Genetic variation and population structure in Oryza malampuzhaensis Krish. et Chand. endemic to Western Ghats, South India.

Oryza malampuzhaensis Krish. et Chand. (2n = 4x = 48; Poaceae, Oryza) is endemic to Western Ghats, South India, and shows a highly localized distribution over a small geographical area in this region. This is the most poorly understood taxon in genus Oryza and is often misidentified as O. officinalis owing to their close morphology. We assessed the nature and distribution of genetic variation among 11 populations of O. malampuzhaensis using random amplified polymorphic DNA markers. The analysis revealed low genetic variation in O. malampuzhaensis. Cluster analysis of pairwise genetic distances of populations revealed three distinct clusters and the grouping of populations largely corresponded to their geographical proximity. Restricted gene flow and a geography-dependent differentiation were evident among populations. The altitude-influenced differences in ecological factors among the natural habitats of the populations seem to be the cause of the geography-dependent differentiation. Genetically isolated smaller populations and a narrow genetic base in O. malampuzhaensis point to its vulnerability to genetic drift and genetic depauperation. Thus O. malampuzhaensis appears to be under the threat of extinction and needs to be conserved by use of suitable methods. The present study also identified molecular markers diagnostic for O. malampuzhaensis.