Microsatellite marker-based genetic variability in Spanish rice cultivars and landraces

The genetic relationships among japonica rice cultivars and landraces were studied. Most of them are of Spanish origin, and were developed and cultivated for varying time periods over more than a century. To uncover genetic diversity within each cultivar, we analysed 30 plants per cultivar or accession using 10 fluorescently labelled primer pairs for SSR markers. Six cultivars were included in the study, with accessions from four different regions of Spain of the traditional cultivar Bomba. A total of 37 alleles were detected with a mean of 3.7 alleles per locus. Polymorphism information content (PIC) ranged from 0 to 0.78 with an average of 0.51 per locus. Genetic diversity for cvs. Albufera, Bahia, Taipei 309 and Jsendra ranged between 0.008 and 0.062. Cultivar Bomba accessions displayed higher number of alleles and genetic diversity, with Tarragona the lowest (0.08) and Valencia the highest (0.16) genetic diversity. Although infrequent, some heterozygous individuals were detected in cvs. Bomba, Bahia and Taipei 309. Cluster analysis enabled to categorize four accessions of cv. Bomba and cv. Albufera in one group and cvs. Bahia, Taipei 309, Jsendra and Senia in a second group supporting previously known relationships among varieties. These results show the utility of SSR markers for characterization of rice cultivars. In addition, the use of high number of individuals per cultivar, enabled to evaluate both inter- and intra-varietal genetic diversity. Therefore, this investigation should be useful in rice breeding programmes for genotype identification and for the evaluation of germplasm purity.