Call of the wild rice: Oryza rufipogon shapes weedy rice evolution in Southeast Asia

Authors: VIGUEIRA, CYNTHIA - High Point University; QI, XINSHUAI - University Of Arizona; SONG, BEN-KAH - University Of Science Malaysia; LI, LIN-FENG - Fudan University; CAICEDO, ANA - University Of Massachusetts; Jia, Yulin; OLSEN, KENNETH - Washington University

Submitted to: Evolutionary Applications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/21/2017
Publication Date: 11/27/2017
Citation: Vigueira, C.C., Qi, X., Song, B., Li, L., Caicedo, A.L., Jia, Y., Olsen, K.M. 2017. Call of the wild rice: Oryza rufipogon shapes weedy rice evolution in Southeast Asia. Evolutionary Applications. https://doi.org:10.1111/eva.12581.
DOI: https://doi.org/10.1111/eva.12581

Interpretive Summary: Weedy rice is an agricultural problem negatively impacting rice yield and quality. In the present study, weedy rice in regions outside the range of wild rice (North America, South Korea) and populations in Southeast Asia were sequenced and compared with DNA sequences of wild rice relatives. We found different introgressions of wild rice alleles into weedy rice populations including genomic regions for invasive weedy traits in Southeast Asia. We also found that nucleotide diversity is also much higher in Southeast Asian weeds than in North American and South Korean weeds. Wild rice populations are commonly found in Southeast Asia. The differences of genomic regions we identified likely reflect introgression from wild rice and from diverse cultivated landraces. These findings suggest that the monitoring of weedy populations during any shift in agricultural practices is useful to ensure the continued effectiveness of a weed management strategy.

Technical Abstract: Agricultural weeds serve as models for studying the genetic basis of rapid adaptation, with weed-adaptive traits potentially evolving independently in geographically distinct but environmentally similar agroecosystems. Weedy relatives of domesticated crops can be especially interesting systems because of the potential for weed adaptive alleles to originate through multiple mechanisms, including introgression from cultivated and/or wild relatives, recombination, and de novo mutations. Weedy rice populations have evolved multiple times through de-domestication from cultivated rice. Much of the genomic work to date in weedy rice has focused on populations that exist outside the range of the wild crop progenitor. In this study, we use genome-wide SNPs generated through genotyping-by sequencing (GBS) to compare the evolution of weedy rice in regions outside the range of wild rice (North America, South Korea) and populations in Southeast Asia, where wild rice populations are present. We find evidence for adaptive introgression of wild rice alleles into weedy rice populations in Southeast Asia, with the relative contributions of wild and cultivated rice alleles varying among Southeast Asian weedy strains; however, the genomic regions underlying several weed-adaptive traits are dominated by genomic contributions from wild rice. Nucleotide diversity is also much higher in Southeast Asian weeds than in North American and South Korean weeds. This difference likely reflects introgression from wild rice as well as genetic contributions from diverse cultivated landraces that may have served as the progenitors of these weedy populations.