AUTHOR=Labroo Marlee R. , Clark Lindsay V. , Zhang Shilai , Hu Fengyi , Tao Dayun , Hamilton Ruaraidh Sackville , Sacks Erik J. 

TITLE=Solving the mystery of Obake rice in Africa: population structure analyses of Oryza longistaminata reveal three genetic groups and evidence of both recent and ancient introgression with O. sativa

JOURNAL=Frontiers in Plant Science

VOLUME=Volume 14 - 2023

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1278196

DOI=10.3389/fpls.2023.1278196

ISSN=1664-462X

ABSTRACT=<p>The undomesticated rice relative <italic>Oryza longistaminata</italic> is a valuable genetic resource for the improvement of the domesticated Asian rice, <italic>Oryza sativa</italic>. To facilitate the conservation, management, and use of <italic>O. longistaminata</italic> germplasm, we sought to quantify the population structure and diversity of this species across its geographic range, which includes most of sub-Saharan Africa, and to determine phylogenetic relationships to other AA-genome species of rice present in Africa, including the prevalence of interspecific hybridization between <italic>O. longistaminata</italic> and <italic>O. sativa</italic>. Though past plant breeding efforts to introgress genes from <italic>O. longistaminata</italic> have improved biotic stress resistance, ratooning ability, and yield in <italic>O. sativa</italic>, progress has been limited by substantial breeding barriers. Nevertheless, despite the strong breeding barriers observed by plant breeders who have attempted this interspecific cross, there have been multiple reports of spontaneous hybrids of <italic>O. sativa</italic> and <italic>O. longistaminata</italic> (aka “Obake”) obtained from natural populations in Africa. However, the frequency and extent of such natural introgressions and their effect on the evolution of <italic>O. longistaminata</italic> had not been previously investigated. We studied 190 <italic>O. longistaminata</italic> accessions, primarily from the International Rice Research Institute genebank collection, along with 309 <italic>O. sativa</italic>, 25 <italic>Oryza barthii</italic>, and 83 <italic>Oryza glaberrima</italic> control outgroups, and 17 control interspecific <italic>O. sativa</italic>/<italic>O. longistaminata</italic> hybrids. We analyzed the materials using 178,651 single-nucleotide polymorphisms (SNPs) and seven plastid microsatellite markers. This study identified three genetic subpopulations of <italic>O. longistaminata</italic>, which correspond geographically to Northwestern Africa, Pan-Africa, and Southern Africa. We confirmed that <italic>O. longistaminata</italic> is, perhaps counterintuitively, more closely related to the Asian species, <italic>O. sativa</italic>, than the African species <italic>O. barthii</italic> and <italic>O. glaberrima</italic>. We identified 19 recent spontaneous interspecific hybrid individuals between <italic>O. sativa</italic> and <italic>O. longistaminata</italic> in the germplasm sampled. Notably, the recent introgression between <italic>O. sativa</italic> and <italic>O. longistaminata</italic> has been bidirectional. Moreover, low levels of <italic>O. sativa</italic> alleles admixed in many predominantly <italic>O. longistaminata</italic> accessions suggest that introgression also occurred in the distant past, but only in Southern Africa.</p>