Tropical Plant Biology

, Volume 5, Issue 4, pp 286–308 | Cite as

Analysis of Starch Gene Diversity in the Wild Relatives of Oryza sativa

  • Shabana Kasem
  • Daniel L. E. Waters
  • Robert J. Henry


Genetic loci influencing traits important to humans have been selected during crop domestication. The starch properties of rice influence the ease of cooking and attractiveness of rice as a human food. Starch biosynthesis genes likely to influence starch properties in the grain were compared in wild and domesticated rice genotypes. Sequence variation was investigated in starch biosynthesis gene exons that have been reported to have a direct influence on rice amylose content, gelatinization temperature, and amylopectin chain length. Exons 6 and 10 of GBSSI, exon 8 of SSIIa and exons 11, 13, 14 and 16 of SBEIIb were amplified and sequenced from 13 wild Oryza species encompassing genome types AA to HHJJ. Thirty two single nucleotide polymorphisms (SNPs) were identified in the exons of GBSSI; 176 in exon 8 of SSIIa, and 43 in SBEIIb, giving a total of 251 SNPs among the species. Eighty six of these SNP caused changes in the encoded amino acid, of which 28 were missense mutations that affected highly conserved amino acids within the protein sequence of GBSSI, SSIIa or SBEIIb. Two indels were identified in Potamophila parviflora, a close relative of Zizania palustris, a North American native wild rice. Most of the nucleotide variations and non-conservative changes were observed in the genomes other than the AA genome species. This represents a genetic resource for use in rice starch manipulation. The impact of human selection at these loci can be deduced by comparison of modern cultivated genotypes with their wild progenitors.


Rice Wild rice Oryza sativa Oryza Phylogeny Genome Starch 



We thank Dr Martin Elphinston for invaluable discussions, Australian Tropical Crops and Forages Collection, Department of Employment, Economic Development and Innovation (DEEDI), Biloela, Australia ( for the providing the materials used in the study. This project was funded by the Grain Foods CRC.


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Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  • Shabana Kasem
    • 1
  • Daniel L. E. Waters
    • 1
  • Robert J. Henry
    • 2
  1. 1.Southern Cross Plant ScienceSouthern Cross UniversityLismoreAustralia
  2. 2.Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandBrisbaneAustralia

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