Theoretical and Applied Genetics

, Volume 131, Issue 1, pp 157–166 | Cite as

Fine mapping of QTL qCTB10-2 that confers cold tolerance at the booting stage in rice

  • Jilong Li
  • Yinghua Pan
  • Haifeng Guo
  • Lei Zhou
  • Shuming Yang
  • Zhanying Zhang
  • Jiazhen Yang
  • Hongliang Zhang
  • Jinjie Li
  • Yawen ZengEmail author
  • Zichao LiEmail author
Original Article


Key message

The QTL qCTB10 - 2 controlling cold tolerance at the booting stage in rice was delimited to a 132.5 kb region containing 17 candidate genes and 4 genes were cold-inducible.


Low temperature at the booting stage is a major abiotic stress-limiting rice production. Although some QTL for cold tolerance in rice have been reported, fine mapping of those QTL effective at the booting stage is few. Here, the near-isogenic line ZL31-2, selected from a BC7F2 population derived from a cross between cold-tolerant variety Kunmingxiaobaigu (KMXBG) and the cold-sensitive variety Towada, was used to map a QTL on chromosome 10 for cold tolerance at the booting stage. Using BC7F3 and BC7F4 populations, we firstly confirmed qCTB10-2 and gained confidence that it could be fine mapped. QTL qCTB10-2 explained 13.9 and 15.9% of the phenotypic variances in those two generations, respectively. Using homozygous recombinants screened from larger BC7F4 and BC7F5 populations, qCTB10-2 was delimited to a 132.5 kb region between markers RM25121 and MM0568. 17 putative predicted genes were located in the region and only 5 were predicted to encode expressed proteins. Expression patterns of these five genes demonstrated that, except for constant expression of LOC_Os10g11820, LOC_Os10g11730, LOC_Os10g11770, and LOC_Os10g11810 were highly induced by cold stress in ZL31-2 compared to Towada, while LOC_Os10g11750 showed little difference. Our results provide a basis for identifying the genes underlying qCTB10-2 and indicate that markers linked to the qCTB10-2 locus can be used to improve the cold tolerance of rice at the booting stage by marker-assisted selection.



We thank Robert A McIntosh (University of Sydney) for critical reading and suggested revisions to the manuscript. This work was supported by grants from Ministry of Science and Technology of China (2016YFD0100101, 2015BAD02B01 and 2013BAD01B02-15), National Natural Science Foundation of China (31471456, 31671649).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interests.

Supplementary material

122_2017_2992_MOESM1_ESM.docx (19 kb)
Supplementary material 1 (DOCX 19 kb)


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Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  1. 1.Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
  2. 2.Biotechnology and Genetic Resources InstituteYunnan Academy of Agricultural SciencesKunmingChina
  3. 3.Rice Research InstituteGuangxi Academy of Agricultural SciencesNanningChina
  4. 4.Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops InstituteHubei Academy of Agricultural SciencesWuhanChina

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