3 Biotech

, 8:235 | Cite as

Genome-wide association study reveals candidate genes related to low temperature tolerance in rice (Oryza sativa) during germination

  • Heng Wang
  • Ah-Rim Lee
  • So-Yeon Park
  • Sang-Hyeon Jin
  • Joohyun Lee
  • Tae-Ho Ham
  • Yongjin Park
  • Wei-Guo Zhao
  • Soon-Wook KwonEmail author
Original Article


In this study, relative germination percentage (RGP) and delayed mean germination time (DMGT) were measured in various rice accessions at the germination stage and carried out association analysis to identify candidate genes related to low temperature germination (LTG) using a natural population comprising 137 rice cultivars and inbred lines selected from the Korean rice core set. Genome-wide association study using ~ 1.44 million high-quality SNPs, which were identified by re-sequencing all rice collections, revealed 48 candidate genes on chromosome 10 and 55 candidate genes on chromosome 11 in the high peak SNP sites of associated loci for RGP and DMGT, respectively. By detecting highly associated variations located inside genic regions and performing functional annotation of the genes, we detected 23 candidate genes for RGP and 18 genes for DMGT for LTG. In addition, the haplotype and sequence analysis of the candidate gene (Os10g0371100) with RGP trait and the candidate gene (Os11t0104240-00) with DMGT revealed correlation between sequences of functional variations and phenotypes. Several novel LTG-related candidate genes previously were known for the function during rice germination and uncovered their substantial natural variations. These candidate genes represent valuable resources for molecular breeding and genetic improvement of cold tolerance during rice germination.


Oryza sativa L. Low temperature germination Re-sequencing GWAS Haplotype 



This work was supported by National Research Foundation of Korea (NRF) grant funded by the Korean government (NRF-2015R1C1A1A01054699).

Compliance with ethical standards

Conflict of interest

All the authors declare that they have on conflict of interest in the publication.

Supplementary material

13205_2018_1252_MOESM1_ESM.docx (48 kb)
Supplementary material 1 (DOCX 48 KB)
13205_2018_1252_MOESM2_ESM.xlsx (13 kb)
Supplementary material 2 (XLSX 12 KB)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Plant Bioscience, College of Natural Resources and Life SciencePusan National UniversityMiryangRepublic of Korea
  2. 2.Department of Applied BioscienceKonkuk UniversitySeoulRepublic of Korea
  3. 3.Department of Agricultural ScienceKorea National Open UniversitySeoulRepublic of Korea
  4. 4.Department of Plant Resources, College of Industrial ScienceKongju National UniversityYesanRepublic of Korea
  5. 5.School of Biology and TechnologyJiangsu University of Science and TechnologyZhenjiangPeople’s Republic of China

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