Dissecting genomic regions and underlying sheath blight resistance traits in rice (Oryza sativa L.) using a genome-wide association study
The productivity of rice is greatly affected by the infection of the plant pathogenic fungus Rhizoctonia solani, which causes a significant grain yield reduction globally. There exist a limited number of rice accessions that are available to develop sheath blight resistance (ShB). Our objective was...
| Autores principales: | , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Wiley
2023
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| Acceso en línea: | https://hdl.handle.net/10568/163884 |
| _version_ | 1855527790198128640 |
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| author | Naveenkumar, R. Anandan, Annamalai Prabhukarthikeyan, Seenichamy Rathinam Mahender, Anumalla Sangeetha, Ganesan Vaish, Shyam Saran Singh, Pawan Kumar Hussain, Waseem Ali, Jauhar |
| author_browse | Ali, Jauhar Anandan, Annamalai Hussain, Waseem Mahender, Anumalla Naveenkumar, R. Prabhukarthikeyan, Seenichamy Rathinam Sangeetha, Ganesan Singh, Pawan Kumar Vaish, Shyam Saran |
| author_facet | Naveenkumar, R. Anandan, Annamalai Prabhukarthikeyan, Seenichamy Rathinam Mahender, Anumalla Sangeetha, Ganesan Vaish, Shyam Saran Singh, Pawan Kumar Hussain, Waseem Ali, Jauhar |
| author_sort | Naveenkumar, R. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | The productivity of rice is greatly affected by the infection of the plant pathogenic fungus Rhizoctonia solani, which causes a significant grain yield reduction globally. There exist a limited number of rice accessions that are available to develop sheath blight resistance (ShB). Our objective was to identify a good source of the ShB resistance, understand the heritability, and trait interactions, and identify the genomic regions for ShB resistance traits by genome‐wide association studies (GWAS). In the present study, a set of 330 traditional landraces and improved rice varieties were evaluated for ShB resistance and created a core panel of 192 accessions used in the GWAS. This panel provides a more considerable amount of genetic variance and found a significant phenotypic variation among the panel of rice accessions for all the agro‐morphological and disease‐resistance traits over the seasons. The infection rate of ShB and disease reaction were calculated as percent disease index (PDI) and area under the disease progress curve (AUDPC). The correlation analysis showed a significant positive association between PDIs and AUPDC and a negative association between PDI and plant height, flag leaf length, and grain yield. The panel was genotyped with 133 SSR microsatellite markers, resulting in a genome coverage of 314.83 Mb, and the average distance between markers is 2.53 Mb. By employing GLM and MLM (Q + K) models, 30 marker–trait associations (MTAs) were identified with targeted traits over the seasons. Among these QTLs, eight were found to be novel and located on 2, 4, 8, 10, and 12 chromosomes, which explained the phenotypic variation ranging from 5% to 15%. With the GWAS approach, six candidate genes were identified. Os05t0566400, Os08t0155900, and Os09t0567300 were found to be associated with defense mechanisms against ShB. These findings provided insights into the novel donors of IC283139, IC 277248, Sivappuchithirai Kar, and Bowalia. The promising genomic regions on 10 of 12 chromosomes associated with ShB would be useful in developing rice varieties with durable disease resistance. |
| format | Journal Article |
| id | CGSpace163884 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Wiley |
| publisherStr | Wiley |
| record_format | dspace |
| spelling | CGSpace1638842025-05-14T10:24:13Z Dissecting genomic regions and underlying sheath blight resistance traits in rice (Oryza sativa L.) using a genome-wide association study Naveenkumar, R. Anandan, Annamalai Prabhukarthikeyan, Seenichamy Rathinam Mahender, Anumalla Sangeetha, Ganesan Vaish, Shyam Saran Singh, Pawan Kumar Hussain, Waseem Ali, Jauhar The productivity of rice is greatly affected by the infection of the plant pathogenic fungus Rhizoctonia solani, which causes a significant grain yield reduction globally. There exist a limited number of rice accessions that are available to develop sheath blight resistance (ShB). Our objective was to identify a good source of the ShB resistance, understand the heritability, and trait interactions, and identify the genomic regions for ShB resistance traits by genome‐wide association studies (GWAS). In the present study, a set of 330 traditional landraces and improved rice varieties were evaluated for ShB resistance and created a core panel of 192 accessions used in the GWAS. This panel provides a more considerable amount of genetic variance and found a significant phenotypic variation among the panel of rice accessions for all the agro‐morphological and disease‐resistance traits over the seasons. The infection rate of ShB and disease reaction were calculated as percent disease index (PDI) and area under the disease progress curve (AUDPC). The correlation analysis showed a significant positive association between PDIs and AUPDC and a negative association between PDI and plant height, flag leaf length, and grain yield. The panel was genotyped with 133 SSR microsatellite markers, resulting in a genome coverage of 314.83 Mb, and the average distance between markers is 2.53 Mb. By employing GLM and MLM (Q + K) models, 30 marker–trait associations (MTAs) were identified with targeted traits over the seasons. Among these QTLs, eight were found to be novel and located on 2, 4, 8, 10, and 12 chromosomes, which explained the phenotypic variation ranging from 5% to 15%. With the GWAS approach, six candidate genes were identified. Os05t0566400, Os08t0155900, and Os09t0567300 were found to be associated with defense mechanisms against ShB. These findings provided insights into the novel donors of IC283139, IC 277248, Sivappuchithirai Kar, and Bowalia. The promising genomic regions on 10 of 12 chromosomes associated with ShB would be useful in developing rice varieties with durable disease resistance. 2023-11 2024-12-19T12:53:10Z 2024-12-19T12:53:10Z Journal Article https://hdl.handle.net/10568/163884 en Open Access Wiley Naveenkumar, R; Anandan, Annamalai; Prabhukarthikeyan, Seenichamy Rathinam; Mahender, Anumalla; Sangeetha, Ganesan; Vaish, Shyam Saran; Singh, Pawan Kumar; Hussain, Waseem and Ali, Jauhar. 2023. Dissecting genomic regions and underlying sheath blight resistance traits in rice (Oryza sativa L.) using a genome-wide association study. Plant Direct, Volume 7, no. 11 |
| spellingShingle | Naveenkumar, R. Anandan, Annamalai Prabhukarthikeyan, Seenichamy Rathinam Mahender, Anumalla Sangeetha, Ganesan Vaish, Shyam Saran Singh, Pawan Kumar Hussain, Waseem Ali, Jauhar Dissecting genomic regions and underlying sheath blight resistance traits in rice (Oryza sativa L.) using a genome-wide association study |
| title | Dissecting genomic regions and underlying sheath blight resistance traits in rice (Oryza sativa L.) using a genome-wide association study |
| title_full | Dissecting genomic regions and underlying sheath blight resistance traits in rice (Oryza sativa L.) using a genome-wide association study |
| title_fullStr | Dissecting genomic regions and underlying sheath blight resistance traits in rice (Oryza sativa L.) using a genome-wide association study |
| title_full_unstemmed | Dissecting genomic regions and underlying sheath blight resistance traits in rice (Oryza sativa L.) using a genome-wide association study |
| title_short | Dissecting genomic regions and underlying sheath blight resistance traits in rice (Oryza sativa L.) using a genome-wide association study |
| title_sort | dissecting genomic regions and underlying sheath blight resistance traits in rice oryza sativa l using a genome wide association study |
| url | https://hdl.handle.net/10568/163884 |
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