Genetic diversity assessment of the Indonesian and Philippine javanica type rice (Oryza sativa L.) based on morphological and simple sequence repeat markers

Javanica rice is grown in Indonesia, Ifugao province in the Philippines, and in mountainous area of Madagascar. Genetic relationship of the javanica accessions from Indonesia and the Philippines was assessed using morphological and Simple Sequence Repeat markers. The mean H' for all morphological traits showed moderate diversity (0.63) in javanica rice accessions from Indonesia and high diversity (0.67) from the Philippines. However, no significant differences was found between the mean H' based on analysis of variance of H' for qualitative and quantitative morphological traits, indicating that the diversity found in the javanica accessions from Indonesia and Philippines is the same. Clustering by SAHN using simple matching coefficient and UPGMA [Unweighted Paired Group Method using Arithmetic Averages] methods of the qualitative traits of the javanica accessions from Indonesia, the Philippines, and combined accessions from Indonesia and the Philippines resulted in 8, 3, and 9 clusters respectively. For quantitative traits, clustering by SAHN using Euclidean coefficient and UPGMA for javanica accessions from Indonesia, the Philippines, and combined Indonesia and the Philippines generated 7, 3, and 9 clusters, respectively. The clustering together of the javanica accessions from Indonesia and the Philippines indicates that they are related. Results of the molecular characterization of 19 simple sequence repeats (SSRs) primers revealed that there are 172 alleles ranging from 4 to 19 per locus in the javanica accessions from Indonesia and the Philippines and the mean diversity index (H' = 0.61). The total number of alleles for Indonesian accessions was 167 ranging from 4 to 18 while, there are 108 alleles which ranged from 3 to 12 for Philippine accessions. The mean of H' = 0.60 was high for Indonesia compared to that of the Philippine accessions (H' = 0.54). However, the analysis of variance of the mean H' revealed no significant differences. The results further confirmed that the diversity found in Indonesia and the Philippines accessions is the same. The allelic data from Indonesian and the Philippine accessions was subjected to clustering using DARwin (Perrier et al., 2003). Three clusters each were generated from javanica accessions from Indonesia, the Philippines and the combined accessions from Indonesia and the Philippines. Results of the morphological and molecular characterization of the javanica accessions from Indonesia and the Philippines showed that they are equally diverse. Rice breeders can therefore tap this diversity from either Indonesian of Philippine javanica rices. Further research on the javanica rices from Indonesia and Philippines is recommended to include additional accessions and primers to assess the total genetic diversity of the javanica collections.