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qLTG-9, a stable quantitative trait locus for low-temperature germination in rice (Oryza sativa L.)

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Low-temperature germination (LTG) is an important agronomic trait for direct seeding of rice in temperate regions of East Asia. To dissect the genetic control of LTG, we constructed a recombinant inbred line (RIL) population derived from a cross of japonica variety USSR5 and indica variety N22. Three putative QTL involved in LTG were detected and named qLTG-7, qLTG-9 and qLTG-12. They explained 9.5, 12.12 and 7.08 % of the phenotypic variation, respectively, and the alleles from USSR5 enhanced LTG. A set of advanced backcross lines selected for the presence of qLTG-9 (with the biggest contribution of the three QTL), by both linked markers and phenotype, was used to validate qLTG-9 in different generations, years and locations. A near-isogenic line in USSR5 background with a qLTG-9 insertion from N22 had retarded germination under low-temperature conditions. Finally, qLTG-9 was fine mapped between markers L9-25D and ID-1, to a 72.3-kb region in chromosome 9, which in the Nipponbare genome contains five predicted genes. This result provides a springboard for map-based cloning of qLTG-9 and is helpful in understanding the mechanism of seed germination under low-temperature conditions.

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Advanced backcross


Near-isogenic line


Marker-assisted selection


Marker-assisted backcrossing


Phenotypic selection


Recombinant inbred line


Low-temperature germination


Quantitative trait loci/locus


Quantitative trait allele for low-temperature germination




Simple sequence repeat


Polymerase chain reaction


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This research was supported by grants from the National Natural Science Foundation of China (No. 30671246), 863 Program (projects 2012AA101101, 2011AA10A101) of China, Jiangsu Cultivar Development Program (projects BE2012303, BK2010016), Jiangsu Independence Innovation Project (CX(12)1003) and PAPD program.

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Correspondence to Jianmin Wan.

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Communicated by M. Wissuwa.

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Fig. S1. Chromosome locations of low temperature germination quantitative trait loci in RIL at the fourth and fifth days of germination (DOC 126 kb)


Fig. S2. Genetic backgrounds of W907 (BC4F2) (A), Y2469 (BC4F3) (B), Y2288 (BC5F2) (C). Black square represent fragments from N22. Hollow square are QTL detected in RIL (DOC 26 kb)


Fig. S3. Breeding scheme employed to develop the advanced backcross lines and mapping populations. Numbers in brackets represent the size of each population. PS: Phenotypic selection. MAS + PS: Marker assistant selection plus phenotypic selection (DOC 717 kb)

Table S1:.Primers used in fine mapping (DOC 32 kb)

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Li, L., Liu, X., Xie, K. et al. qLTG-9, a stable quantitative trait locus for low-temperature germination in rice (Oryza sativa L.). Theor Appl Genet 126, 2313–2322 (2013).

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