Skip to main content

Advertisement

SpringerLink
Log in

Genetic analysis of a local population of Oryza glumaepatula using SSR markers: implications for management and conservation programs

  • Published:
Genetica Aims and scope Submit manuscript

Abstract

Knowledge of natural diversity and population structures of wild species, which might be related to cultivated species, is fundamental for conservation and breeding purposes. In this study, a genetic characterization of a large population of Oryza glumaepatula, occurring in a 10 km2 area located at Tamengo Basin (Paraguay River, Brazil), was performed using SSR markers. This population is annually dragged from the river to permit navigation; one goal of this study was to examine the impact of this removal on genetic variability. From 18 polymorphic SSR markers, a total of 190 alleles were detected in a sample of 126 individuals, with an average of 10.3 alleles/locus, and a H e of 0.67. The five QTL-related markers showed an average H e value of 0.56, while the remaining 13 markers detected an average estimate of 0.70. An apparent outcrossing rate of 30%, a high proportion of alleles at low frequencies (56%), and the presence of exclusive alleles (9.5%) were found, with strong evidence of the establishment of individuals from different populations upstream in the Paraguay River. For conservation purposes, the river drag has no effect on the population. However, periodical seed collection from the Corumbá population can preserve part of the genetic variability present in upstream populations reducing the need for upriver collecting expeditions.

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.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Akimoto M, Shimamoto Y, Morishima H (1998) Population genetic structure of wild rice Oryza glumaepatula distributed in the Amazon flood area influenced by its life-history traits. Mol Ecol 7:1371–1381

    Article  Google Scholar 

  • Belkhir K, Borsa P, Chikhi L et al. (2001) GENETIX. Université de Montpellier Version 4.05.2. Available via DIALOG http://www.univ-montp2.fr/~genetix/genetix/genetix.htm Accessed 17 Jan 2008

  • Brondani RPV, Grattapaglia D (2001) Cost-effective method to synthesize a fluorescent internal DNA standard for automated fragment sizing. BioTechniques 31:793–800

    PubMed  CAS  Google Scholar 

  • Brondani C, Brondani RPV, Rangel PHN et al (2001) Development and mapping of Oryza glumaepatula-derived microsatellite markers in the interspecific cross Oryza glumaepatula × O. sativa. Hereditas 134:59–71

    Article  PubMed  CAS  Google Scholar 

  • Brondani C, Rangel PHN, Brondani RPV et al (2002) QTL mapping and introgression of yield-related traits from O. glumaepatula to cultivated rice (Oryza sativa) using microsatellite markers. Theor Appl Genet 104:1192–1203

    Article  PubMed  CAS  Google Scholar 

  • Brondani RPV, Zucchi MI, Brondani C et al (2005) Genetic structure of wild rice Oryza glumaepatula populations in three Brazilian biomes using microsatellite markers. Genetica 125:115–123

    Article  PubMed  CAS  Google Scholar 

  • Brondani C, Borba TCO, Rangel PHN et al (2006) Determination of genetic variability of traditional varieties of Brazilian rice using microsatellite markers. Genet Mol Biol 29:676–684

    Article  CAS  Google Scholar 

  • Buso GSC, Rangel PH, Ferreira ME (1998) Analysis of genetic variability of South American wild rice populations (Oryza glumaepatula) with isozymes and RAPD markers. Mol Ecol 7:107–117

    Article  CAS  Google Scholar 

  • Chabane K, Ablett GA, Cordeiro GM et al (2005) EST versus genomic derived microsatellite markers for genotyping wild and cultivated barley. Genet Res Crop Evol 52:903–909

    Article  CAS  Google Scholar 

  • Creste S, Tulmann Neto A, Figueira A (2001) Detection of single sequence repeat polymorphisms in denaturing polyacrylamide sequencing gels by silver staining. Plant Mol Biol Rep 19:299–306

    Article  CAS  Google Scholar 

  • Gao LZ (2004) Population structure and conservation genetics of wild rice Oryza rufipogon (Poaceae): a region-wide perspective from microsatellite variation. Mol Ecol 13:1009–1024

