Population Structure and Diversity of the Aa Genome of Rice Based on Simple Sequence Repeats Variation in Organelle Genome

Maternally inherited mitochondrial and chloroplast genomes based Simple Sequence Repeat (SSR) variations were examined for their contribution to diversity of rice genome. Population structure and diversity analysis based on mitochondria and chloroplast inherited genome has been studied less as compared to nuclear genome inheritance. The present study was designed to evaluate the population structure and diversity of rice grown in Pakistan along with other countries based on maternally inherited mitochondria and chloroplast genome. The mitochondrial and chloroplast genomes were analyzed by using 42 mitochondrial and 20 chloroplast pairs of SSR primers. A slightly higher percentage of polymorphism was observed in chloroplast (30%) than mitochondria (28.57%). The average gene diversity for both mitochondrial and chloroplast was 0.32 oscillating from 0.041 to 0.620. The Polymorphism Information Content (PIC) value ranged from 0.040 to 0.543 with an average of 0.282, while the allelic richness ranged from two to four alleles with an average of 2.779 alleles. Mononucleotide repeats stood first (50% polymorphic) for detecting polymorphism for organelle genomes followed by tri(25%), tetra(14.29%) and dinucleotide (12.5%), respectively. Cluster and population structure analysis revealed two groups of accessions. On the basis of our results the AA genome of Asian cultivated rice diverges from the same origin during evolution. Key words; Mitochondrial and chloroplast genomes; SSR variation; Oryza sativa; Population structure; Genetic diversity.