Skip to main content
SpringerLink
Log in

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

  • Research Article
  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Bao Y, Xu S, Jing X, Meng L, Qin Z (2015) De Novo assembly and characterization of Oryza officinalis leaf transcriptome by using RNA-Seq. BioMed Res Int. doi:10.1155/2015/982065

    Google Scholar 

  • Bon SG, Borromeo TH, Altoveros NC, Brar DS, Raymundo AD (2005) Morpho-agronomic diversity of thirty-nine Philippine populations of Oryza officinalis Wall ex Watt. Philipp Agric Sci 88(3):281–291

    Google Scholar 

  • Bon SG, Borromeo TH, Altoveros NC, Raymundo AD (2006) Isozyme characterization and diversity among the Philippine populations of Oryza officinalis Wall. ex Watt conserved ex situ. Philipp Jour Sci 135(2):93–104

    Google Scholar 

  • Bao Y, Zhou HF, Hong DY (2006) Genetic diversity and evolutionary relationships of Oryza species with the B- and C- genomes as revealed by SSR markers. J Plant Biol 49(5):339–347

    Article  CAS  Google Scholar 

  • Brondani RPV, Zucchi MI, Brondani C, Rangel PHN, De Oliveira Borba TC, Rangel PN, Magalhães MR, Vencovsky R (2005) Genetic structure of wild rice Oryza glumaepatula populations in three Brazilian biomes using microsatellite markers. Genetica 125:115–123

    Article  CAS  PubMed  Google Scholar 

  • Devanna NB, Vijayan J, Sharma TR (2014) The blast resistance gene Pi54of Cloned from Oryza officinalis interacts with Avr-Pi54 through Its Novel NonLRR Domains. PLoS ONE 9(8):e104840. doi:10.1371/journal.pone.0104840

    Article  PubMed  PubMed Central  Google Scholar 

  • Evanno G, Regnaut S, Gaudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587

    CAS  PubMed  PubMed Central  Google Scholar 

  • Federici MT, Shcherban AB, Capdevielle F, Francis M, Vaughan D (2002) Analysis of genetic diversity in the Oryza officinalis complex. Electron J Biotechnol 5:173–181

    Article  Google Scholar 

  • Fulton TM, Chunwongse J, Tanksley SD (1995) Microprep protocol for extraction of DNA from tomato and other herbaceous plants. Plant Mol Biol Reporter 13:207–209

    Article  CAS  Google Scholar 

  • Gao LZ, Ge S, Hong DY (2001) High levels of genetic differentiation of Oryza officinalis Wall. ex Watt. from China. J Hered 92(6):511–516

    Article  CAS  PubMed  Google Scholar 

  • Gao LZ, Zhang CH (2005) Comparisons of microsatellite variability and population genetic structure of two endangered wild rice species, Oryza rufipogon and O. o fficinalis, and their conservation implications. Biodivers Conserv 14:1663–1679

    Article  Google Scholar 

  • Gao LZ (2005) Microsatellite variation within and among populations of Oryza officinalis (Poaceae), an endangered wild rice from China. Mol Ecol 14(14):4287–4297

    Article  CAS  PubMed  Google Scholar 

  • Hammer K (2003) A paradigm shift in the discipline of plant genetic resources. Genet Resour Crop Evol 50:3–10

    Article  CAS  Google Scholar 

  • Hirabayashi H, Kaji R, Okamoto M, Ogawa T, Brar DS, Angeles ER, and Khush GS (2003) Mapping QTLs for brown planthopper (BPH) resistance introgressed from Oryza officinalis in rice. In: Khush GS, Brar DS, Hardy B (eds) Advances in rice genetics. International Rice Research Institute

  • Hu C-H, Chang C-H (1967) Cytogenetic studies of Oryza officinalis complex. Bot Bull Acad Sinica 8:8–19

    Google Scholar 

  • Huang Z, He G, Shu L, Li X, Zhang Q (2001) Identification and mapping of two brown planthopper resistance genes in rice. Theor Appl Genet 102:929–934

    Article  CAS  Google Scholar 

  • Hughes NM (2009) The photoreactive role of anthocyanin pigments in leaf tissues. Dissertation, Wake Forest University Graduate School of Arts and Sciences

  • Jacquemin J, Bhatia D, Singh K, Wing RA (2013) The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question. Curr Opin Plant Biol 16(2):147–156

