Quantitative and molecular analyses reveal a deep genetic divergence between the ancient medicinal rice ( Oryza sativa) Njavara and syntopic traditional cultivars.

We analysed 76 accessions of the medicinal and nutritive rice ( Oryza sativa) landrace Njavara ( Shashtika in Sanskrit) and 67 traditional cultivars of Kerala state using phenotypic traits and microsatellite markers. Multivariate analyses of 13 quantitative phenotypic traits revealed two distinct clusters, the Njavara accessions and the traditional cultivars ( Qst = 0.4753). Njavara accessions belonging to the same morphotype were clustered together, although no specific pattern could be deciphered from the clustering of traditional cultivars. A total of 222 alleles were generated at the 24 microsatellite loci, with a mean number of 4.42 and 6.623 alleles per locus and a mean gene diversity ( He) of 0.479 and 0.596 in Njavara and traditional cultivars, respectively. Different diversity analyses clearly separated Njavara and traditional cultivars from each other. As with the phenotypic analysis, Njavara accessions clustered according to their morphotypes, but the topology of the two dendrograms were different. However, the clustering pattern of traditional cultivars in genotypic dendrogram was inconsistent with that of phenotypic dendrogram. The scented rice cultivars formed a distinct cluster while the remaining traditional cultivars were clustered according to their photosensitivity. Significant ( P < 0.0000) partitioning of molecular diversity was recorded between Njavara and traditional cultivars ( Fst = 0.4293), within Njavara types ( Fst = 0.5616) and traditional cultivars ( Fst = 0.2546). The results indicate that Njavara is a cryptic variant within the traditional rice gene pool in Kerala. The study provided valuable information on the genetic structure and population differentiation of traditional rice cultivars in Kerala, which are relevant in breeding and conservation. [ABSTRACT FROM AUTHOR]