Genetic relationships of selected traditional and newly improved Sri Lankan rice germplasm

Abstract

Rice (Oryza sativa L.) germplasm of Sri Lanka consists of many traditional accessions(TAs) and newly improved varieties (NIVs). However, the genetic relationships betweenthese rice accessions/varieties are not fully understood. In the current study, the geneticrelationships of a panel of 64 Sri Lankan rice accessions/varieties (representing 24 TAsand 40 NIVs) were deduced using a Bayesian approach and a hierarchical clusteranalysis, with 12 unlinked molecular markers representing all rice chromosomes. TheBayesian genetic assignment analysis was conducted in Structure v2.3.4. adopting anadmixture model and the optimum most probable number of ancestral clusters (K) werederived based on the log-likelihood values in Structure Harvester v0.6.93. (K = 2; group-1 and group-2). Of the two genetically distinct groups recovered (≥ 95% assignmentprobability), group 1 corresponded to 90% of the NIVs and group 2 to 79% of the TAs inthe study panel. The remaining NIVs (10%) and TAs (21%) shared alleles indicatingpossible historical genetic admixture. The resulted two genetically isolated gene poolsare indicative that the contribution of TAs in the development of NIVs has been at aminimum. Based on the hierarchical cluster analysis adopting Ward‘s method as thealgorithm with squared Euclidian distance as the interval, two clusters (cluster 1 andcluster 2) were defined at the fifth rescaled distance cluster combine. The NIVs formedcluster-1, with the exception of Bg 357, At 311 and Bg 94-1, which were clustered withTAs in the cluster-2. Of the TAs, only Kalu baala wee clustered with NIVs in thecluster-1. The study clearly reflects a genetic separation in the gene pools of TAs andNIVs, warranting the need to further characterize the Sri Lankan TAs for the better useof their desirable gene alleles in future rice breeding programs.