Abstract
Key message
By deploying a multi-omics approach, we unraveled the mechanisms that might help rice to combat Yellow Stem Borer infestation, thus providing insights and scope for developing YSB resistant rice varieties.
Abstract
Yellow Stem Borer (YSB), Scirpophaga incertulas (Walker) (Lepidoptera: Crambidae), is a major pest of rice, that can lead to 20–60% loss in rice production. Effective management of YSB infestation is challenged by the non-availability of adequate sources of resistance and poor understanding of resistance mechanisms, thus necessitating studies for generating resources to breed YSB resistant rice and to understand rice-YSB interaction. In this study, by using bulk-segregant analysis in combination with next-generation sequencing, Quantitative Trait Loci (QTL) intervals in five rice chromosomes were mapped that could be associated with YSB resistance at the vegetative phase in a resistant rice line named SM92. Further, multiple SNP markers that showed significant association with YSB resistance in rice chromosomes 1, 5, 10, and 12 were developed. RNA-sequencing of the susceptible and resistant lines revealed several genes present in the candidate QTL intervals to be differentially regulated upon YSB infestation. Comparative transcriptome analysis revealed a putative candidate gene that was predicted to encode an alpha-amylase inhibitor. Analysis of the transcriptome and metabolite profiles further revealed a possible link between phenylpropanoid metabolism and YSB resistance. Taken together, our study provides deeper insights into rice-YSB interaction and enhances the understanding of YSB resistance mechanism. Importantly, a promising breeding line and markers for YSB resistance have been developed that can potentially aid in marker-assisted breeding of YSB resistance among elite rice cultivars.
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Data availability
SM and SM92 parent whole genome sequences are deposited in NCBI-SRA under the accession PRJNA658718. The F2 bulk DNA data are deposited under the accession PRJNA972670. The transcriptome data are deposited in NCBI-Gene Expression Omnibus (GEO) under the accession GSE245213.
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Acknowledgements
This study was supported by grants to MSM, HKP, and RVS from the Council of Scientific and Industrial Research (CSIR), Government of India (MLP0121 Phase-I and Phase-II) and the JC Bose Fellowship of RVS granted by the Science and Engineering Research Board (SERB), Department of Science and Technology, Government of India (SB/S2/JCB-12/2014). We thank Dr. Rajkanwar Nathawat (Current address: Yale University) for her guidance and suggestions on protein structure prediction analysis. We thank the skilled workers at ICAR-IIRR and CSIR-CCMB for their support in field activities and maintenance.
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This study was funded by Council of Scientific and Industrial Research (CSIR), Government of India, New Delhi and the Science and Engineering Research Board (SERB), Department of Science and Technology, Government of India, New Delhi.
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Conceptualization—RVS, MSM, HKP, and PAP. Investigation—GCG (QTL-seq, RNA-seq, metabolomics analyses and KASP genotyping); UB, VB, SB, PAP (studies with YSB larvae, F2 population generation, and screening of rice plants); DR (QTLseq data analysis); PV, NM, KJ, SM, PAP (screening of plants and phenotyping). Assessment and supervision of the work—GSL, SRLV, KMB, MSR, PAP, HKP, MSM, and RVS. Writing of original draft – GCG. Manuscript review and editing—PAP, KMB, HKP, MSM, and RVS. Funding acquisition – MSM, HKP, and RVS.
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Gokulan, C.G., Bangale, U., Balija, V. et al. Multiomics-assisted characterization of rice-Yellow Stem Borer interaction provides genomic and mechanistic insights into stem borer resistance in rice. Theor Appl Genet 137, 122 (2024). https://doi.org/10.1007/s00122-024-04628-7
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DOI: https://doi.org/10.1007/s00122-024-04628-7