    Article  CAS  PubMed  Google Scholar 

  • Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806

    Article  CAS  PubMed  Google Scholar 

  • Jena KK, Khush GS (1990) Introgression of genes from Oryza officinalis Wall ex Watt to cultivated rice, O. s ativa L. Theor Appl Genet 80:737–745

    Article  CAS  PubMed  Google Scholar 

  • Jena KK, Khush GS, Kochert G (1992) RFLP analysis of rice (Oryza sativa L.) introgression lines. Theor Appl Genet 84:608–616

    CAS  PubMed  Google Scholar 

  • Karasawa MMG, Vencovsky R, Silva CM, Zucchi MI, Oliveira GCX, Veasey EA (2007) Genetic structure of Brazilian wild rice (Oryza glumaepatula Steud., Poaceae) populations analyzed using microsatellite markers. Genet MolBiol 30(2):400–410

    CAS  Google Scholar 

  • Karasawa MMG, Vencovsky R, Silva CM, Zucchi MI, Cardim DC, Bressan EdA, Oliveira GCX, Veasey EA (2012) Comparison of microsatellites and isozymes in genetic diversity studies of Oryza glumaepatula (Poaceae) populations. Rev Biol Trop (Int J Trop Biol) 60(4):1463–1478

    Google Scholar 

  • Koo B, Pardey P, Wright B (2003) The price of conserving agricultural biodiversity. Nat Biotechnol 21:126–128

    Article  CAS  PubMed  Google Scholar 

  • Koski MH, Ashman T-L (2015) Floral pigmentation patterns provide an example of Gloger’s rule in plants. Nat Plants 1:14007

    Article  CAS  PubMed  Google Scholar 

  • Lê S, Josse J, Husson F (2008) FactoMineR: an R package for multivariate analysis. J Stat Softw 25(1):1–18

    Article  Google Scholar 

  • Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129

    Article  CAS  PubMed  Google Scholar 

  • Lu BR (1999) Taxonomy of the genus Oryza (Poaceae): historical perspective and current status. Int Rice Res Notes 24:4–8

    Google Scholar 

  • Maechler M, Rousseeuw P, Struyf A, Hubert M, Hornik K (2015) cluster: cluster Analysis Basics and Extensions. R package version 2:3

    Google Scholar 

  • Melaku G, Haileselassie T, Feyissa T, Kiboi S (2013) Genetic diversity of the African wild rice (Oryza longistaminata Chev. et Roehr) from Ethiopia as revealed by SSR markers. Genet Resour Crop Ev 60:1047–1056

    Article  CAS  Google Scholar 

  • Oka HI (1991) Genetic diversity of wild and cultivated rice. In: Khush GS, Toenienssen GH (eds) Rice Biotechnology. CAB International UK and International Rice Research Institute, Manila, pp 55–82

    Google Scholar 

  • Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Science Enfield (ed) Genetic diversity of cultivated tropical plants, Hamon P, Sequin M, Perrier X, Glaszmann JC. Publishers, Montpellier, pp 43–76

    Google Scholar 

  • Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000) Association mapping in structured populations. Am J Hum Genet 67:170–181

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • R Development Core Team (2013) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. http://www.R-project.org

  • Renganayaki K, Fritz AK, Sadasivam S, Pammi S, Harrington SE, McCouch SR, Kumar SM, Reddy AS (2002) Mapping and progress toward map-based cloning of brown planthopper biotype-4 resistance gene introgressed from Oryza officinalis into cultivated rice. O. sativa. Crop Sci 42:2112–2117

    Article  CAS  Google Scholar 

  • Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138

    Article  Google Scholar 

  • Sharma SD, Shastry SVS (1965) Taxonomic studies in genus Oryza L. VI. A modified classification. Indian J Genet Pl Br 25(2):173–178

    Google Scholar 

  • Song Z, Li B, Chen J, Lu BR (2005) Genetic diversity and conservation of common wild rice (Oryza rufipogon) in China. Plant Species Biol 20:83–92

    Article  Google Scholar 

  • Tateoka T (1962) Taxonomic studies of Oryza. I. O. latifolia complex. Bot Mag Tokyo 75:418–427

    Article  Google Scholar 

  • Tateoka T, Pancho JV (1963) A cytotaxonomic study of Oryza minuta and O. officinalis. Bot Mag Tokyo 76:366–373

    Article  Google Scholar 

  • Thomas G, Joseph L, Varghese G, Kalyanaraman K, Kuriachan P, Das MR (2001) Discrimination between Oryza malampuzhaensis Krish. et Chand. and Oryza officinalis Wall. ex Watt based on RAPD markers and morphological traits. Euphytica 122:181–189

