African Journal of
Biotechnology

  • Abbreviation: Afr. J. Biotechnol.
  • Language: English
  • ISSN: 1684-5315
  • DOI: 10.5897/AJB
  • Start Year: 2002
  • Published Articles: 12487

Full Length Research Paper

The use of multiplexed simple sequence repeat (SSR) markers for analysis of genetic diversity in African rice genotypes

Bonny M. Oloka*
  • Bonny M. Oloka*
  • Cereals Program, National Crops Resources Research Institute P. O. Box 7084 Kampala, Uganda; Department of Agricultural Production, Makerere University, P. O. Box 7062 Kampala, Uganda.
  • Google Scholar
Jimmy Lamo
  • Jimmy Lamo
  • Cereals Program, National Crops Resources Research Institute P. O. Box 7084 Kampala, Uganda.
  • Google Scholar
Patrick Rubaihayo
  • Patrick Rubaihayo
  • Department of Agricultural Production, Makerere University, P. O. Box 7062 Kampala, Uganda.
  • Google Scholar
Paul Gibson
  • Paul Gibson
  • Department of Agricultural Production, Makerere University, P. O. Box 7062 Kampala, Uganda.
  • Google Scholar
Juan Vorster
  • Juan Vorster
  • Department of Plant Production and Soil Science, University of Pretoria, Private Bag X20, Hilcrest, Pretoria, South Africa.
  • Google Scholar


  •  Received: 05 February 2015
  •  Accepted: 04 May 2015
  •  Published: 06 May 2015

References

Akagi H, Yokozeki Y, Fujimura T (1997). Highly polymorphic microsatellites of rice consist of AT repeats, and a classification of closely related cultivars with these microsatellite loci. Theor. Appl. Genet. 94:61-67.
Crossref

 

Chakravarthi KB, Naravaneni R (2006). SSR marker based DNA fingerprinting and diversity study in rice (Oryza sativa. L). Afr. J. Biotechnol. 5(9):684-688.

 
 

Cuevas-Pe’rez FE, Guimara˜es EP, Berrio LE, Gonzalez DI (1992). Genetic base of irrigated rice in Latin America and the Caribbean, 1971-1989. Crop Sci. 32:1054-1059.
Crossref

 
 

Drame KE, Sanchez I, Gregorio G, Ndjiondjop MN (2011). Suitability of a selected set of simple sequence repeats (SSR) markers for multiplexing and rapid molecular characterization of African rice (Oryza glaberrima Steud.). Afr. J. Biotechnol. 10(35): 6675-6685.

 
 

Evanno G, Regnaut S, Goudet J, 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14:2611-2620.
Crossref

 
 

FAO (1987). An Illustrated Manual of Kenyan Grasses, Rome, Italy: FAO.

 
 

FAOSTAT (2012). Statistics database of the Food and Agriculture Organization FAO Publications, Rome, Italy: s.n.

 
 

Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S (2005). Genetic Structure and Diversity in Oryza sativa L. Genetics 169: 131-138.

 
 

Glaszmann JC, Arraudeau M, 1986. Rice plant type variation, "japonica" – "javanica" relationship. Rice Genet. Newslett. 3:41-41.

 
 

Guichoux E, Lagache L, Wagner S, Chaumeil P, Léger P, Lepais O, Lepoittevin C, Malausa T, Revardel E, Salin F, Petit RJ (2011). Current trends in microsatellite genotyping. Mol. Ecol. Resour. 11: 591-611.
Crossref

 
 

Guimaraes EP (2009). Rice Breeding. In: Carena MJ, ed. Cereals. Rome: Springer. pp. 99 -126.
Crossref

 
 

Harushima Y, Nakagahra M, Yano M, Sasaki T (2002). Diverse variation of reproductive barriers in three intraspecific rice crosses. Genetics 160: 313–322.
Pubmed

 
 

Kijima Y, Otusuka K, Sserunkuuma D (2012). On the Possibility of Lowland Rice Green Revolution in Sub-Saharan Africa: Evidance from Eastern Uganda. In: T. Yamano, K. Otsuka & F. Place, eds. Emerging Development of Agriculture in East Africa: Markets, Soil and Innovations. London: Springer, pp. 169-187.

 
 

Masi P, Spagnoletti PL, Donini P (2003). Development and analysis of multiplex microsatellite markers sets in common bean (Phaseolus vulgaris L.). Mol. Breed. 11:303-313.
Crossref

 
 

Masudaab M, Throwerab F, Nicholas KM (2009). The Effects of Violating Hardy-Weinberg equillibrium Assumptions on a Cluster-based Population Mixture Analysis of Stealhead Populations in Southeast Alaska. N. Am. J. Fish. Manage. 29(1):140-150.
Crossref

 
 

McCouch SR, Susan R, Teytelman L, Xu Y, YLobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M (2002). Development and Mapping of 2240 New SSR Markers for Rice (Oryza sativa L). DNA Res. 9: 199-207.
Crossref

 
 

Miller PJ, Parfitt DE, Weinbaum SA (1989). Out crossing in Peach. Hort. Sci. 24:359-360.

 
 

Morishima H, Oka HI (1981). Phylogenetic differentiation of cultivated rice. XXVII Numerical evaluation of the Indica – Japonica differentiation. Jpn. J. Breed. 31:402-413.
Crossref

 
 

Ni J, Colowit PM, Mackill DJ (2002). Evaluation of genetic diversity in rice subspecis using microsatellite markers. Crop Sci. 42: 601-607.
Crossref

 
 

Ogumbayo SA, Ojo DK, Guei RG, Oyelakin OO, Sanni KA (2005). Phylogenetic diversity and relationships among 40 rice accessions using morphological and RAPDs techniques. Afr. J. Biotechnol. 4(11): 1234-1244.

 
 

Peakall R, Smouse PE (2006). GENEALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes 6: 288-295.
Crossref

 
 

Pritchard JK, Stephens M, Donnelly P (2000). Inference of Population Structure Using Multilocus Genotype Data. Genetics 155: 945-959.
Pubmed

 
 

QIAGEN (2006). DNeasy Blood and Tissue Handbook. Austin, Texas.

 
 

Semon M, Nielsen R, Jones MP, McCouch SR (2005). 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(3):1639-1647.
Crossref

 
 

Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch S, 2000. Mapping and genome organization of microsatellites sequencies in rice (Oryza sativa L). Theor. Appl. Genet. 100:697-712.
Crossref