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Title: Little white lies: pericarp color provides insights into the origins and evolution of Southeast Asian weedy rice

Author
item CUI, YONGXIA - Washington University
item SONG, BENG KAH - University Of Science Malaysia
item LI, LIN-FENG - Washington University
item LI, YA-LING - Chinese Academy Of Sciences
item HUANG, ZHONGYUN - University Of Massachusetts
item CAICEDO, ANA - University Of Massachusetts
item Jia, Yulin
item OLSEN, KENNETH - Washington University

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/7/2016
Publication Date: 12/1/2016
Citation: Cui, Y., Song, B., Li, L., Li, Y., Huang, Z., Caicedo, A.L., Jia, Y., Olsen, K.M. 2016. Little white lies: pericarp color provides insights into the origins and evolution of Southeast Asian weedy rice. G3, Genes/Genomes/Genetics. doi:10.1534/g3.116.035881.

Interpretive Summary: Weedy red (Oryza sativa L.) competing with cultivated rice is a damaging crop weed. Different origination of weedy rice has been found worldwide. In Malaysian, weedy rice was predicted to have multiple origins based on DNA marker analyses for hull color and seed shattering. In the present study, we examined the rice Rc gene responsible for proanthocyanidin pigmentation of the pericarp, a trait found in most wild and weedy Oryza species and associated with seed dormancy; nonfunctional rc alleles were strongly favored during rice domestication, and most cultivated varieties have non-pigmented pericarps. Phenotypic analysis of 52 Malaysian weeds showed that most strains are characterized by the pigmented pericarp; however, some weeds have white pericarps, suggesting close relationships to cultivated rice. Phylogenetic analyses indicate that the Rc variants present in Malaysian weeds likely have at least three distinct origins: wild O. rufipogon, white-pericarp cultivated rice, and red-pericarp cultivated rice. These diverse origins contribute to high Rc nucleotide diversity in the Malaysian weeds. Comparison of Rc allelic distributions with other rice domestication genes suggests that functional Rc alleles may confer particular fitness benefits in weedy rice populations, for example, by conferring seed dormancy. This may promote functional Rc introgression from local wild Oryza populations. These findings are useful for the development of effective strategies to manage weedy rice in commercial rice fields worldwide.

Technical Abstract: Weedy rice is a conspecific form of cultivated rice (Oryza sativa L.) that infests rice fields and results in severe crop losses. Weed strains in different world regions appear to have originated multiple times from different domesticated and/or wild rice progenitors. In the case of Malaysian weedy rice, a multiple-origin model has been proposed based on neutral markers and analyses of domestication genes for hull color and seed shattering. Here we examined variation in pericarp (bran) color and its molecular basis to address how this trait evolved in Malaysian weeds and its possible role in weed adaptation. Functional alleles of the Rc gene confer proanthocyanidin pigmentation of the pericarp, a trait found in most wild and weedy Oryzas and associated with seed dormancy; nonfunctional rc alleles were strongly favored during rice domestication, and most cultivated varieties have non-pigmented pericarps. Phenotypic characterizations of 52 Malaysian weeds revealed that most strains are characterized by the pigmented pericarp; however, some weeds have white pericarps, suggesting close relationships to cultivated rice. Phylogenetic analyses indicate that the Rc haplotypes present in Malaysian weeds likely have at least three distinct origins: wild O. rufipogon, white-pericarp cultivated rice, and red-pericarp cultivated rice. These diverse origins contribute to high Rc nucleotide diversity in the Malaysian weeds. Comparison of Rc allelic distributions with other rice domestication genes suggests that functional Rc alleles may confer particular fitness benefits in weedy rice populations, for example, by conferring seed dormancy. This may promote functional Rc introgression from local wild Oryza populations.