title: Little White Lies: Pericarp Color Provides Insights into the Origins and Evolution of Southeast Asian Weedy Rice.
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 nonpigmented 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.
authors.affiliation: College of Science, Sichuan Agricultural University, Ya'an 625014, China.|Department of Biology, Washington University in St Louis, Missouri 63130.
authors.forename: Yongxia
authors.initials: Y
authors.lastname: Cui
authors.affiliation: School of Science, Monash University Malaysia, 46150 Bandar Sunway, Selangor, Malaysia song.beng.kah@monash.edu kolsen@wustl.edu.
authors.forename: Beng Kah
authors.initials: BK
authors.lastname: Song
authors.affiliation: Department of Biology, Washington University in St Louis, Missouri 63130.|Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
authors.forename: Lin-Feng
authors.initials: LF
authors.lastname: Li
authors.affiliation: Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
authors.forename: Ya-Ling
authors.initials: YL
authors.lastname: Li
authors.affiliation: Department of Biology, University of Massachusetts, Amherst, Massachusetts 01003.
authors.forename: Zhongyun
authors.initials: Z
authors.lastname: Huang
authors.affiliation: Department of Biology, University of Massachusetts, Amherst, Massachusetts 01003.
authors.forename: Ana L
authors.initials: AL
authors.lastname: Caicedo
authors.affiliation: Dale Bumpers National Rice Research Center, United States Department of Agriculture-Agricultural Research Service, Stuttgart, Arkansas 72160.
authors.forename: Yulin
authors.initials: Y
authors.lastname: Jia
authors.affiliation: Department of Biology, Washington University in St Louis, Missouri 63130 song.beng.kah@monash.edu kolsen@wustl.edu.
authors.forename: Kenneth M
authors.identifier: 0000-0002-8338-3638
authors.initials: KM
authors.lastname: Olsen
mesh_terms: D000220:Adaptation, Biological; D018556:Crops, Agricultural / Q000235:genetics; D019143:Evolution, Molecular; D017343:Genes, Plant; D056726:Genetic Association Studies; D014644:Genetic Variation; D018745:Genome, Plant; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010641:Phenotype; D010802:Phylogeny; D010858:Pigmentation / Q000235:genetics*; D017422:Sequence Analysis, DNA
keywords: Rc gene; adaptive introgression; seed dormancy; targeted genome sequencing; weedy crop relatives