Identification of novel Single Nucleotide Polymorphisms (SNPs) associated with brown planthopper, Nilaparvata lugens (Stal.) resistance in rice (Oryza sativa L.)
The brown planthopper (BPH) is one of the most predominant rice insect pests in Asia. Changes in the virulence pattern of BPHacross the regions and breakdown of resistance in many released resistant cultivars warrant identification of novel and diverse germplasm resources that can be deployed for de...
| Main Authors: | , , , , , , , , , , , , , |
|---|---|
| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Horizon E-Publishing Group
2025
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/179646 |
| _version_ | 1855516583081803776 |
|---|---|
| author | Varma, N. R. G. Mohan, Y. Chandra Babu, T. Kiran Singh, T. Virender Jeet Ramakrishna, A. Harikrishna, J. Kumar, Aravind Singh, Vikas Kumar Singh, Uma Maheshwar Kalia, Sanjay Sinha, Pallavi Krishna, T. S. Niranjani, G. Jagadeeshwar, R. |
| author_browse | Babu, T. Kiran Harikrishna, J. Jagadeeshwar, R. Kalia, Sanjay Krishna, T. S. Kumar, Aravind Mohan, Y. Chandra Niranjani, G. Ramakrishna, A. Singh, T. Virender Jeet Singh, Uma Maheshwar Singh, Vikas Kumar Sinha, Pallavi Varma, N. R. G. |
| author_facet | Varma, N. R. G. Mohan, Y. Chandra Babu, T. Kiran Singh, T. Virender Jeet Ramakrishna, A. Harikrishna, J. Kumar, Aravind Singh, Vikas Kumar Singh, Uma Maheshwar Kalia, Sanjay Sinha, Pallavi Krishna, T. S. Niranjani, G. Jagadeeshwar, R. |
| author_sort | Varma, N. R. G. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | The brown planthopper (BPH) is one of the most predominant rice insect pests in Asia. Changes in the virulence pattern of BPHacross the regions and breakdown of resistance in many released resistant cultivars warrant identification of novel and diverse germplasm resources that can be deployed for developing new rice varieties with a broader genetic base. Accordingly, the field phenotypic screening was conducted over two years during kharif 2020 and 2021 using 300 rice genotypes (selected from 3 K subset of BPH panel) along with eight checks in an augmented block design to identify the BPH-resistant donor lines. Two rice genotypes viz., IRGC 126266 and IRGC 128206 exhibited consistent resistant reaction during both years. Mechanism of resistance studies (conducted duringrabi 2021-2022) revealed that, among the two promising germplasm, IRGC 126266 exhibited all the three mechanisms of resistance by recording lower honey dew excretion (72.5 mm2), lower nymphal survival rate (47.5 %), longer nymphal development period (17.20 days), lowest growth index (2.4) and took more days to wilt (27.2) compared to the susceptible check, TN1. Genome Wide Association Studies (GWAS) analysis was conducted in the 3K subset of BPH panel using four single locus models to identify the SNPs associated with BPH resistance. Significant SNPs were identified in proximity with several BPH resistance genes viz., Bph33(t), Bph13(t), Bph6, Bph34, Bph3, Bph4, Bph25, Bph29, Bph32, Bph28(t), Bph2, Bph26, Bph7, Bph9, Bph18(t) and Bph21(t). Candidate gene analysis study revealed that 9 Quantitative Trait Nucleotides (QTNs) associated with stress tolerance genes played a significant role in BPH resistance. |
| format | Journal Article |
| id | CGSpace179646 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Horizon E-Publishing Group |
| publisherStr | Horizon E-Publishing Group |
| record_format | dspace |
| spelling | CGSpace1796462026-01-12T02:01:54Z Identification of novel Single Nucleotide Polymorphisms (SNPs) associated with brown planthopper, Nilaparvata lugens (Stal.) resistance in rice (Oryza sativa L.) Varma, N. R. G. Mohan, Y. Chandra Babu, T. Kiran Singh, T. Virender Jeet Ramakrishna, A. Harikrishna, J. Kumar, Aravind Singh, Vikas Kumar Singh, Uma Maheshwar Kalia, Sanjay Sinha, Pallavi Krishna, T. S. Niranjani, G. Jagadeeshwar, R. Nilaparvata lugens single nucleotide polymorphisms genome-wide association studies rice defence mechanisms field experimentation genes Hemiptera The brown planthopper (BPH) is one of the most predominant rice insect pests in Asia. Changes in the virulence pattern of BPHacross the regions and breakdown of resistance in many released resistant cultivars warrant identification of novel and diverse germplasm resources that can be deployed for developing new rice varieties with a broader genetic base. Accordingly, the field phenotypic screening was conducted over two years during kharif 2020 and 2021 using 300 rice genotypes (selected from 3 K subset of BPH panel) along with eight checks in an augmented block design to identify the BPH-resistant donor lines. Two rice genotypes viz., IRGC 126266 and IRGC 128206 exhibited consistent resistant reaction during both years. Mechanism of resistance studies (conducted duringrabi 2021-2022) revealed that, among the two promising germplasm, IRGC 126266 exhibited all the three mechanisms of resistance by recording lower honey dew excretion (72.5 mm2), lower nymphal survival rate (47.5 %), longer nymphal development period (17.20 days), lowest growth index (2.4) and took more days to wilt (27.2) compared to the susceptible check, TN1. Genome Wide Association Studies (GWAS) analysis was conducted in the 3K subset of BPH panel using four single locus models to identify the SNPs associated with BPH resistance. Significant SNPs were identified in proximity with several BPH resistance genes viz., Bph33(t), Bph13(t), Bph6, Bph34, Bph3, Bph4, Bph25, Bph29, Bph32, Bph28(t), Bph2, Bph26, Bph7, Bph9, Bph18(t) and Bph21(t). Candidate gene analysis study revealed that 9 Quantitative Trait Nucleotides (QTNs) associated with stress tolerance genes played a significant role in BPH resistance. 