A combination of joint linkage and genome-wide association study reveals putative candidate genes associated with resistance to northern corn leaf blight in tropical maize
Northern corn leaf blight (NCLB), caused by Setosphaeria turcica, is a major fungal disease affecting maize production in sub-Saharan Africa. Utilizing host plant resistance to mitigate yield losses associated with NCLB can serve as a cost-effective strategy. In this study, we conducted a high-resol...
| Autores principales: | , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Frontiers Media
2024
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/169952 |
| _version_ | 1855521789733502976 |
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| author | Ndlovu, Noel Gowda, Manje Beyene, Yoseph Das, Biswanath Mahabaleswara, Suresh L. Makumbi, Dan Ogugo, Veronica Burgueño, Juan Crossa, Jose Spillane, Charles McKeown, Peter C. Brychkova, Galina Prasanna, Boddupalli M. |
| author_browse | Beyene, Yoseph Brychkova, Galina Burgueño, Juan Crossa, Jose Das, Biswanath Gowda, Manje Mahabaleswara, Suresh L. Makumbi, Dan McKeown, Peter C. Ndlovu, Noel Ogugo, Veronica Prasanna, Boddupalli M. Spillane, Charles |
| author_facet | Ndlovu, Noel Gowda, Manje Beyene, Yoseph Das, Biswanath Mahabaleswara, Suresh L. Makumbi, Dan Ogugo, Veronica Burgueño, Juan Crossa, Jose Spillane, Charles McKeown, Peter C. Brychkova, Galina Prasanna, Boddupalli M. |
| author_sort | Ndlovu, Noel |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Northern corn leaf blight (NCLB), caused by Setosphaeria turcica, is a major fungal disease affecting maize production in sub-Saharan Africa. Utilizing host plant resistance to mitigate yield losses associated with NCLB can serve as a cost-effective strategy. In this study, we conducted a high-resolution genome-wide association study (GWAS) in an association mapping panel and linkage mapping with three doubled haploid (DH) and three F3 populations of tropical maize. These populations were phenotyped for NCLB resistance across six hotspot environments in Kenya. Across environments and genotypes, NCLB scores ranged from 2.12 to 5.17 (on a scale of 1–9). NCLB disease severity scores exhibited significant genotypic variance and moderate-to-high heritability. From the six biparental populations, 23 quantitative trait loci (QTLs) were identified, each explaining between 2.7% and 15.8% of the observed phenotypic variance. Collectively, the detected QTLs explained 34.28%, 51.37%, 41.12%, 12.46%, 12.11%, and 14.66% of the total phenotypic variance in DH populations 1, 2, and 3 and F3 populations 4, 5, and 6, respectively. GWAS, using 337,110 high-quality single nucleotide polymorphisms (SNPs), identified 15 marker–trait associations and several putative candidate genes linked to NCLB resistance in maize. Joint linkage association mapping (JLAM) identified 37 QTLs for NCLB resistance. Using linkage mapping, JLAM, and GWAS, several QTLs were identified within the genomic region spanning 4 to 15 Mbp on chromosome 2. This genomic region represents a promising target for enhancing NCLB resistance via marker-assisted breeding. Genome-wide predictions revealed moderate correlations with mean values of 0.45, 0.44, 0.55, and 0.42 for within GWAS panel, DH pop1, DH pop2, and DH pop3, respectively. Prediction by incorporating marker-by-environment interactions did not show much improvement. Overall, our findings indicate that NCLB resistance is quantitative in nature and is controlled by few major-effect and many minor-effect QTLs. We conclude that genomic regions consistently detected across mapping approaches and populations should be prioritized for improving NCLB resistance, while genome-wide prediction results can help incorporate both major- and minor-effect genes. This study contributes to a deeper understanding of the genetic and molecular mechanisms driving maize resistance to NCLB. |
| format | Journal Article |
| id | CGSpace169952 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1699522025-12-08T10:29:22Z A combination of joint linkage and genome-wide association study reveals putative candidate genes associated with resistance to northern corn leaf blight in tropical maize Ndlovu, Noel Gowda, Manje Beyene, Yoseph Das, Biswanath Mahabaleswara, Suresh L. Makumbi, Dan Ogugo, Veronica Burgueño, Juan Crossa, Jose Spillane, Charles McKeown, Peter C. Brychkova, Galina Prasanna, Boddupalli M. genome-wide association studies quantitative trait loci mapping marker-assisted selection maize Northern corn leaf blight (NCLB), caused by Setosphaeria turcica, is a major fungal disease affecting maize production in sub-Saharan Africa. Utilizing host