New insights into the history of rice domestication

The history of rice domestication has long been a subject of debate. Recently obtained genetic evidence provides new insights into this complex story. Genome-wide studies of variation demonstrate that the two varietal groups in Oryza sativa (indica and japonica) arose from genetically distinct gene pools within a common wild ancestor, Oryza rufipogon, suggesting multiple domestications of O. sativa. However, the evolutionary history of recently cloned domestication genes adds another layer of complexity to the domestication of rice. Although some alleles exist only within specific subpopulations, as would be expected if the domestications occurred independently, other major domestication alleles are common to all cultivated O. sativa varieties. Our current view of rice domestication supports multiple domestications coupled with limited introgression that transferred key domestication alleles between divergent rice gene pools. The history of rice domestication has long been a subject of debate. Recently obtained genetic evidence provides new insights into this complex story. Genome-wide studies of variation demonstrate that the two varietal groups in Oryza sativa (indica and japonica) arose from genetically distinct gene pools within a common wild ancestor, Oryza rufipogon, suggesting multiple domestications of O. sativa. However, the evolutionary history of recently cloned domestication genes adds another layer of complexity to the domestication of rice. Although some alleles exist only within specific subpopulations, as would be expected if the domestications occurred independently, other major domestication alleles are common to all cultivated O. sativa varieties. Our current view of rice domestication supports multiple domestications coupled with limited introgression that transferred key domestication alleles between divergent rice gene pools. a zone of cells at the interface of plant organs that breaks down during senescence, promoting the organ to fall off. a sample of seed collected to represent a species, population or variety. an organism whose genome contains DNA inherited from different subpopulations as the result of outcrossing and recombination. the tip of the lemma or palea; a small point at the tip of the seed hull. a physiological period of quiescence during which a mature seed will not germinate. a measure of population differentiation based on polymorphism data. It compares the genetic variability within and between populations. If two populations have completely divergent DNA sequences, their Fst value equals 1, indicating complete differentiation. If two populations have identical DNA sequences, their Fst value equals 0, indicating no differentiation. Therefore, when comparing two populations, the larger the Fst value (the closer to 1), the more differentiated those populations are from one another. small bract found at the base of cereal grains. seed abscission; when ripe seed falls from the panicle before harvesting occurs. a combination of alleles or sequence variants at multiple linked loci that are transmitted together. the result of successful outcrossing and fertilization of two genetically distinct plants. the movement of a discrete portion of a genome from one genotype into another via meiotic recombination. variants of an enzyme; proteins that differ in amino-acid sequence, but catalyze the same reaction. a primative variety consisting of a heterogeneous mixture of genotypes selected and maintained by early farmers. the reproductive cycle of a plant; annual habit refers to plants that live, reproduce and die in one year or season, whereas perennial habit refers to plants whose life cycle spans more than one year. using DNA polymorphisms between the sequences of two organisms to deduce the amount of time that has elapsed since they diverged from a common ancestor. a compound raceme; the inflorescence of a rice plant. the outermost layer of cells in the seed coat. a plant's ability to flower in response to increasing or decreasing day length. referring to the evolutionary relationships between organisms. a type of transposable element (mobile DNA) that moves through an RNA intermediate inserting new copies of itself throughout the genome of an organism. restriction fragment length polymorphism; a DNA marker that detects genetic differences between individuals based on the presence or absence of restriction enzyme sites. single nucleotide polymorphism. simple sequence repeat; a DNA marker that detects genetic differences between individuals based on the length of short repetitive sequences found throughout the genome. a population within a species that is genetically divergent from other populations within that species. a branch of the rice plant including roots, culms, leaves and panicle. the process of removing ripe grains from harvested panicles. a protein that affects the transcription and thus expression of specific target genes.