Allelic sequence variation in the Sub1A, Sub1B and Sub1C genes among diverse rice cultivars and its association with submergence tolerance
Erratic rainfall leading to flash flooding causes huge yield losses in lowland rice. The traditional varieties and landraces of rice possess variable levels of tolerance to submergence stress, but gene discovery and utilization of these resources has been limited to the Sub1A-1 allele from variety F...
| Autores principales: | , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2020
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| Acceso en línea: | https://hdl.handle.net/10568/164502 |
| _version_ | 1855540089198739456 |
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| author | Singh, Anuradha Singh, Yashi Mahato, Ajay K. Jayaswal, Pawan K. Singh, Sangeeta Singh, Renu Yadav, Neera Singh, A.K. Singh, P.K. Singh, Rakesh Kumar, Rajesh Septiningsih, Endang M. Balyan, H.S. Singh, Nagendra K. Rai, Vandna |
| author_browse | Balyan, H.S. Jayaswal, Pawan K. Kumar, Rajesh Mahato, Ajay K. Rai, Vandna Septiningsih, Endang M. Singh, A.K. Singh, Anuradha Singh, Nagendra K. Singh, P.K. Singh, Rakesh Singh, Renu Singh, Sangeeta Singh, Yashi Yadav, Neera |
| author_facet | Singh, Anuradha Singh, Yashi Mahato, Ajay K. Jayaswal, Pawan K. Singh, Sangeeta Singh, Renu Yadav, Neera Singh, A.K. Singh, P.K. Singh, Rakesh Kumar, Rajesh Septiningsih, Endang M. Balyan, H.S. Singh, Nagendra K. Rai, Vandna |
| author_sort | Singh, Anuradha |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Erratic rainfall leading to flash flooding causes huge yield losses in lowland rice. The traditional varieties and landraces of rice possess variable levels of tolerance to submergence stress, but gene discovery and utilization of these resources has been limited to the Sub1A-1 allele from variety FR13A. Therefore, we analysed the allelic sequence variation in three Sub1 genes in a panel of 179 rice genotypes and its association with submergence tolerance. Population structure and diversity analysis based on a 36-plex genome wide genic-SNP assay grouped these genotypes into two major categories representing Indica and Japonica cultivar groups with further sub-groupings into Indica, Aus, Deepwater and Aromatic-Japonica cultivars. Targetted re-sequencing of the Sub1A, Sub1B and Sub1C genes identfied 7, 7 and 38 SNPs making 8, 9 and 67 SNP haplotypes, respectively. Haplotype networks and phylogenic analysis revealed evolution of Sub1B and Sub1A genes by tandem duplication and divergence of the ancestral Sub1C gene in that order. The alleles of Sub1 genes in tolerant reference variety FR13A seem to have evolved most recently. However, no consistent association could be found between the Sub1 allelic variation and submergence tolerance probably due to low minor allele frequencies and presence of exceptions to the known Sub1A-1 association in the genotype panel. We identified 18 cultivars with non-Sub1A-1 source of submergence tolerance which after further mapping and validation in bi-parental populations will be useful for development of superior flood tolerant rice cultivars. |
| format | Journal Article |
| id | CGSpace164502 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1645022025-05-14T10:39:59Z Allelic sequence variation in the Sub1A, Sub1B and Sub1C genes among diverse rice cultivars and its association with submergence tolerance Singh, Anuradha Singh, Yashi Mahato, Ajay K. Jayaswal, Pawan K. Singh, Sangeeta Singh, Renu Yadav, Neera Singh, A.K. Singh, P.K. Singh, Rakesh Kumar, Rajesh Septiningsih, Endang M. Balyan, H.S. Singh, Nagendra K. Rai, Vandna Erratic rainfall leading to flash flooding causes huge yield losses in lowland rice. The traditional varieties and landraces of rice possess variable levels of tolerance to submergence stress, but gene discovery and utilization of these resources has been limited to the Sub1A-1 allele from variety FR13A. Therefore, we analysed the allelic sequence variation in three Sub1 genes in a panel of 179 rice genotypes and its association with submergence tolerance. Population structure and diversity analysis based on a 36-plex genome wide genic-SNP assay grouped these genotypes into two major categories representing Indica and Japonica cultivar groups with further sub-groupings into Indica, Aus, Deepwater and Aromatic-Japonica cultivars. Targetted re-sequencing of the Sub1A, Sub1B and Sub1C genes identfied 7, 7 and 38 SNPs making 8, 9 and 67 SNP haplotypes, respectively. Haplotype networks and phylogenic analysis revealed evolution of Sub1B and Sub1A genes by tandem duplication and divergence of the ancestral Sub1C gene in that order. The alleles of Sub1 genes in tolerant reference variety FR13A seem to have evolved most recently. However, no consistent association could be found between the Sub1 allelic variation and submergence tolerance probably due to low minor allele frequencies and presence of exceptions to the known Sub1A-1 association in the genotype panel. We identified 18 cultivars with non-Sub1A-1 source of submergence tolerance which after further mapping and validation in bi-parental populations will be useful for development of superior flood tolerant rice cultivars. 2020-05-25 2024-12-19T12:53:59Z 2024-12-19T12:53:59Z Journal Article https://hdl.handle.net/10568/164502 en Open Access Springer Singh, Anuradha; Singh, Yashi; Mahato, Ajay K.; Jayaswal, Pawan K.; Singh, Sangeeta; Singh, Renu; Yadav, Neera; Singh, A. K.; Singh, P. K.; Singh, Rakesh; Kumar, Rajesh; Septiningsih, Endang M.; Balyan, H. S.; Singh, Nagendra K. and Rai, Vandna. 2020. Allelic sequence variation in the Sub1A, Sub1B and Sub1C genes among diverse rice cultivars and its association with submergence tolerance. Sci Rep, Volume 10, no. 1 |
| spellingShingle | Singh, Anuradha Singh, Yashi Mahato, Ajay K. Jayaswal, Pawan K. Singh, Sangeeta Singh, Renu Yadav, Neera Singh, A.K. Singh, P.K. Singh, Rakesh Kumar, Rajesh Septiningsih, Endang M. Balyan, H.S. Singh, Nagendra K. Rai, Vandna Allelic sequence variation in the Sub1A, Sub1B and Sub1C genes among diverse rice cultivars and its association with submergence tolerance |
| title | Allelic sequence variation in the Sub1A, Sub1B and Sub1C genes among diverse rice cultivars and its association with submergence tolerance |
| title_full | Allelic sequence variation in the Sub1A, Sub1B and Sub1C genes among diverse rice cultivars and its association with submergence tolerance |
| title_fullStr | Allelic sequence variation in the Sub1A, Sub1B and Sub1C genes among diverse rice cultivars and its association with submergence tolerance |
| title_full_unstemmed | Allelic sequence variation in the Sub1A, Sub1B and Sub1C genes among diverse rice cultivars and its association with submergence tolerance |
| title_short | Allelic sequence variation in the Sub1A, Sub1B and Sub1C genes among diverse rice cultivars and its association with submergence tolerance |
| title_sort | allelic sequence variation in the sub1a sub1b and sub1c genes among diverse rice cultivars and its association with submergence tolerance |
| url | https://hdl.handle.net/10568/164502 |
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