Plant Genetic Resources

Research Article

Genetic diversity and structure of indica rice varieties from two heterotic pools of southern China and IRRI

Fangming Xiea1 c1, Longbiao Guoa2, Guangjun Rena3, Peisong Hua2, Feng Wanga4, Jianlong Xua5, Xinqi Lia6, Fulin Qiua1 and Madonna Angelita dela Paza1

a1 International Rice Research Institute, Metro Manila, DAPO Box 7777, Philippines

a2 China National Rice Research Institute, Hangzhou 310006, People' Republic of China

a3 Sichuan Academy of Agricultural Sciences, Chengdu 610066, People' Republic of China

a4 Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, People' Republic of China

a5 Crop Science Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People' Republic of China

a6 China National Hybrid Rice Research and Development Center, Changsha 410125, People' Republic of China


Investigation of genetic diversity and the relationships among varieties and breeding lines is of great importance to facilitate parental selection in the development of inbred and hybrid rice varieties and in the construction of heterotic groups. The technology of single nucleotide polymorphism (SNP) is being advanced for the assessment of population diversity and genetic structures. We characterized 215 widely cultivated indica rice varieties developed in southern China and at the International Rice Research Institute (IRRI) using IRRI-developed SNP oligonucleotide pooled assay (OPA) to provide grouping information of rice mega-varieties for further heterotic pool study. The results revealed that the Chinese varieties were more divergent than the IRRI varieties. Two major subpopulations were clustered for the varieties using a model-based grouping method. The IRRI varieties were closely grouped and separated clearly from the majority of the Chinese varieties. The Chinese varieties were subclustered into three subgroups, but there was no clear evidence to separate the Chinese varieties into subgroups geographically, indicating a great degree of genetic integration of alleles and shared ancestries among those high-yielding modern varieties.

(Received May 16 2012)

(Accepted July 31 2012)

(Online publication October 14 2012)

Key Words:

  • Chinese variety;
  • genetic diversity;
  • hybrid rice;
  • IRRI variety;
  • single nucleotide polymorphism markers


c1 Corresponding author. E-mail:


  Fangming Xie and Longbiao Guo contributed equally to this work.