A meta-QTL analysis highlights genomic hotspots associated with phosphorus use efficiency in rice (Oryza sativa L.)
Phosphorus use efficiency (PUE) is a complex trait, governed by many minor quantitative trait loci (QTLs) with small effects. Advances in molecular marker technology have led to the identification of QTLs underlying PUE. However, their practical use in breeding programs remains challenging due to th...
| Autores principales: | , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Frontiers Media
2023
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/163912 |
| _version_ | 1855516602774061056 |
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| author | Navea, Ian Paul Maung, Phyu Phyu Yang, Shiyi Han, Jae-Hyuk Jing, Wen Shin, Na-Hyun Zhang, Wenhua Chin, Joong Hyoun |
| author_browse | Chin, Joong Hyoun Han, Jae-Hyuk Jing, Wen Maung, Phyu Phyu Navea, Ian Paul Shin, Na-Hyun Yang, Shiyi Zhang, Wenhua |
| author_facet | Navea, Ian Paul Maung, Phyu Phyu Yang, Shiyi Han, Jae-Hyuk Jing, Wen Shin, Na-Hyun Zhang, Wenhua Chin, Joong Hyoun |
| author_sort | Navea, Ian Paul |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Phosphorus use efficiency (PUE) is a complex trait, governed by many minor quantitative trait loci (QTLs) with small effects. Advances in molecular marker technology have led to the identification of QTLs underlying PUE. However, their practical use in breeding programs remains challenging due to the unstable effects in different genetic backgrounds and environments, interaction with soil status, and linkage drag. Here, we compiled PUE QTL information from 16 independent studies. A total of 192 QTLs were subjected to meta-QTL (MQTL) analysis and were projected into a high-density SNP consensus map. A total of 60 MQTLs, with significantly reduced number of initial QTLs and confidence intervals (CI), were identified across the rice genome. Candidate gene (CG) mining was carried out for the 38 MQTLs supported by multiple QTLs from at least two independent studies. Genes related to amino and organic acid transport and auxin response were found to be abundant in the MQTLs linked to PUE. CGs were cross validated using a root transcriptome database (RiceXPro) and haplotype analysis. This led to the identification of the eight CGs (OsARF8, OsSPX-MFS3, OsRING141, OsMIOX, HsfC2b, OsFER2, OsWRKY64, and OsYUCCA11) modulating PUE. Potential donors for superior PUE CG haplotypes were identified through haplotype analysis. The distribution of superior haplotypes varied among subspecies being mostly found in indica but were largely scarce in japonica. Our study offers an insight on the complex genetic networks that modulate PUE in rice. The MQTLs, CGs, and superior CG haplotypes identified in our study are useful in the combination of beneficial alleles for PUE in rice. |
| format | Journal Article |
| id | CGSpace163912 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1639122025-12-08T10:29:22Z A meta-QTL analysis highlights genomic hotspots associated with phosphorus use efficiency in rice (Oryza sativa L.) Navea, Ian Paul Maung, Phyu Phyu Yang, Shiyi Han, Jae-Hyuk Jing, Wen Shin, Na-Hyun Zhang, Wenhua Chin, Joong Hyoun candidate genes quantitative trait loci haplotypes phosphorus Phosphorus use efficiency (PUE) is a complex trait, governed by many minor quantitative trait loci (QTLs) with small effects. Advances in molecular marker technology have led to the identification of QTLs underlying PUE. However, their practical use in breeding programs remains challenging due to the unstable effects in different genetic backgrounds and environments, interaction with soil status, and linkage drag. Here, we compiled PUE QTL information from 16 independent studies. A total of 192 QTLs were subjected to meta-QTL (MQTL) analysis and were projected into a high-density SNP consensus map. A total of 60 MQTLs, with significantly reduced number of initial QTLs and confidence intervals (CI), were identified across the rice genome. Candidate gene (CG) mining was carried out for the 38 MQTLs supported by multiple QTLs from at least two independent studies. Genes related to amino and organic acid transport and auxin response were found to be abundant in the MQTLs linked to PUE. CGs were cross validated using a root transcriptome database (RiceXPro) and haplotype analysis. This led to the identification of the eight CGs (OsARF8, OsSPX-MFS3, OsRING141, OsMIOX, HsfC2b, OsFER2, OsWRKY64, and OsYUCCA11) modulating PUE. Potential donors for superior PUE CG haplotypes were identified through haplotype analysis. The distribution of superior haplotypes varied among subspecies being mostly found in indica but were largely scarce in japonica. Our study offers an insight on the complex genetic networks that modulate PUE in rice. The MQTLs, CGs, and superior CG haplotypes identified in our study are useful in the combination of beneficial alleles for PUE in rice. 2023-08-18 2024-12-19T12:53:11Z 2024-12-19T12:53:11Z Journal Article https://hdl.handle.net/10568/163912 en Open Access Frontiers Media Navea, Ian Paul; Maung, Phyu Phyu; Yang, Shiyi; Han, Jae-Hyuk; Jing, Wen; Shin, Na-Hyun; Zhang, Wenhua and Chin, Joong Hyoun. 2023. A meta-QTL analysis highlights genomic hotspots associated with phosphorus use efficiency in rice (Oryza sativa L.). Front. Plant Sci., Volume 14 |
| spellingShingle | candidate genes quantitative trait loci haplotypes phosphorus Navea, Ian Paul Maung, Phyu Phyu Yang, Shiyi Han, Jae-Hyuk Jing, Wen Shin, Na-Hyun Zhang, Wenhua Chin, Joong Hyoun A meta-QTL analysis highlights genomic hotspots associated with phosphorus use efficiency in rice (Oryza sativa L.) |
| title | A meta-QTL analysis highlights genomic hotspots associated with phosphorus use efficiency in rice (Oryza sativa L.) |
| title_full | A meta-QTL analysis highlights genomic hotspots associated with phosphorus use efficiency in rice (Oryza sativa L.) |
| title_fullStr | A meta-QTL analysis highlights genomic hotspots associated with phosphorus use efficiency in rice (Oryza sativa L.) |
| title_full_unstemmed | A meta-QTL analysis highlights genomic hotspots associated with phosphorus use efficiency in rice (Oryza sativa L.) |
| title_short | A meta-QTL analysis highlights genomic hotspots associated with phosphorus use efficiency in rice (Oryza sativa L.) |
| title_sort | meta qtl analysis highlights genomic hotspots associated with phosphorus use efficiency in rice oryza sativa l |
| topic | candidate genes quantitative trait loci haplotypes phosphorus |
| url | https://hdl.handle.net/10568/163912 |
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