Genome-wide association mapping in a rice MAGIC Plus population detects QTLs and genes useful for biofortification
The development of rice genotypes with micronutrient-dense grains and disease resistance is one of the major priorities in rice improvement programs. We conducted Genome-wide association studies (GWAS) using a Multi-parent Advanced Generation Inter-Cross (MAGIC) Plus population to identify QTLs and...
| Autores principales: | , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Frontiers Media
2018
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/164801 |
| _version_ | 1855525106957156352 |
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| author | Descalsota, Gwen Iris L. Swamy, B.P. Mallikarjuna Zaw, Hein Inabangan-Asilo, Mary Ann Amparado, Amery Mauleon, Ramil Chadha-Mohanty, Prabhjit Arocena, Emily C. Raghavan, Chitra Leung, Hei Hernandez, Jose E. Lalusin, Antonio B. Mendioro, Merlyn S. Diaz, Ma. Genaleen Q. Reinke, Russell |
| author_browse | Amparado, Amery Arocena, Emily C. Chadha-Mohanty, Prabhjit Descalsota, Gwen Iris L. Diaz, Ma. Genaleen Q. Hernandez, Jose E. Inabangan-Asilo, Mary Ann Lalusin, Antonio B. Leung, Hei Mauleon, Ramil Mendioro, Merlyn S. Raghavan, Chitra Reinke, Russell Swamy, B.P. Mallikarjuna Zaw, Hein |
| author_facet | Descalsota, Gwen Iris L. Swamy, B.P. Mallikarjuna Zaw, Hein Inabangan-Asilo, Mary Ann Amparado, Amery Mauleon, Ramil Chadha-Mohanty, Prabhjit Arocena, Emily C. Raghavan, Chitra Leung, Hei Hernandez, Jose E. Lalusin, Antonio B. Mendioro, Merlyn S. Diaz, Ma. Genaleen Q. Reinke, Russell |
| author_sort | Descalsota, Gwen Iris L. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | The development of rice genotypes with micronutrient-dense grains and disease resistance is one of the major priorities in rice improvement programs. We conducted Genome-wide association studies (GWAS) using a Multi-parent Advanced Generation Inter-Cross (MAGIC) Plus population to identify QTLs and SNP markers that could potentially be integrated in biofortification and disease resistance breeding. We evaluated 144 MAGIC Plus lines for agronomic and biofortification traits over two locations for two seasons, while disease resistance was screened for one season in the screen house. X-ray fluorescence technology was used to measure grain Fe and Zn concentrations. Genotyping was carried out by genotype by sequencing and a total of 14,242 SNP markers were used in the association analysis. We used Mixed linear model (MLM) with kinship and detected 57 significant genomic regions with a -log10 (P- value) ≥3.0. The PH1.1 and Zn7.1 were consistently identified in all the four environments, ten QTLs qDF3.1, qDF6.2 qDF9.1 qPH5.1 qGL3.1, qGW3.1, qGW11.1 and qZn6.2 were detected in two environments, while two major loci qBLB11.1 and qBLB5.1 were identified for Bacterial Leaf Blight (BLB) resistance. The associated SNP markers were found to co-locate with known major genes and QTLs such as OsMADS50 for days to flowering, osGA20ox2 for plant height, and GS3 for grain length. Similarly, Xa4 and Xa5 genes were identified for BLB resistance and Pi5(t), Pi28(t) and Pi30(t) genes were identified for Blast resistance. A number of metal homeostasis genes OsMTP6, OsNAS3, OsMT2D, OsVIT1 and OsNRAMP7 were co-located with QTLs for Fe and Zn. The marker-trait relationships from Bayesian network analysis showed consistency with the results of GWAS. A number of promising candidate genes reported in our study can be further validated. We identified several QTLs/genes pyramided lines with high grain Zn and acceptable yield potential, which are a good resource for further evaluation to release as varieties as well as for use in breeding programs |
| format | Journal Article |
| id | CGSpace164801 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1648012025-12-08T09:54:28Z Genome-wide association mapping in a rice MAGIC Plus population detects QTLs and genes useful for biofortification Descalsota, Gwen Iris L. Swamy, B.P. Mallikarjuna Zaw, Hein Inabangan-Asilo, Mary Ann Amparado, Amery Mauleon, Ramil Chadha-Mohanty, Prabhjit Arocena, Emily C. Raghavan, Chitra Leung, Hei Hernandez, Jose E. Lalusin, Antonio B. Mendioro, Merlyn S. Diaz, Ma. Genaleen Q. Reinke, Russell biofortification breeding programmes chromosome mapping gene pyramiding genomes grain quality quantitative trait loci rice genes trace elements programmes single nucleotide polymorphisms agronomic characters disease resistance breeding xanthomonas oryzae plant breeding iron zinc genome-wide association studies bayesian theory The development of rice genotypes