Genetic Resources and Crop Evolution

, Volume 64, Issue 4, pp 733–744 | Cite as

Genetic diversity patterns in ex situ collections of Oryza officinalis Wall. ex G. Watt revealed by morphological and microsatellite markers

  • Maria Elizabeth Boncodin NaredoEmail author
  • Sheila Mae Quilloy Mercado
  • Maria Celeste Naynes Banaticla-Hilario
  • Myrricar Loren Berdos
  • Mario Alcantara Rodriguez
  • Kenneth Lee McNally
  • Ruaraidh Sackville Hamilton
Research Article


This study was conducted to understand variation patterns and establish the population structure in the wild rice species, Oryza officinalis, using accessions collected across the 11 regions/areas of endemism in Asia and Oceania and conserved ex situ in the International Rice Genebank at the International Rice Research Institute. Morphological and microsatellite data detected a tendency for latitudinal divergence in O. officinalis and divided the accessions into (1) Malesian and (2) South and East Asian populations. Cluster and ordination analyses of morphological characters revealed that accessions from Malesia (Regions 1–6), Vietnam (Region 7), and Central Thailand (Region 8) showed short (16.19 ± 3.70 cm) and slender (1.53 ± 2.06 cm) flag leaves that are erect to almost horizontal, short panicles (25.19 ± 3.02 cm) and mainly purple internodes; and (3) accessions from Northern Thailand and Myanmar (Region 9), India (Region 10) and China (Region 11) characterized by long (29.57 ± 4.94 cm) and broad (2.18 ± 3.33 cm) flag leaves that are horizontal to drooping, long panicles (35.26 ± 2.63 cm) and green internodes. With 79.3 % of the SSR markers being polymorphic, molecular analyses detected an average of 5.31 alleles per marker with a total of 154 alleles. Differentiation was evident among the regions with FST = 0.2173, although there is an apparent loss of heterozygosity across regions indicated by an over-all positive FIS. Based on the results, issues related to the management of O. officinalis, specifically filling gaps in the collection and the formulation of seed multiplication practices are addressed.


Ex situ conservation Geographic differentiation Oryza officinalis Population structure Wild Oryza germplasm 


Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Supplementary material 1 (pdf 145 kb)
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Supplementary material 2 (pdf 104 kb)
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Supplementary material 3 (pdf 101 kb)
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Supplementary material 4 (pdf 3764 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Maria Elizabeth Boncodin Naredo
    • 1
    Email author
  • Sheila Mae Quilloy Mercado
    • 1
  • Maria Celeste Naynes Banaticla-Hilario
    • 1
  • Myrricar Loren Berdos
    • 1
  • Mario Alcantara Rodriguez
    • 1
  • Kenneth Lee McNally
    • 1
  • Ruaraidh Sackville Hamilton
    • 1
  1. 1.International Rice Research InstituteLos BañosPhilippines

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