Assessment of genetic diversity among rice (Oryza sativa L.) landrace populations under traditional production using microsatellite (SSR) markers

Despite the surge of support for on farm conservation of plant genetic resources on global scale, no agreed set of scientific principles yet exists for its effective implementation. Farming communities in traditional agroecosystem have been playing an important role in conserving agricultural diversity and assessment at genetic level is a prerequisite for understanding detrimental evolutionary patterns and devising suitable strategies for their conservation and sustainable use. The present investigation was undertaken with the objectives of understanding farmer management of population structure of rice landraces in traditional farming systems as well as inter- and intra-population molecular diversity at microsatellite loci. The microsatellites (STMS) markers were used for analysing selected eleven rice landrace populations from various parts of Uttarakhand state in north-western Himalayas. A total number of 98 alleles were recorded, of which 91 were common and seven were rare. The mean number of alleles per locus was 6.13 and for different groups of rice landrace populations, namely eight populations of common landrace and three populations of rare landraces were 4.96 and 4.37, respectively. The study also compared genebank-conserved (ex situ) and on-farm-managed (in situ) landrace populations of same named common landraces Jaulia and Thapachini, and revealed greater number of alleles per locus for on-farm-managed populations as compared to the populations under static management. Significant number of alleles specific to populations under dynamic management could also be recorded. Changes in yield parameters also seemed affected under dynamic farmer management for same rice landrace populations. Further, the rare landraces included in the present study were more diverse than the common landrace populations. The rare landraces were distinct entities largely representing locally common alleles. Genetic differentiation results from the joint effects of various evolutionary forces, which in turn must operate within the historical and biological context of the crop. The present investigation about the population genetic structure is therefore helpful in monitoring diversity loss over time and space, and also for devising a rational conservation plan, particularly on-farm management of farmer landraces under traditional production.