Analysis of genetic diversity and relationships in waxy rice (Oryza sativa L.) using AFLP and ISSR markers

Jinsong Bao*, Harold Corke, Mei Sun

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

23 Scopus citations


Opaque endosperm is the main phenotypic indicator for waxy rice, but other phenotypic and genotypic variation among waxy rice accessions has largely been ignored. Previous studies showed that wide diversity in starch physiochemical properties exists in both indica and japonica waxy rices, especially for starch gelatinization temperature (GT) which could be divided into a high- and a low-GT group. In the present study, amplified fragment length polymorphism (AFLP) and inter-simple sequence repeat (ISSR) molecular markers were employed to examine genetic diversity and relationships of 56 waxy rice accessions. A total of 358 AFLP fragments were amplified with five primer combinations, showing a high level of polymorphism (78.3%). A total of 190 ISSR bands were generated with a single primer and a primer pair, showing a very high level of polymorphism (92.2%). The genetic distance matrices obtained from the two sets of markers were significantly correlated (r = 0.731, P = 0.004). The dendrogram generated with combined AFLP and ISSR markers could clearly differentiate the indica and japonica groups. Newly released varieties and breeding lines within each subspecies tended to be clustered together, whereas landraces were more distantly placed in the dendrogram. Only one AFLP band was found specific to the indica type, while no specific bands were found for starch GT. The implications for the conservation and breeding of waxy rice are discussed.

Original languageEnglish
Pages (from-to)323-330
Number of pages8
JournalGenetic Resources and Crop Evolution
Issue number2
StatePublished - Mar 2006
Externally publishedYes


  • AFLP
  • Genetic diversity
  • ISSR
  • Starch quality
  • Waxy rice


Dive into the research topics of 'Analysis of genetic diversity and relationships in waxy rice (Oryza sativa L.) using AFLP and ISSR markers'. Together they form a unique fingerprint.

Cite this