Genetic diversity of African wild rice (Oryza longistaminata Chev. et Roehr) at the edge of its distribution

Ethiopia is at the edge of the distribution for African wild rice, Oryza longistaminata. Here, chloroplast (cp) and simple sequence repeat (SSR) markers were applied to wild rice accessions in Ethiopia to evaluate how they differ from control O. longistaminata, O. barthii and O. glaberrima accessions which originated from African countries. Based on the cp genomes of African wild rice species, maternally inherited cpINDEL markers were developed. The cp indels helped to elucidate 20 plastid types. African cultivated rice shared a particular plastid type with one of annual O. barthii. Parts of northern wild rice in Ethiopia shared Type 6 with control O. longistaminata. The north group shared another type with parts of the south group. The 16 SSR markers amplified a total of 155 alleles in 215 rice accessions, with mean allelic richness of 9.688 per locus, observed heterozygosity of 0.241, expected heterozygosity of 0.724, polymorphic information content of 0.700, and a significant genetic differentiation of 0.215. Both cpINDEL and nuclear markers analyses suggested that wild rice in Ethiopia belongs to O. longistaminata. However, they carry both a unique plastid type and different population structure from control O. longistaminata collected from other areas in Africa. We concluded that the edge of its distribution maintains unique variation. These populations are regarded as valuable genetic resources for future rice breeding.