Background Rice is staple food for over two billion people. Planthoppers like BPH and WBPH occur together in most of rice growing regions across Asia and cause extensive yield loss by feeding and transmission of disease-causing viruses. Chemical control of the pest is expensive and ecologically disastrous; breeding resistant varieties is an acceptable option. But most of such efforts are focused on BPH with an assumption that these varieties will also be effective against WBPH. No critical studies are available to understand rice resistance, common or otherwise, against these two planthoppers. Results Our studies aimed to understand the defense mechanisms in rice line RP2068 against BPH and WBPH through RNA sequencing analysis of a RIL line TR3RR derived from the cross TN1 (susceptible) and RP2068 (resistant) after infestation with BPH or WBPH. Results revealed higher number of differentially expressed genes (DEGs) in BPH infested plants than in WBPH infested plants when compared with the uninfested plants. These DEGs could be grouped into UPUP, DNDN, UPDN and DNUP groups based on whether the DEGs were up (UP) or down (DN) regulated against BPH and WBPH, respectively. Gene ontology analysis, specially of members of the last two groups, revealed differences in plant response to the two planthoppers. Abundance of miRNAs and detection of their target genes also indicated that separate sets of genes were suppressed or induced against BPH and WBPH. These results were validated through the analysis of expression of 27 genes through semi-quantitative and quantitative real-time RT-PCR using a set of five RILs that were genetically identical but with different reaction against the two planthoppers. Coupled with data obtained through pathway analysis involving these 27 genes, expression studies revealed common and differential response of rice RP2068 against BPH and WBPH. Trehalose biosynthesis, proline transport, methylation were key pathways commonly upregulated; glucosinolate biosynthesis, response to oxidative stress, proteolysis, cytokinesis pathways were commonly down regulated; photosynthesis, regulation of transcription, expression and transport of peptides and defense related pathways were exclusively upregulated against WBPH; MYB transcription factor mediated defense induction was exclusive to BPH. Conclusion Rice defense against the two sympatric planthoppers: BPH and WBPH has distinct features in RP2068. Hence, a conscious combination of resistance to these two pests is essential for effective field management.
The Asian rice gall midge (ARGM), Orseolia oryzae is an important insect pest causing an annual yield loss of about US$ 80 million in India. Till now 11 R genes and seven biotypes of the pest have been characterized and reported. The indica rice variety Aganni, a landrace from the state of Kerala, is known to carry the gall midge resistance gene Gm8 with HR-type of resistance. This gene has been fine mapped within 0.43 Mb region with the flanking markers RM22685 and RM22709. We identified 63 possible candidate genes through in silico analysis in the reference Nipponbare rice genome between 7.5 and 9.5 Mb region. One of the markers targeting the proline rich protein (PRP) gene (LOC_Os08g15080) showed polymorphism between the parents and also exhibited complete co-segregation with the trait in 426 F RIL populations. Functional validation of this gene through RT-PCR in contrasting parents and Pre-NILs (near isogenic lines) revealed that this is an early responsive gene with rapid induction at 24 h after gall midge infestation (hai) followed by subsequent reduction in the expression levels at late hours. Validation of this gene in five gall midge resistant rice varieties carrying different resistance genes revealed that the induction was unique to Aganni rice carrying Gm8 gene. Further, cloning and sequencing of the alleles of this gene including promoter region from TN1 (susceptible parent) and Aganni (resistant parent) revealed 153 nucleotide substitution, four amino acid substitutions and three mutations at putative cis-acting elements in TN1 when compared to Aganni. In addition, we also developed a functional marker (PRP-del) for detection of the gene for use in marker-assisted introgression of Gm8.
The brown planthopper (BPH; Nilaparvata lugens) is one of India’s most destructive pests of rice. BPH, a monophagous migratory insect, reported from all major rice-growing ecosystems of the country, is capable of traversing large distances and causing massive crop loss. A crucial step for developing viable management strategies is understanding its population dynamics. Very few reliable markers are currently available to screen BPH populations for their diversity. In the current investigation, we developed a combinatorial approach using the polymorphism present within the mitochondrial Control Region of BPH and in the nuclear genome (genomic simple sequence repeats; gSSRs) to unravel the diversity present in BPH populations collected from various rice-growing regions of India. Using two specific primer pairs, the complete Control Region (1112 to 2612 bp) was PCR amplified as two overlapping fragments, cloned and sequenced from BPH individuals representing nine different populations. Results revealed extensive polymorphism within this region due to a variable number of tandem repeats. The three selected gSSR markers also exhibited population-specific amplification patterns. Overall genetic diversity between the nine populations was high (>5%). Further, in silico double-digestion of the consensus sequences of the Control Region, with HpyCH4IV and Tsp45I restriction enzymes, revealed unique restriction fragment length polymorphisms (digital-RFLPs; dRFLPs) that differentiated all the nine BPH populations. To the best of our knowledge, this is the first report of markers developed from the Control Region of the BPH mitogenome that can differentiate populations. Eventually, such reliable and rapid marker-based identification of BPH populations will pave the way for an efficient pest management strategy.
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