Genetic Structure Analysis Of Wild Rice Populations (oryza Longistaminata) From Kwale District Of Kenya Using Microsatellite Markers

Abstract

The most agriculturally important wild rice species found in Kenya is Oryza longistaminata, which can act as a source of useful traits for improvement of cultivated rice. Knowledge of the amount of genetic diversity in natural populations is needed for development of good strategies for in-situ and ex-situ conservation so as to sustain this diversity and prevent it's erosion through man made activities. Likewise the genetic diversity and genetic structure of these populations can act as a pointer to whether gene flow from cultivated rice species has occurred and the consequences of gene flow if transgenic rice is introduced. The genetic structure and genetic diversity of natural populations of Oryza longistaminata on a fine scale has not been well documented. Microsatellite loci were used to unravel the fine scale genetic variation within and between populations of Oryza longistaminata from Kwale District of Kenya. To better estimate the genetic diversity and structure of the Kwale populations a total of 244 individuals from ten discretely distributed populations were analysed using five Oryza saliva microsatellites (SSRs). To estimate the differentiation and the 'connectivity among the populations the study relied on Wright's (1951) FST and FST estimator (8) while the effective number of alleles (Ae), the observed heterozygosity (Ho), ex~e~ted heterozygosity (H~) and Shannon's index were used to demonstrate the level of population genetic diversity and locus genetic diversity. FSTwas used to indirectly estimate gene flow through its link with effective number of migrants (Nm) i.e.[ Nn = (1/4)(I-FsT)/FsT). Microsatellite genotyping resulted in a tptal of 40 alleles and an average of 8 alleles per locus which revealed high polymorphism. The genetic diversity indices indicated the observed heterozygosity is higher than expected heterozygosity resulting to a general increase in diversity within populations i.e. mean (F1s = -0.14023). The fixation index (FST= 0.4049) shows considerable population differentiation while FSTestimator (8 = 0.42331) is also proportionally high and significant (P < 0.05). The gene flow (Nn = 0.3629) is quite low which could have '\ x influenced the differentiation through isolation by distance. In general the parameters reveal high levels of variation in the populations of Oryza longistaminata and this diversity is higher within the populations than between populations. The increased diversity suggests that alleles from cultivated rice may have introgressed into wild rice as cultivated rice in this region grows sympatrically with Oryza longistaminata. There is therefore need to consider identifying a safe distance between Oryza longistaminata populations and cultivated transgenic rice to avoid contamination and erosion of the inherent diversity.