Rice Genetics IV - IRRI books - International Rice Research Institute

Molecular wt (bp)15 cultivars241 cultivarsWild speciesCT308OSM35CT309 CT404 CT206Microsatellite markerFig. 5. Range of allele sizes at five SSR markers as detected in three groups ofgermplasm: (1) a group of 15 diverse O. sativa cultivars, (2) a group of 241diverse O. sativa cultivars, and (3) a set of 76 wild AA genome Oryza species(described by Harrington 2000). Allele size ranges are illustrated in terms ofmolecular weight of alleles as detected on silver-stained gels for each set ofgermplasm.personal communication), and japonica rice from California (Ni et al 2001) and Korea(Ji et al 1998, Kwon et al 2000).When evolutionarily divergent accessions of Oryza and other grasses are beingcompared, chloroplast SSRs have proven to be a reliable tool for comparative phylogeneticanalysis (Provan et al 1996, 1997, Ishii and McCouch 2000, Ishii et al 2001).SSR loci vary considerably in the amount of allelic diversity detected per locus.Harrington (2000) demonstrated that the relative number of alleles per locus detectedin wild and cultivated AA genome species of Oryza varies greatly with the specificSSR marker (Fig. 5). Loci that tend to be hypervariable in a specific set of germplasmare most useful for differentiating among closely related genotypes, whereas SSRloci that are more conserved and have fewer alleles per locus can be used more reliablyfor evaluating genetic relationships among more distantly related accessions.Ultimately, sequence analysis is required to determine whether SSR amplicons thatare determined to be identical in size based on electrophoretic migration patterns arehomoplasic or are truly common by descent (X. Chen, personal communication).Thus, only when sequence analysis has confirmed the identity of alleles can phylogeneticreconstruction be reliably undertaken using SSR data (Doyle et al 1998).In both public and private settings, SSRs are economically employed in hybridrice breeding programs. These markers have also been used to help define heteroticgroups in rice (Xiao et al 1996); to evaluate parental and hybrid seed purity (Q. Zhangand J. Mann, personal communication); to study the genetics of heterosis (Hua et al2000), transgressive variation (Xiao et al 1998, J. Li, personal communication); andhybrid fertility (Zhang et al 1997); and to transfer traits via marker-assisted selection(He et al 2000).128 McCouch et al