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Gao LZ, Schaal B, Zhang CH et al (2002) Assessment of population genetic structure of common wild rice Oryza rufipogon Griff. detected by microsatellite DNA and allozyme loci. Theor Appl Genet 106:173–180

    PubMed  CAS  Google Scholar 

  • Jain S, Jain RK, McCouch SR (2004) Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers. Theor Appl Genet 109:965–977

    Article  PubMed  CAS  Google Scholar 

  • Junk JW, Cunha CN, Wantzen KM et al (2006) Biodiversity and its conservation in the Pantanal of Mato Grosso, Brazil. Aquat Sci 68:278–309

    Article  Google Scholar 

  • Kang HW, Cho YG, Yoon UH (1998) A rapid DNA extraction method for RFLP and PCR analysis from a single dry seed. Plant Mol Biol Rep 16:1–9

    Article  Google Scholar 

  • Karasawa MMG, Vencovsky R, Silva CM et al (2007a) Genetic structure of South American Oryza glumaepatula Steud. populations using microsatellite molecular markers. Genet Mol Biol 30:400–410

    Article  CAS  Google Scholar 

  • Karasawa MMG, Vencovsky R, Silva CM et al (2007b) Mating system of Brazilian Oryza glumaepatula Steud. populations detected with microsatellite markers. Ann Bot 99:245–253

    Article  PubMed  CAS  Google Scholar 

  • Kuroda Y, Sato Y, Bounphanousay C et al (2007) Genetic structure of three Oryza AA genome species (O. rufipogon, O. nivara and O. sativa) as assessed by SSR analysis on the Vientiane Plain of Laos. Conserv Genet 8:149–158

    Article  CAS  Google Scholar 

  • Leigh F, Lea V, Law J et al (2003) Assessment of EST- and genomic microsatellite markers for variety discrimination and genetic diversity studies in wheat. Euphytica 133:359–366

    Article  CAS  Google Scholar 

  • Lewis PO, Zaykin D (2001) Genetic data analysis: computer program for the analysis of allelic data. Version 1.0 (d16c), available via DIALOG http://lewis.eeb.uconn.edu/lewishome/software.html Accessed 8 Nov 2007

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

    Article  PubMed  CAS  Google Scholar 

  • MaCkay JK, Latta RG (2002) Adaptive population divergence: markers, QTL and traits. Trends Ecol Evol 17:285–291

    Article  Google Scholar 

  • Margules C, Pressey RL (2000) Systematic planning for biodiversity conservation. Nature 405:243–253

    Article  PubMed  CAS  Google Scholar 

  • Meir E, Andelman S, Possingham HP (2004) Does conservation planning matter in a dynamic and uncertain world? Ecol Letters 7:615–622

    Article  Google Scholar 

  • Nei M (1972) Genetic distance between populations. Am Nat 106:283–292

    Article  Google Scholar 

  • Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323

    Article  PubMed  CAS  Google Scholar 

  • Panaud O, Chen X, McCouch SR (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 252:597–607

    PubMed  CAS  Google Scholar 

  • Perrier X, Jacquemoud-Collet JP (2006) DARwin software. Available via DIALOG http://darwin.cirad.fr/darwin Accessed 8 Nov 2007

  • Possingham H, Ball I, Andelman S (2000) Mathematical methods for identifying representative reserve networks. In: Ferson S, Burgman M (eds) Quantitative methods for conservation biology. Springer, New York, pp 291–306

    Chapter  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–995

    PubMed  CAS  Google Scholar 

  • Rangel PN (2005) Construção de mapa de ligação e mapeamento de QTLs utilizando marcadores SSRs, ESTs e SNPs em cruzamento interespecífico Oryza glumaepatula e Oryza sativa. Dissertation, Universidade Federal de Goiás

  • Rangel PHN, Brondani C, Fonseca JR (2006) Mapeamento da distribuição geográfica das espécies brasileiras de Oryza, com vistas à conservação dos parentes silvestres e das variedades crioulas de arroz (O. sativa L.). In: Coradin L (ed) Parentes silvestres das espécies de plantas cultivadas, vol 1. Ministério do Meio Ambiente, Brasília, pp 16–19

