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

Abstract

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.

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Acknowledgements

This research was supported by the Japan International Cooperation Agency (JICA) through the EthioRice Project. This work was funded by a Grant-in-aid B (Overseas project, No. 16H05777), partly by a Grant-in-Aid for Scientific Research on Innovative Areas (15H05968), partly by a Grant-in-Aid for Scientific Research on Innovative Areas (19H00542), and partly by a Grant-in-Aid for Scientific Research on Innovative Areas (19H00549). The valuable Core collections of O. longistaminata and O. barthii used as controls in this study were provided by the National Institute of Agrobiological Sciences (NIAS), Japan. Wild rice accessions from Ethiopia were collected with kind cooperation of research technicians at the Gambella and Fogera research centers.

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Correspondence to Ryuji Ishikawa.

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Lakew, T., Tanaka, K. & Ishikawa, R. Genetic diversity of African wild rice (Oryza longistaminata Chev. et Roehr) at the edge of its distribution. Genet Resour Crop Evol 68, 1769–1784 (2021). https://doi.org/10.1007/s10722-020-01080-6

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Keywords

  • Chloroplast
  • Oryza longistaminata
  • Ethiopian wild rice
  • Diversity