was resistant to both piercing-sucking and chewing insects via a gene deficiency in mitochondria is discussed.