Identification of genomic regions associated with agronomic and biofortification traits in DH populations of rice
Rice provides energy and nutrition to more than half of the world’s population. Breeding rice varieties with the increased levels of bioavailable micronutrients is one of the most sustainable approaches to tackle micronutrient malnutrition. So, high zinc and iron content in the grain are primary tar...
| Main Authors: | , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
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Public Library of Science
2018
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| Online Access: | https://hdl.handle.net/10568/164820 |
| _version_ | 1855520263769161728 |
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| author | Swamy, B.P. Mallikarjuna Descalsota, Gwen Iris L. Nha, Chau Thanh Amparado, Amery Inabangan-Asilo, Mary Ann Manito, Christine Tesoro, Frances Reinke, Russell |
| author_browse | Amparado, Amery Descalsota, Gwen Iris L. Inabangan-Asilo, Mary Ann Manito, Christine Nha, Chau Thanh Reinke, Russell Swamy, B.P. Mallikarjuna Tesoro, Frances |
| author_facet | Swamy, B.P. Mallikarjuna Descalsota, Gwen Iris L. Nha, Chau Thanh Amparado, Amery Inabangan-Asilo, Mary Ann Manito, Christine Tesoro, Frances Reinke, Russell |
| author_sort | Swamy, B.P. Mallikarjuna |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Rice provides energy and nutrition to more than half of the world’s population. Breeding rice varieties with the increased levels of bioavailable micronutrients is one of the most sustainable approaches to tackle micronutrient malnutrition. So, high zinc and iron content in the grain are primary targets in rice biofortification breeding. In this study, we conducted QTL mapping using doubled haploid (DH) populations, PSBRc82 x Joryeongbyeo and PSBRc82 x IR69428, phenotyped for agronomic traits and micronutrients during two growing seasons and using genotypic information from analysis with the 6K SNP chip. A number of DH lines were identified as having high grain Zn and Fe content in polished rice. Importantly, we identified 20 QTLs for agronomic traits and 59 QTLs for a number of biofortification traits. Of the 79 QTLs, 12 were large-effect QTLs (>25% PVE), nine QTLs were consistent across seasons in either population, and one QTL was identified in both populations. Moreover, at least two QTLs were clustered in defined regions of chromosomes 1, 2, 3, 4, 5, 7 and 9. Eight epistatic interactions were detected for Cu, Mg, Na, and Zn in population 1. Furthermore, we identified several candidate genes near QTLs for grain Zn (OsNRAMP, OsNAS, OsZIP, OsYSL, OsFER, and OsZIFL family) and grain yield (OsSPL14 and OsSPL16). These new QTLs and candidate genes help to further elucidate the genetic basis for grain micronutrient concentration, and may prove useful for marker assisted breeding for this important trait. |
| format | Journal Article |
| id | CGSpace164820 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| publisher | Public Library of Science |
| publisherStr | Public Library of Science |
| record_format | dspace |
| spelling | CGSpace1648202025-05-14T10:23:58Z Identification of genomic regions associated with agronomic and biofortification traits in DH populations of rice Swamy, B.P. Mallikarjuna Descalsota, Gwen Iris L. Nha, Chau Thanh Amparado, Amery Inabangan-Asilo, Mary Ann Manito, Christine Tesoro, Frances Reinke, Russell agronomic traits biofortification chromosomes food supply genomics health human nutrition plant breeding identification genomes genetics agronomic characters rice oryza energy nutrition malnutrition famine trace elements zinc iron grain Rice provides energy and nutrition to more than half of the world’s population. Breeding rice varieties with the increased levels of bioavailable micronutrients is one of the most sustainable approaches to tackle micronutrient malnutrition. So, high zinc and iron content in the grain are primary targets in rice biofortification breeding. In this study, we conducted QTL mapping using doubled haploid (DH) populations, PSBRc82 x Joryeongbyeo and PSBRc82 x IR69428, phenotyped for agronomic traits and micronutrients during two growing seasons and using genotypic information from analysis with the 6K SNP chip. A number of DH lines were identified as having high grain Zn and Fe content in polished rice. Importantly, we identified 20 QTLs for agronomic traits and 59 QTLs for a number of biofortification traits. Of the 79 QTLs, 12 were large-effect QTLs (>25% PVE), nine QTLs were consistent across seasons in either population, and one QTL was identified in both populations. Moreover, at least two QTLs were clustered in defined regions of chromosomes 1, 2, 3, 4, 5, 7 and 9. Eight epistatic interactions were detected for Cu, Mg, Na, and Zn in population 1. Furthermore, we identified several candidate genes near QTLs for grain Zn (OsNRAMP, OsNAS, OsZIP, OsYSL, OsFER, and OsZIFL family) and grain yield (OsSPL14 and OsSPL16). These new QTLs and candidate genes help to further elucidate the genetic basis for grain micronutrient concentration, and may prove useful for marker assisted breeding for this important trait. 2018-08-10 2024-12-19T12:54:20Z 2024-12-19T12:54:20Z Journal Article https://hdl.handle.net/10568/164820 en Open Access Public Library of Science Swamy, B. P. Mallikarjuna; Descalsota, Gwen Iris L.; Nha, Chau Thanh; Amparado, Amery; Inabangan-Asilo, Mary Ann; Manito, Christine; Tesoro, Frances and Reinke, Russell. 2018. Identification of genomic regions associated with agronomic and biofortification traits in DH populations of rice. PLoS ONE, Volume 13 no. 8 p. e0201756 |
| spellingShingle | agronomic traits biofortification chromosomes food supply genomics health human nutrition plant breeding identification genomes genetics agronomic characters rice oryza energy nutrition malnutrition famine trace elements zinc iron grain Swamy, B.P. Mallikarjuna Descalsota, Gwen Iris L. Nha, Chau Thanh Amparado, Amery Inabangan-Asilo, Mary Ann Manito, Christine Tesoro, Frances Reinke, Russell Identification of genomic regions associated with agronomic and biofortification traits in DH populations of rice |
| title | Identification of genomic regions associated with agronomic and biofortification traits in DH populations of rice |
| title_full | Identification of genomic regions associated with agronomic and biofortification traits in DH populations of rice |
| title_fullStr | Identification of genomic regions associated with agronomic and biofortification traits in DH populations of rice |
| title_full_unstemmed | Identification of genomic regions associated with agronomic and biofortification traits in DH populations of rice |
| title_short | Identification of genomic regions associated with agronomic and biofortification traits in DH populations of rice |
| title_sort | identification of genomic regions associated with agronomic and biofortification traits in dh populations of rice |
| topic | agronomic traits biofortification chromosomes food supply genomics health human nutrition plant breeding identification genomes genetics agronomic characters rice oryza energy nutrition malnutrition famine trace elements zinc iron grain |
| url | https://hdl.handle.net/10568/164820 |
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