plant resistance to mitigate yield losses associated with NCLB can serve as a cost-effective strategy. In this study, we conducted a high-resolution genome-wide association study (GWAS) in an association mapping panel and linkage mapping with three doubled haploid (DH) and three F3 populations of tropical maize. These populations were phenotyped for NCLB resistance across six hotspot environments in Kenya. Across environments and genotypes, NCLB scores ranged from 2.12 to 5.17 (on a scale of 1–9). NCLB disease severity scores exhibited significant genotypic variance and moderate-to-high heritability. From the six biparental populations, 23 quantitative trait loci (QTLs) were identified, each explaining between 2.7% and 15.8% of the observed phenotypic variance. Collectively, the detected QTLs explained 34.28%, 51.37%, 41.12%, 12.46%, 12.11%, and 14.66% of the total phenotypic variance in DH populations 1, 2, and 3 and F3 populations 4, 5, and 6, respectively. GWAS, using 337,110 high-quality single nucleotide polymorphisms (SNPs), identified 15 marker–trait associations and several putative candidate genes linked to NCLB resistance in maize. Joint linkage association mapping (JLAM) identified 37 QTLs for NCLB resistance. Using linkage mapping, JLAM, and GWAS, several QTLs were identified within the genomic region spanning 4 to 15 Mbp on chromosome 2. This genomic region represents a promising target for enhancing NCLB resistance via marker-assisted breeding. Genome-wide predictions revealed moderate correlations with mean values of 0.45, 0.44, 0.55, and 0.42 for within GWAS panel, DH pop1, DH pop2, and DH pop3, respectively. Prediction by incorporating marker-by-environment interactions did not show much improvement. Overall, our findings indicate that NCLB resistance is quantitative in nature and is controlled by few major-effect and many minor-effect QTLs. We conclude that genomic regions consistently detected across mapping approaches and populations should be prioritized for improving NCLB resistance, while genome-wide prediction results can help incorporate both major- and minor-effect genes. This study contributes to a deeper understanding of the genetic and molecular mechanisms driving maize resistance to NCLB. 2024 2025-01-26T02:12:53Z 2025-01-26T02:12:53Z Journal Article https://hdl.handle.net/10568/169952 en Open Access application/pdf Frontiers Media Ndlovu, N., Gowda, M., Beyene, Y., Das, B., Mahabaleswara, S. L., Makumbi, D., Ogugo, V., Burgueno, J., Crossa, J., Spillane, C., McKeown, P. C., Brychkova, G., & Prasanna, B. M. (2024). A combination of joint linkage and genome-wide association study reveals putative candidate genes associated with resistance to northern corn leaf blight in tropical maize. Frontiers in Plant Science, 15, 1448961. https://doi.org/10.3389/fpls.2024.1448961 |
| spellingShingle | genome-wide association studies quantitative trait loci mapping marker-assisted selection maize Ndlovu, Noel Gowda, Manje Beyene, Yoseph Das, Biswanath Mahabaleswara, Suresh L. Makumbi, Dan Ogugo, Veronica Burgueño, Juan Crossa, Jose Spillane, Charles McKeown, Peter C. Brychkova, Galina Prasanna, Boddupalli M. A combination of joint linkage and genome-wide association study reveals putative candidate genes associated with resistance to northern corn leaf blight in tropical maize |
| title | A combination of joint linkage and genome-wide association study reveals putative candidate genes associated with resistance to northern corn leaf blight in tropical maize |
| title_full | A combination of joint linkage and genome-wide association study reveals putative candidate genes associated with resistance to northern corn leaf blight in tropical maize |
| title_fullStr | A combination of joint linkage and genome-wide association study reveals putative candidate genes associated with resistance to northern corn leaf blight in tropical maize |
| title_full_unstemmed | A combination of joint linkage and genome-wide association study reveals putative candidate genes associated with resistance to northern corn leaf blight in tropical maize |
| title_short | A combination of joint linkage and genome-wide association study reveals putative candidate genes associated with resistance to northern corn leaf blight in tropical maize |
| title_sort | combination of joint linkage and genome wide association study reveals putative candidate genes associated with resistance to northern corn leaf blight in tropical maize |
| topic | genome-wide association studies quantitative trait loci mapping marker-assisted selection maize |
| url | https://hdl.handle.net/10568/169952 |
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