2025-08-15 2026-01-12T01:01:20Z 2026-01-12T01:01:20Z Journal Article https://hdl.handle.net/10568/179646 en Open Access application/pdf Horizon E-Publishing Group Varma, N. R. G.,Y Chandra Mohan, T Kiran Babu, T Virender Jeet Singh, A Ramakrishna, J Harikrishna, Aravind Kumar, Vikas Kumar Singh, Uma Maheshwar Singh, Sanjay Kalia, Pallavi Sinha, T S Krishna, G Niranjani and R Jagadeeshwar (2025). Identification of novel Single Nucleotide Polymorphisms (SNPs) associated with brownplanthopper, Nilaparvata lugens(Stal.) resistance in rice (Oryza sativa L.). Plant Science Today 12, no. 3: 1-11. |
| spellingShingle | Nilaparvata lugens single nucleotide polymorphisms genome-wide association studies rice defence mechanisms field experimentation genes Hemiptera Varma, N. R. G. Mohan, Y. Chandra Babu, T. Kiran Singh, T. Virender Jeet Ramakrishna, A. Harikrishna, J. Kumar, Aravind Singh, Vikas Kumar Singh, Uma Maheshwar Kalia, Sanjay Sinha, Pallavi Krishna, T. S. Niranjani, G. Jagadeeshwar, R. Identification of novel Single Nucleotide Polymorphisms (SNPs) associated with brown planthopper, Nilaparvata lugens (Stal.) resistance in rice (Oryza sativa L.) |
| title | Identification of novel Single Nucleotide Polymorphisms (SNPs) associated with brown planthopper, Nilaparvata lugens (Stal.) resistance in rice (Oryza sativa L.) |
| title_full | Identification of novel Single Nucleotide Polymorphisms (SNPs) associated with brown planthopper, Nilaparvata lugens (Stal.) resistance in rice (Oryza sativa L.) |
| title_fullStr | Identification of novel Single Nucleotide Polymorphisms (SNPs) associated with brown planthopper, Nilaparvata lugens (Stal.) resistance in rice (Oryza sativa L.) |
| title_full_unstemmed | Identification of novel Single Nucleotide Polymorphisms (SNPs) associated with brown planthopper, Nilaparvata lugens (Stal.) resistance in rice (Oryza sativa L.) |
| title_short | Identification of novel Single Nucleotide Polymorphisms (SNPs) associated with brown planthopper, Nilaparvata lugens (Stal.) resistance in rice (Oryza sativa L.) |
| title_sort | identification of novel single nucleotide polymorphisms snps associated with brown planthopper nilaparvata lugens stal resistance in rice oryza sativa l |
| topic | Nilaparvata lugens single nucleotide polymorphisms genome-wide association studies rice defence mechanisms field experimentation genes Hemiptera |
| url | https://hdl.handle.net/10568/179646 |
| work_keys_str_mv | AT varmanrg identificationofnovelsinglenucleotidepolymorphismssnpsassociatedwithbrownplanthoppernilaparvatalugensstalresistanceinriceoryzasatival AT mohanychandra identificationofnovelsinglenucleotidepolymorphismssnpsassociatedwithbrownplanthoppernilaparvatalugensstalresistanceinriceoryzasatival AT babutkiran identificationofnovelsinglenucleotidepolymorphismssnpsassociatedwithbrownplanthoppernilaparvatalugensstalresistanceinriceoryzasatival AT singhtvirenderjeet identificationofnovelsinglenucleotidepolymorphismssnpsassociatedwithbrownplanthoppernilaparvatalugensstalresistanceinriceoryzasatival AT ramakrishnaa identificationofnovelsinglenucleotidepolymorphismssnpsassociatedwithbrownplanthoppernilaparvatalugensstalresistanceinriceoryzasatival AT harikrishnaj identificationofnovelsinglenucleotidepolymorphismssnpsassociatedwithbrownplanthoppernilaparvatalugensstalresistanceinriceoryzasatival AT kumararavind identificationofnovelsinglenucleotidepolymorphismssnpsassociatedwithbrownplanthoppernilaparvatalugensstalresistanceinriceoryzasatival AT singhvikaskumar identificationofnovelsinglenucleotidepolymorphismssnpsassociatedwithbrownplanthoppernilaparvatalugensstalresistanceinriceoryzasatival AT singhumamaheshwar identificationofnovelsinglenucleotidepolymorphismssnpsassociatedwithbrownplanthoppernilaparvatalugensstalresistanceinriceoryzasatival AT kaliasanjay identificationofnovelsinglenucleotidepolymorphismssnpsassociatedwithbrownplanthoppernilaparvatalugensstalresistanceinriceoryzasatival AT sinhapallavi identificationofnovelsinglenucleotidepolymorphismssnpsassociatedwithbrownplanthoppernilaparvatalugensstalresistanceinriceoryzasatival AT krishnats identificationofnovelsinglenucleotidepolymorphismssnpsassociatedwithbrownplanthoppernilaparvatalugensstalresistanceinriceoryzasatival AT niranjanig identificationofnovelsinglenucleotidepolymorphismssnpsassociatedwithbrownplanthoppernilaparvatalugensstalresistanceinriceoryzasatival AT jagadeeshwarr identificationofnovelsinglenucleotidepolymorphismssnpsassociatedwithbrownplanthoppernilaparvatalugensstalresistanceinriceoryzasatival |