Comparison of Microsatellite DNA Fingerprints of Original Seed Files and Conserved Rice Germplasm Collections

Abstract

The understanding of the genetic identity and composition of germplasm collections conserved in a genebank is vital for the proper management of germplasm resources and utilization in various plant breeding programs. A study was conducted at the Genebank of the Philippine Rice Research Institute (PhilRice) to examine the genetic similarity of the original seed files (SF) and regenerated seeds conserved as an active collection (AC) using 18 microsatellite DNA markers and to explore their underlying intra-varietal heterogeneity. Here, 74 rice germplasm collections regenerated from 1992–2012 were randomly selected for the comparative DNA fingerprinting. The genetic similarity between the original SF and regenerated AC was examined through the Dice coefficient (DC) analysis, while the extent of intra-varietal genetic heterogeneity was determined via average-linkage cluster analysis based on binary genetic distance. Of the 74 collections studied, 68 showed paired clustering of SF and AC, indicating high genetic similarity. The DCs of these collections ranged from 0.79–1. On the other hand, SF and AC comparison of six germplasm collections yielded very low DCs ranging from 0.62–0.77, with their corresponding SF and AC pair dissociated in the dendrogram owing to their high intra-varietal genetic heterogeneity. The intra-varietal polymorphic alleles between SF and AC were observed in all markers analyzed – especially in RM562, RM547, and RM154 microsatellite markers –suggesting their potential use in assessing the levels of intra-varietal genetic heterogeneity in rice cultivars. This pilot study provides baseline information that may be used for potential integration of intra-varietal similarity or variability tests in the Genebank which are important aspects for effective germplasm conservation, management, and utilization. Also discussed in this paper are other insights regarding the intra-varietal genetic heterogeneity of the selected rice accessions.