Genes & Genomics

, Volume 39, Issue 3, pp 341–352 | Cite as

Genetic architecture of flag leaf length and width in rice (Oryza sativa L.) revealed by association mapping

  • Jiantao Wu
  • Yongwen Qi
  • Guanglong Hu
  • Jinjie Li
  • Zichao Li
  • Hongliang Zhang
Research Article


Rice flag leaf is the main photosynthetic organ and plays a key role in grain yield. In this study, 106 loci associated with flag leaf length and width were identified using association mapping in a rice mini core collection. Analyzing the phenotypic effects of each allele represented 156 positive and 167 negative alleles, with a few alleles showing inconsistent effect in different environments. Among the 106 loci, 69 were environment-specific loci, 16 were environmentally stable and 21 were environmentally sensitive. Fifteen associated markers were shared by two traits and were designated as pleiotropic markers. According to the frequency distribution of alleles in different variety types, 343 alleles were categorized into three types based on geographic source and usage in breeding. Among these, 156 were used alleles, 138 were unused and 49 were foreign alleles. The results further our understanding of the genetic mechanisms of flag leaf length and width.


Rice mini core collection Flag leaf length and width Association mapping Phenotype effect 



This study was supported by 948 Projects (2011-G1(5)-25 and 2011-G2B), Projects of Ministry of Science and technology (2013BAD01B02-15 and 2015BAD02B01), the Earmarked Fund for China Agriculture Research System (CARS-20-1-4 and CARS-20-3-1), and the Science and Technology Planning Project of Guangdong Province (2012B020301008 and Yue Ke Cai Zi [2013] No.82). We thank Dongling Zhang and Guoxin Yao for technical assistance with data analysis.

Compliance with ethical standards

Conflict of interest

Jiantao Wu declares that he has no conflict of interest. Yongwen Qi. declares that he has no conflict of interest. Guanglong Hu declares that he has no conflict of interest. Jinjie Li declares that she has no conflict of interest. Zichao Li declares that he has no conflict of interest. Hongliang Zhang declares that he has no conflict of interest.

Human and animal participants

The article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

13258_2016_501_MOESM1_ESM.pdf (442 kb)
Supplementary material 1 (PDF 442 KB)


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Copyright information

© The Genetics Society of Korea and Springer-Science and Media 2016

Authors and Affiliations

  • Jiantao Wu
    • 1
    • 2
  • Yongwen Qi
    • 2
  • Guanglong Hu
    • 3
  • Jinjie Li
    • 1
  • Zichao Li
    • 1
  • Hongliang Zhang
    • 1
  1. 1.Key Lab of Crop Heterosis and Utilization, Beijing Key Lab of Crop Genetic Improvement, Ministry of EducationChina Agricultural UniversityBeijingChina
  2. 2.Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute)Guangzhou CityChina
  3. 3.Beijing Academy of Agricultural and Forestry SciencesBeijingChina

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