Euphytica

, Volume 191, Issue 1, pp 9–21

Association analysis of physicochemical traits on eating quality in rice (Oryza sativa L.)

  • Wei-Guo Zhao
  • Jong-Wook Chung
  • Soon-Wook Kwon
  • Jeong-Heui Lee
  • Kyung-Ho Ma
  • Yong-Jin Park
Article

DOI: 10.1007/s10681-012-0820-z

Cite this article as:
Zhao, W., Chung, J., Kwon, S. et al. Euphytica (2013) 191: 9. doi:10.1007/s10681-012-0820-z

Abstract

Improvement of rice eating quality is an important objective in current breeding programs. In this study, 130 rice accessions of diverse origin were genotyped using 170 SSR markers to identify marker–trait associations with physicochemical traits on eating quality. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r2 value for all intrachromosomal loci pairs was 0.0940. LD between linked markers decreased with distance. Marker–trait associations were investigated using the unified mixed-model approach, considering both population structure (Q) and kinship (K). In total, 101 marker–trait associations (p < 0.05) were identified using 52 different SSR markers covering 12 chromosomes. The results suggest that association mapping in rice is a viable alternative to quantitative trait loci mapping, and detection of new marker–trait associations associated with rice eating quality will also provide important information for marker-assisted breeding and functional analysis of rice grain quality.

Keywords

RiceAssociation mapping (AM)Linkage disequilibrium (LD)Population structureEating quality

Supplementary material

10681_2012_820_MOESM1_ESM.xls (40 kb)
Supplementary material 1 (XLS 39 kb)
10681_2012_820_MOESM2_ESM.xls (53 kb)
Supplementary material 2 (XLS 53 kb)
10681_2012_820_MOESM3_ESM.xls (32 kb)
Supplementary material 3 (XLS 31 kb)
10681_2012_820_MOESM4_ESM.tif (1.8 mb)
Supplementary material 4 Model-based ancestry for each of the 130 rice accessions examined based on the 170 SSR markers used to build the Q matrix. The accession numbers correspond to those listed on supplemental Table 1 (TIFF 1883 kb)

Copyright information

© Springer Science+Business Media Dordrecht 2012

Authors and Affiliations

  • Wei-Guo Zhao
    • 1
    • 2
  • Jong-Wook Chung
    • 3
  • Soon-Wook Kwon
    • 1
    • 4
  • Jeong-Heui Lee
    • 5
  • Kyung-Ho Ma
    • 3
  • Yong-Jin Park
    • 1
    • 4
  1. 1.Department of Plant ResourcesCollege of Industrial Science, Kongju National UniversityYesanRepublic of Korea
  2. 2.Sericultural Research Institute, Chinese Academy of Agricultural SciencesJiangsu University of Science and TechnologyZhenjiangPeople’s Republic of China
  3. 3.National Agrobiodiversity Center, National Academy of Agricultural ScienceRural Development AdministrationSuwonRepublic of Korea
  4. 4.Legume Bio-Resource Center of Green ManureKongju National UniversityYesanRepublic of Korea
  5. 5.National Institute of Crop ScienceRural Development AdministrationSuwonRepublic of Korea