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Abstract


In silico SSRs Analysis of Mitochondrial Genome (mtDNA) of Oryza rufipogon Griff.
Cultivated rice is one of the most important crops for human diet. The Oryza genus includes 21 wild species and 2 cultivated species. Oryza rufipogon Griff. is the wild ancestor of cultivated rice and has AA genome structure as cultivated rice species (Oryza sativa L. and Oryza glaberrima Steud. ). Microsatellites also known as simple sequence repeats (SSRs) are small tandem repeats (1-6 bp) that are interspersed throughout the genome. In this study, in silico we identified mitochondrial SSRs (mtSSR) in O. rufipogon mitochondrial genome (mtDNA) by using bioinformatics tools. We determined 594 SSRs in the mitochondrial genome with an average of 1 SSR/1.06 kb and a total of 4% mtSSRs were observed in genic regions while a total of 96% mtSSRs were observed in intergenic regions. Trinucleotide SSRs were the most abundant repeats in mitochondrial genome while mononucleotide SSRs were predominant in genic regions. The most frequent motifs were A/T (85.5%) for mononucleotide repeats, AG/CT (70.59%) for dinucleotide repeats , AAG/CTT (30.9%) for trinucleotide repeats, AAAG/CTTT (24.5%) for tetranucleotide repeats, AAATT/AATTT, AAGAT/ATCTT, AATTC/GAATT and CCCGG/CCGGG were equal (16.7%) for pentanucleotide repeats and AAAAAT/ATTTTT (100%) for hexanucleotide repeats. In conclusion, this study results provide scientific basis for phylogenetics, evolutionary genetics, genetic mapping and diversity studies based on mtSSRs for different Oryza species in future.

Keywords
Oryza rufipogon, rice, mtDNA, SSR, in silico analysis.


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