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Fine mapping of a major quantitative trait locus, qLG-9, that controls seed longevity in rice (Oryza sativa L.)

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We fine-mapped a quantitative trait locus, qLG - 9, for seed longevity detected between Japonica-type and Indica-type cultivars. qLG - 9 was mapped in a 30-kb interval of the Nipponbare genome sequence.


A quantitative trait locus, qLG-9, for seed longevity in rice has previously been detected on chromosome 9 by using backcross inbred lines derived from a cross between Japonica-type (Nipponbare) and Indica-type (Kasalath) cultivars. In the present study, the chromosomal location of qLG-9 was precisely determined by fine-scale mapping. Firstly, allelic difference in qLG-9 was verified by QTL analysis of an F2 population derived from a cross between Nipponbare and NKSL-1, in which a segment of Kasalath chromosome 9 was substituted in Nipponbare genetic background. Then, we selected F2 plants in which recombination had occurred near qLG-9 and performed F3 progeny testing on these plants to determine the genotype classes of qLG-9. Eventually, qLG-9 was mapped in a 30-kb interval (defined by two markers, CAPSb and CHPa12) of the Nipponbare genome sequence. This allowed us to nominate positional candidate genes of qLG-9. Additionally, we developed near-isogenic lines (NIL) for qLG-9 by marker-assisted selection. qLG-9 NIL showed significantly higher seed longevity than isogenic control of Nipponbare. These results will facilitate cloning of the gene(s) underlying qLG-9 as well as marker-assisted transfer of desirable genes for seed longevity improvement in rice.

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This work was supported in part by a Grant-in-Aid from the Ministry of Agriculture, Forestry and Fisheries, Japan (Green Technology Project QT-2008 and Genomics for Agricultural Innovation, QTL-4009). K. Sasaki was a recipient of a Research Fellowship for Young Scientists from the Japan Society for the Promotion of Science (18-5156). Grateful acknowledgement is extended to Dr. K. Sugimoto and Mr. T. Shimizu (National Institute of Agrobiological Sciences), Dr. M. Obara (Japan International Research Centre for Agricultural Sciences) and Ms. E. Hanzawa (Tohoku University) for their helpful suggestions in analyzing the data.

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The authors declare that they have no conflict of interest.

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The experiments comply with the current laws of the country in which they were performed.

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Correspondence to K. Sasaki.

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Communicated by L. Jiang.

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Sasaki, K., Takeuchi, Y., Miura, K. et al. Fine mapping of a major quantitative trait locus, qLG-9, that controls seed longevity in rice (Oryza sativa L.). Theor Appl Genet 128, 769–778 (2015).

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