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Fine mapping a QTL qCTB7 for cold tolerance at the booting stage on rice chromosome 7 using a near-isogenic line

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Abstract

Low temperature at the booting stage is a serious abiotic stress in rice, and cold tolerance is a complex trait controlled by many quantitative trait loci (QTL). A QTL for cold tolerance at the booting stage in cold-tolerant near-isogenic rice line ZL1929-4 was analyzed. A total of 647 simple sequence repeat (SSR) markers distributed across 12 chromosomes were used to survey for polymorphisms between ZL1929-4 and the cold-sensitive japonica cultivar Towada, and nine were polymorphic. Single marker analysis revealed that markers on chromosome 7 were associated with cold tolerance. By interval mapping using an F2 population from ZL1929-4 × Towada, a QTL for cold tolerance was detected on the long arm of chromosome 7. The QTL explained 9 and 21% of the phenotypic variances in the F2 and F3 generations, respectively. Recombinant plants were screened for two flanking markers, RM182 and RM1132, in an F2 population with 2,810 plants. Two-step substitution mapping suggested that the QTL was located in a 92-kb interval between markers RI02905 and RM21862. This interval was present in BAC clone AP003804. We designated the QTL as qCTB7 (quantitative trait locus for cold tolerance at the booting stage on chromosome 7), and identified 12 putative candidate genes.

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Acknowledgments

We thank Professor Robert A McIntosh, University of Sydney, for critically reading and revising the manuscript. This work was funded by the “973” Project of the Ministry of Sciences and Technology of China (2010CB125900-G), the 863 project (2006AA10Z158, 2006AA100101), the National Natural Science Foundation of China (30571140), the Key Project of Transgenic Crop Improvement in China (2009ZX08009-073B) and China National Key Technologies R&D Program (2009BADA2B01, 2006BAD13B01-6).

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  1. Lei Zhou

    Present address: Hybrid Rice Research Center, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China

Authors and Affiliations

  1. Key Laboratory of Crop Genomics and Genetic Improvement, Ministry of Agriculture, and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China

    Lei Zhou, Weiwei Zheng, Bo Tang, Hongliang Zhang, Jinjie Li & Zichao Li

  2. Biotechnology and Genetic Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China

    Yawen Zeng & Shuming Yang

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  1. Lei Zhou
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Correspondence to Zichao Li.

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Communicated by T. Close.

L. Zhou and Y. Zeng contributed equally to this work.

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Zhou, L., Zeng, Y., Zheng, W. et al. Fine mapping a QTL qCTB7 for cold tolerance at the booting stage on rice chromosome 7 using a near-isogenic line. Theor Appl Genet 121, 895–905 (2010). https://doi.org/10.1007/s00122-010-1358-x

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