Assessment of genetic diversity of Philippine rice cultivars carrying good quality traits using SSR markers

Microsatellite markers, also known as simple sequence repeat (SSR) markers have been useful for the detection of genetic diversity. Twenty-four rice cultivars carrying good quality traits were evaluated for genetic diversity using 164 SSR markers. A total of 890 alleles were detected by 151 polymorphic markers with an average of 5.89 per locus. Out of these markers, 89 generated a total of 147 rare alleles. Based on Shannon's diversity index, an overall genetic diversity of 0.71 was revealed indicating a high level of genetic variation among these cultivars. Polymorphism information content (PIC) values of the markers ranged from 0.18 (RM420) to 0.91 (RM473B) with an average of 0.68 per marker. Cluster analysis of these cultivars enabled to identify 3 groups at 40% level of similarity with additional sub-clusters within each group. Group I corresponded to the 8 japonica subspecies, whereas Groups 2 and 3 comprised the indica. Cultivars under groups I and 2 are known for their aroma and good cooking and eating quality traits. Between the 2 rice subspecies, indica gave more alleles than japonica and likewise displayed a higher genetic diversity. Genetic diversity of indica was high on chromosome 11, while that for japonica was high on chromosome 2. The study revealed that SSR markers facilitated the classification of these cultivars according to their subspecies. The results also indicated that these quality rice cultivars exhibited a higher genetic diversity and therefore very useful for rice breeding programs, especially for genetic mapping studies and eventually for application of marker-assisted selection (MAS) in the programs.