    Article  CAS  Google Scholar 

  • Tsunoda S (1984) Adjustment of photosynthetic structures in three steps of rice evolution. In: Tsunoda S, Takahashi N (eds) Biology of Rice. Japan Sci. Soc. Press, Elsevier, Tokyo, pp 89–115

    Chapter  Google Scholar 

  • Turner H, Hovenkamp P, van Welsen PC (2001) Biogeography of Southeast Asia and the West Pacific. J Biogeogr 28:217–230

    Article  Google Scholar 

  • Vaughan DA (1989) The genus Oryza L. Current status of taxonomy. The International Rice Research Institute, Los Banos

    Google Scholar 

  • Vaughan DA (1994) The wild relatives of rice. International Rice Research Institute, Los Banos

    Google Scholar 

  • Vaughan DA, Ge S, Kaga A, Tomooka N (2008) Phylogeny and biogeography of the genus Oryza. In: Rice Biology in the Genomics Era. Biotechnology in Agriculture and Forestry 62. Springer, Berlin, pp. 219–233

  • Van Welsen PC, Slick JWF, Alahuhta J (2005) Plant distribution patterns and plate tectonics in Malesia. Biol. Skr. 55:199-217. ISSN 0366-3612. ISBN 87-7304-304-4

  • Walesiak M, Dudek A (2015) Department of Econometrics and Computer Science, University of Economics, Wroclaw, Poland http://keii.ue.wroc.pl/clusterSim

  • Wang B, Ding Z, Liu W, Pan J, Li C, Ge S, Zhang D (2009) Polyploid evolution in Oryza officinalis complex of the genus Oryza. BMC Evol Biol 9:250. doi:10.1186/1471-2148-9-250

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang HY, You AQ, Yang ZF, Zhang F, He RF, Zhu LL, He G (2004) High-resolution genetic mapping at the Bph15 locus for brown planthopper resistance in rice (Oryza sativa L.). Theor Appl Genet 110:182–191

    Article  CAS  PubMed  Google Scholar 

  • Yoshida S (1972) Physiological aspects of grain yield. Annu Rev Plant Physiol 23:437–464

    Article  Google Scholar 

  • Yoshida S, Forno DA, Cock JH, Gomez KA (1976) Routine procedures for growing rice plants in culture solution. International Rice Resaerch Institute, Los Baños

    Google Scholar 

  • Zang LL, Zou XH, Zhang FM, Yang ZH, Ge S (2011) Phylogeny and species delimitation of the C-genome diploid species in Oryza. J Syst Evol 49(5):386–395

    Article  Google Scholar 

  • Zhang W, Dong Y, Yang L, Ma B, Ma R, Huang F, Wang C, Hu H, Li C, Chen J (2014) Small brown planthopper resistance loci in wild rice (Oryza officinalis). Mol Genet Genomics 289:373–382

    Article  CAS  PubMed  Google Scholar 

  • Zhang LB, Ge S (2007) Multilocus analysis of nucleotide variation in Oryza officinalis and its close relatives. Mol Biol Evol 24(3):769–783

    Article  CAS  PubMed  Google Scholar 

  • http://www.worldclim.org/

  • http://www.iucnredlist.org/

  • http://www.geonames.org/

Download references

Author information

Authors and Affiliations

  1. International Rice Research Institute, Los Baños, Laguna, Philippines

    Maria Elizabeth Boncodin Naredo, Sheila Mae Quilloy Mercado, Maria Celeste Naynes Banaticla-Hilario, Myrricar Loren Berdos, Mario Alcantara Rodriguez, Kenneth Lee McNally & Ruaraidh Sackville Hamilton

Authors
  1. Maria Elizabeth Boncodin Naredo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sheila Mae Quilloy Mercado
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Maria Celeste Naynes Banaticla-Hilario
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Myrricar Loren Berdos
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Mario Alcantara Rodriguez
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Kenneth Lee McNally
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Ruaraidh Sackville Hamilton
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Maria Elizabeth Boncodin Naredo.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Naredo, M.E.B., Mercado, S.M.Q., Banaticla-Hilario, M.C.N. et al. Genetic diversity patterns in ex situ collections of Oryza officinalis Wall. ex G. Watt revealed by morphological and microsatellite markers. Genet Resour Crop Evol 64, 733–744 (2017). https://doi.org/10.1007/s10722-016-0396-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-016-0396-x

Keywords

Search

Navigation