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Fuchs EJ, Meneses Martínez A, Calvo A, Muñoz M, Arrieta-Espinoza G. (2015) Genetic structure of Oryza glumaepatula wild rice populations and evidence of introgression from O. sativa in Costa Rica. PeerJ PrePrints3:e1095v1https://doi.org/10.7287/peerj.preprints.1095v1
Wild crop relatives are an important source of genetic diversity for crop improvement. However, gene flow from cultivated species into wild species may prove detrimental. Introgression may lead to changes in wild species by incorporating alleles from domesticated species, which may increase the likelihood of extinction. The objective of the present study is to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated if there is evidence of introgression between wild rice and commercial varieties of O. sativa since it is cultivated commonly in close proximity to wild rice populations. Individuals from all known O. glumaepatula populations in Costa Rica were collected. With the aid of 455 AFLP markers, we characterized the genetic diversity and structure among seven populations in northern Costa Rica. Given the dominant nature of our markers, Bayesian estimates of genetic structure were used. We also compared genetic diversity estimates between O. glumaepatula individuals and O. sativa commercial rice. Our results show that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. This is likely a result of large population size. Despite the restricted distributions of this wild species, in Costa Rica most populations are composed of several thousand individuals, thus reducing the effects of drift on genetic diversity. Our results also found low but significant structure (\theta=0.03±0.001) among populations that are separated by ~10 Km within a single river. The position of the population along the river did not influence genetic diversity estimates or differences among populations. This river does not have a strong current and meadows or seeds may easily move upstream, thus homogenizing genetic diversity across populations regardless of river position. Ample gene flow through pollen, seeds or detached culms within the same river reduces genetic structure. A Bayesian structure analysis showed that individuals from two populations share a significant proportion of their genomes with O. sativa genome. These results suggest that the low levels of genetic structure found in these populations are likely the result of introgression from cultivated O. sativa populations. These results expose an important biohazard as recurrent hybridization may reduce genetic diversity of this wild rice species. Introgression may transfer commercial traits into the only populations of O. glumaepatula in Costa Rica, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica.
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Supplemental Table 1
Geographic coordinates and sample sizes of O. glumaepatula populations in MQ and Guanacaste
AFLP dataset for O. glumaepatula populations in CR and six O. sativa individuals
AFLP data set for Oryza glumaepatula individuals in Costa Rica and six Oryza sativa individuals. The data file includes a header row. First column indicates individual ID numbers. Second column indicates the location of analysed individuals. Successive columns hold AFLP data, with ones (1) indicating a band presence and (0) indicating the absence of a scorable band.
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