Mapping of a Novel Quantitative Trait Locus Conferring Bacterial Blight Resistance in the Indigenous Upland Rice Variety ULR207 Using the QTL–Seq Approach
Bacterial blight (BB) disease is a serious stress that affects up to 80% of rice yield. Utilizing an elite resistant variety was previously thought to be an alternative way to control disease outbreaks. The indigenous upland rice variety ULR207 is a high-potential donor for the BB resistance breedin...
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2025-07-01
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| author | Tanawat Wongsa Sompong Chankaew Tidarat Monkham Meechai Siangliw Niranjan Baisakh Jirawat Sanitchon |
| author_facet | Tanawat Wongsa Sompong Chankaew Tidarat Monkham Meechai Siangliw Niranjan Baisakh Jirawat Sanitchon |
| author_sort | Tanawat Wongsa |
| collection | DOAJ |
| description | Bacterial blight (BB) disease is a serious stress that affects up to 80% of rice yield. Utilizing an elite resistant variety was previously thought to be an alternative way to control disease outbreaks. The indigenous upland rice variety ULR207 is a high-potential donor for the BB resistance breeding program. However, the quantitative trait loci (QTLs) associated with bacterial blight resistance in this variety have not yet been discovered. Therefore, QTLs associated with BB resistance need to be identified. In this study, we identified the QTLs associated with BB resistance in the F<sub>2:3</sub> population crossed between the BB resistance variety ULR207 and Maled Phai, as well as a susceptible variety, via QTL-seq analysis and bulk-segregant analysis. We found a new QTL-associated BB resistance locus (<i>qBBchr8</i>) mapped on chromosome 8. Five positions were candidates, including <i>Os08g0110700</i>, <i>Os08g0115200</i>, <i>Os08g0131300</i>, <i>Os08g0139500</i>, and <i>Os08g0163900</i>. Afterwards, Kompetitive Allele-Specific PCR (KASP) markers specific to the SNP variant and the position of each gene were designed. These markers, associated with the disease lesion length phenotype, were validated with another 178 individual plants of the F<sub>2</sub> population via single-marker analysis. This analysis revealed that the position <i>Os08g0110700</i> was the strongest locus, with a PVE of 15.00%. The results suggest that this KASP SNP marker could be used to improve elite rice for BB resistance. |
| format | Article |
| id | doaj-art-c92bda714292463a86e46c68e9e99bc4 |
| institution | DOAJ |
| issn | 2223-7747 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | MDPI AG |
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| series | Plants |
| spelling | doaj-art-c92bda714292463a86e46c68e9e99bc42025-08-20T02:47:21ZengMDPI AGPlants2223-77472025-07-011414211310.3390/plants14142113Mapping of a Novel Quantitative Trait Locus Conferring Bacterial Blight Resistance in the Indigenous Upland Rice Variety ULR207 Using the QTL–Seq ApproachTanawat Wongsa0Sompong Chankaew1Tidarat Monkham2Meechai Siangliw3Niranjan Baisakh4Jirawat Sanitchon5Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, ThailandDepartment of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, ThailandDepartment of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, ThailandNational Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology, Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, ThailandSchool of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USADepartment of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, ThailandBacterial blight (BB) disease is a serious stress that affects up to 80% of rice yield. Utilizing an elite resistant variety was previously thought to be an alternative way to control disease outbreaks. The indigenous upland rice variety ULR207 is a high-potential donor for the BB resistance breeding program. However, the quantitative trait loci (QTLs) associated with bacterial blight resistance in this variety have not yet been discovered. Therefore, QTLs associated with BB resistance need to be identified. In this study, we identified the QTLs associated with BB resistance in the F<sub>2:3</sub> population crossed between the BB resistance variety ULR207 and Maled Phai, as well as a susceptible variety, via QTL-seq analysis and bulk-segregant analysis. We found a new QTL-associated BB resistance locus (<i>qBBchr8</i>) mapped on chromosome 8. Five positions were candidates, including <i>Os08g0110700</i>, <i>Os08g0115200</i>, <i>Os08g0131300</i>, <i>Os08g0139500</i>, and <i>Os08g0163900</i>. Afterwards, Kompetitive Allele-Specific PCR (KASP) markers specific to the SNP variant and the position of each gene were designed. These markers, associated with the disease lesion length phenotype, were validated with another 178 individual plants of the F<sub>2</sub> population via single-marker analysis. This analysis revealed that the position <i>Os08g0110700</i> was the strongest locus, with a PVE of 15.00%. The results suggest that this KASP SNP marker could be used to improve elite rice for BB resistance.https://www.mdpi.com/2223-7747/14/14/2113KASP markerSNP indexR genebulk segregant analysisrice germplasm |
| spellingShingle | Tanawat Wongsa Sompong Chankaew Tidarat Monkham Meechai Siangliw Niranjan Baisakh Jirawat Sanitchon Mapping of a Novel Quantitative Trait Locus Conferring Bacterial Blight Resistance in the Indigenous Upland Rice Variety ULR207 Using the QTL–Seq Approach Plants KASP marker SNP index R gene bulk segregant analysis rice germplasm |
| title | Mapping of a Novel Quantitative Trait Locus Conferring Bacterial Blight Resistance in the Indigenous Upland Rice Variety ULR207 Using the QTL–Seq Approach |
| title_full | Mapping of a Novel Quantitative Trait Locus Conferring Bacterial Blight Resistance in the Indigenous Upland Rice Variety ULR207 Using the QTL–Seq Approach |
| title_fullStr | Mapping of a Novel Quantitative Trait Locus Conferring Bacterial Blight Resistance in the Indigenous Upland Rice Variety ULR207 Using the QTL–Seq Approach |
| title_full_unstemmed | Mapping of a Novel Quantitative Trait Locus Conferring Bacterial Blight Resistance in the Indigenous Upland Rice Variety ULR207 Using the QTL–Seq Approach |
| title_short | Mapping of a Novel Quantitative Trait Locus Conferring Bacterial Blight Resistance in the Indigenous Upland Rice Variety ULR207 Using the QTL–Seq Approach |
| title_sort | mapping of a novel quantitative trait locus conferring bacterial blight resistance in the indigenous upland rice variety ulr207 using the qtl seq approach |
| topic | KASP marker SNP index R gene bulk segregant analysis rice germplasm |
| url | https://www.mdpi.com/2223-7747/14/14/2113 |
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