Genetic mapping by sequencing more precisely detects loci responsible for anaerobic germination tolerance in rice
Direct seeded rice (DSR) is a mainstay for planting rice in the Americas, and it is rapidly becoming more popular in Asia. It is essential to develop rice varieties that are suitable for this type of production system. ASD1, a landrace from India, possesses several traits desirable for direct-seeded...
| Main Authors: | , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
MDPI
2021
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| Online Access: | https://hdl.handle.net/10568/164301 |
| _version_ | 1855538869586362368 |
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| author | Ignacio, John Carlos I. Zaidem, Maricris Casal, Carlos Dixit, Shalabh Kretzschmar, Tobias Samaniego, Jaime M. Mendioro, Merlyn S. Weigel, Detlef Septiningsih, Endang M. |
| author_browse | Casal, Carlos Dixit, Shalabh Ignacio, John Carlos I. Kretzschmar, Tobias Mendioro, Merlyn S. Samaniego, Jaime M. Septiningsih, Endang M. Weigel, Detlef Zaidem, Maricris |
| author_facet | Ignacio, John Carlos I. Zaidem, Maricris Casal, Carlos Dixit, Shalabh Kretzschmar, Tobias Samaniego, Jaime M. Mendioro, Merlyn S. Weigel, Detlef Septiningsih, Endang M. |
| author_sort | Ignacio, John Carlos I. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Direct seeded rice (DSR) is a mainstay for planting rice in the Americas, and it is rapidly becoming more popular in Asia. It is essential to develop rice varieties that are suitable for this type of production system. ASD1, a landrace from India, possesses several traits desirable for direct-seeded fields, including tolerance to anaerobic germination (AG). To map the genetic basis of its tolerance, we examined a population of 200 F2:3 families derived from a cross between IR64 and ASD1 using the restriction site-associated DNA sequencing (RAD-seq) technology. This genotyping platform enabled the identification of 1921 single nucleotide polymorphism (SNP) markers to construct a high-resolution genetic linkage map with an average interval of 0.9 cM. Two significant quantitative trait loci (QTLs) were detected on chromosomes 7 and 9, qAG7 and qAG9, with LOD scores of 7.1 and 15.0 and R2 values of 15.1 and 29.4, respectively. Here, we obtained more precise locations of the QTLs than traditional simple sequence repeat and low-density SNP genotyping methods and may help further dissect the genetic factors of these QTLs. |
| format | Journal Article |
| id | CGSpace164301 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | CGSpace1643012024-12-22T05:45:01Z Genetic mapping by sequencing more precisely detects loci responsible for anaerobic germination tolerance in rice Ignacio, John Carlos I. Zaidem, Maricris Casal, Carlos Dixit, Shalabh Kretzschmar, Tobias Samaniego, Jaime M. Mendioro, Merlyn S. Weigel, Detlef Septiningsih, Endang M. Direct seeded rice (DSR) is a mainstay for planting rice in the Americas, and it is rapidly becoming more popular in Asia. It is essential to develop rice varieties that are suitable for this type of production system. ASD1, a landrace from India, possesses several traits desirable for direct-seeded fields, including tolerance to anaerobic germination (AG). To map the genetic basis of its tolerance, we examined a population of 200 F2:3 families derived from a cross between IR64 and ASD1 using the restriction site-associated DNA sequencing (RAD-seq) technology. This genotyping platform enabled the identification of 1921 single nucleotide polymorphism (SNP) markers to construct a high-resolution genetic linkage map with an average interval of 0.9 cM. Two significant quantitative trait loci (QTLs) were detected on chromosomes 7 and 9, qAG7 and qAG9, with LOD scores of 7.1 and 15.0 and R2 values of 15.1 and 29.4, respectively. Here, we obtained more precise locations of the QTLs than traditional simple sequence repeat and low-density SNP genotyping methods and may help further dissect the genetic factors of these QTLs. 2021-04-06 2024-12-19T12:53:43Z 2024-12-19T12:53:43Z Journal Article https://hdl.handle.net/10568/164301 en Open Access MDPI Ignacio, John Carlos I.; Zaidem, Maricris; Casal, Carlos; Dixit, Shalabh; Kretzschmar, Tobias; Samaniego, Jaime M.; Mendioro, Merlyn S.; Weigel, Detlef and Septiningsih, Endang M. 2021. Genetic mapping by sequencing more precisely detects loci responsible for anaerobic germination tolerance in rice. Plants, Volume 10 no. 4 p. 705 |
| spellingShingle | Ignacio, John Carlos I. Zaidem, Maricris Casal, Carlos Dixit, Shalabh Kretzschmar, Tobias Samaniego, Jaime M. Mendioro, Merlyn S. Weigel, Detlef Septiningsih, Endang M. Genetic mapping by sequencing more precisely detects loci responsible for anaerobic germination tolerance in rice |
| title | Genetic mapping by sequencing more precisely detects loci responsible for anaerobic germination tolerance in rice |
| title_full | Genetic mapping by sequencing more precisely detects loci responsible for anaerobic germination tolerance in rice |
| title_fullStr | Genetic mapping by sequencing more precisely detects loci responsible for anaerobic germination tolerance in rice |
| title_full_unstemmed | Genetic mapping by sequencing more precisely detects loci responsible for anaerobic germination tolerance in rice |
| title_short | Genetic mapping by sequencing more precisely detects loci responsible for anaerobic germination tolerance in rice |
| title_sort | genetic mapping by sequencing more precisely detects loci responsible for anaerobic germination tolerance in rice |
| url | https://hdl.handle.net/10568/164301 |
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