with micronutrient-dense grains and disease resistance is one of the major priorities in rice improvement programs. We conducted Genome-wide association studies (GWAS) using a Multi-parent Advanced Generation Inter-Cross (MAGIC) Plus population to identify QTLs and SNP markers that could potentially be integrated in biofortification and disease resistance breeding. We evaluated 144 MAGIC Plus lines for agronomic and biofortification traits over two locations for two seasons, while disease resistance was screened for one season in the screen house. X-ray fluorescence technology was used to measure grain Fe and Zn concentrations. Genotyping was carried out by genotype by sequencing and a total of 14,242 SNP markers were used in the association analysis. We used Mixed linear model (MLM) with kinship and detected 57 significant genomic regions with a -log10 (P- value) ≥3.0. The PH1.1 and Zn7.1 were consistently identified in all the four environments, ten QTLs qDF3.1, qDF6.2 qDF9.1 qPH5.1 qGL3.1, qGW3.1, qGW11.1 and qZn6.2 were detected in two environments, while two major loci qBLB11.1 and qBLB5.1 were identified for Bacterial Leaf Blight (BLB) resistance. The associated SNP markers were found to co-locate with known major genes and QTLs such as OsMADS50 for days to flowering, osGA20ox2 for plant height, and GS3 for grain length. Similarly, Xa4 and Xa5 genes were identified for BLB resistance and Pi5(t), Pi28(t) and Pi30(t) genes were identified for Blast resistance. A number of metal homeostasis genes OsMTP6, OsNAS3, OsMT2D, OsVIT1 and OsNRAMP7 were co-located with QTLs for Fe and Zn. The marker-trait relationships from Bayesian network analysis showed consistency with the results of GWAS. A number of promising candidate genes reported in our study can be further validated. We identified several QTLs/genes pyramided lines with high grain Zn and acceptable yield potential, which are a good resource for further evaluation to release as varieties as well as for use in breeding programs 2018-09-20 2024-12-19T12:54:19Z 2024-12-19T12:54:19Z Journal Article https://hdl.handle.net/10568/164801 en Open Access application/pdf Frontiers Media Descalsota, Gwen Iris L.; Swamy, B. P. Mallikarjuna; Zaw, Hein; Inabangan-Asilo, Mary Ann; Amparado, Amery; Mauleon, Ramil; Chadha-Mohanty, Prabhjit; Arocena, Emily C.; Raghavan, Chitra; Leung, Hei; Hernandez, Jose E.; Lalusin, Antonio B.; Mendioro, Merlyn S.; Diaz, Ma. Genaleen Q. and Reinke, Russell. 2018. Genome-wide association mapping in a rice MAGIC Plus population detects QTLs and genes useful for biofortification. Front. Plant Sci., Volume 9 |
| spellingShingle | biofortification breeding programmes chromosome mapping gene pyramiding genomes grain quality quantitative trait loci rice genes trace elements programmes single nucleotide polymorphisms agronomic characters disease resistance breeding xanthomonas oryzae plant breeding iron zinc genome-wide association studies bayesian theory Descalsota, Gwen Iris L. Swamy, B.P. Mallikarjuna Zaw, Hein Inabangan-Asilo, Mary Ann Amparado, Amery Mauleon, Ramil Chadha-Mohanty, Prabhjit Arocena, Emily C. Raghavan, Chitra Leung, Hei Hernandez, Jose E. Lalusin, Antonio B. Mendioro, Merlyn S. Diaz, Ma. Genaleen Q. Reinke, Russell Genome-wide association mapping in a rice MAGIC Plus population detects QTLs and genes useful for biofortification |
| title | Genome-wide association mapping in a rice MAGIC Plus population detects QTLs and genes useful for biofortification |
| title_full | Genome-wide association mapping in a rice MAGIC Plus population detects QTLs and genes useful for biofortification |
| title_fullStr | Genome-wide association mapping in a rice MAGIC Plus population detects QTLs and genes useful for biofortification |
| title_full_unstemmed | Genome-wide association mapping in a rice MAGIC Plus population detects QTLs and genes useful for biofortification |
| title_short | Genome-wide association mapping in a rice MAGIC Plus population detects QTLs and genes useful for biofortification |
| title_sort | genome wide association mapping in a rice magic plus population detects qtls and genes useful for biofortification |
| topic | biofortification breeding programmes chromosome mapping gene pyramiding genomes grain quality quantitative trait loci rice genes trace elements programmes single nucleotide polymorphisms agronomic characters disease resistance breeding xanthomonas oryzae plant breeding iron zinc genome-wide association studies bayesian theory |
| url | https://hdl.handle.net/10568/164801 |
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