    Google Scholar 

  • Rohlf FJ (1989) NTSYS-Pc: numerical taxonomy and multivariate analysis system (version 2.02). Exeter Publisher, New York

    Google Scholar 

  • Rosa M, Santos PP, Veasey EA (2006) Caracterização agromorfológica interpopulacional em Oryza glumaepatula, vol 65. Bragantia, Campinas, pp 1–10

    Google Scholar 

  • Sánchez E, Espinoza AM (2003) Ultrastructure of Oryza glumaepatula, a wild rice species endemic of tropical America. Rev Biol Trop 53:15–22

    Google Scholar 

  • Semon M, Nielsen R, Jones MP et al (2004) The population structure of African cultivated rice Oryza glaberrima (Steud.): evidence for elevated levels of linkage disequilibrium caused by admixture with O. sativa and ecological adaptation. Genetics 169:1639–1647

    Article  PubMed  CAS  Google Scholar 

  • Slatkin M (1985) Rare alleles as an indicator of gene flow. Evolution 39:53–65

    Article  Google Scholar 

  • Song ZP, Xu X, Wang B et al (2003) Genetic diversity in the northernmost Oryza rufipogon populations estimated by SSR markers. Theor Appl Genet 107:1492–1499

    Article  PubMed  CAS  Google Scholar 

  • Temnykh S, Park WD, Ayres N et al (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712

    Article  CAS  Google Scholar 

  • Wright S (1978) Evolution and the genetics of populations, vol. 4: variability within and among natural populations. University of Chicago Press, Chicago

    Google Scholar 

  • Xu X, Lu B-R, Chen YH et al (2006) Inferring population history from fine-scale spatial genetic analysis in Oryza rufipogon (Poaceae). Mol Ecol 5:1535–1544

    Article  CAS  Google Scholar 

Download references

Acknowledgments

We acknowledge the Brazilian National Research Council (CNPq) for financial support and research fellowships to RPVB, PHNR and JAFDF and Guilherme de Oliveira for his help with statistical analysis.

Author information

Authors and Affiliations

  1. Laboratório de Biotecnologia Vegetal, Embrapa, Centro Nacional de Pesquisa de Arroz e Feijão, Goiânia, GO, 75375-000, Brazil

    Ana Rosa de Campos Vaz, Tereza Cristina de Oliveira Borba, Claudio Brondani, Paulo Hideo Nakano Rangel & Rosana Pereira Vianello Brondani

  2. Departamento de Biologia, Universidade Católica de Goiás, Goiânia, GO, 74605-010, Brazil

    Ana Rosa de Campos Vaz

  3. Departamento de Biologia, Universidade Anhanguera Centro Universitário de Goiás, Goiânia, GO, Brazil

    Graziela Silvia de Oliveira Camargo

  4. Departamento de Zootecnia, Universidade Católica de Goiás, Goiânia, GO, 74605-010, Brazil

    Mariana Pires de Campos Telles

  5. Departamento de Ecologia e Evolução, Universidade Federal de Goiás, Goiânia, GO, 74001-970, Brazil

    José Alexandre Felizola Diniz Filho

Authors
  1. Ana Rosa de Campos Vaz
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tereza Cristina de Oliveira Borba
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Claudio Brondani
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Paulo Hideo Nakano Rangel
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Graziela Silvia de Oliveira Camargo
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Mariana Pires de Campos Telles
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. José Alexandre Felizola Diniz Filho
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Rosana Pereira Vianello Brondani
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Rosana Pereira Vianello Brondani.

Rights and permissions

Reprints and permissions

About this article

Cite this article

de Campos Vaz, A.R., de Oliveira Borba, T.C., Brondani, C. et al. Genetic analysis of a local population of Oryza glumaepatula using SSR markers: implications for management and conservation programs. Genetica 137, 221–231 (2009). https://doi.org/10.1007/s10709-009-9393-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10709-009-9393-8

Keywords

Search

Navigation