TY - JOUR

T1 - Genome-wide patterns of nucleotide polymorphism in domesticated rice

AU - Caicedo, Ana L

AU - Williamson, Scott H

AU - Hernandez, Ryan D

AU - Boyko, Adam

AU - Fledel-Alon, Adi

AU - York, Thomas L

AU - Polato, Nicholas R

AU - Olsen, Kenneth M

AU - Nielsen, Rasmus

AU - McCouch, Susan R

AU - Bustamante, Carlos D

AU - Purugganan, Michael D

N1 - Keywords: Alleles; Base Pairing; Base Sequence; Computer Simulation; Crops, Agricultural; Evolution, Molecular; Founder Effect; Gene Frequency; Genetic Variation; Genetics, Population; Genome, Plant; Likelihood Functions; Models, Genetic; Molecular Sequence Data; Oryza sativa; Polymerase Chain Reaction; Polymorphism, Single Nucleotide; Recombination, Genetic; Selection (Genetics); Sequence Analysis, DNA

PY - 2007

Y1 - 2007

N2 - Domesticated Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild ancestor, O. rufipogon, across 111 randomly chosen gene fragments, and use these to infer the evolutionary dynamics that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide polymorphisms (SNPs) in O. sativa varieties, a pattern that has not been reported for other crop species. We developed several alternative models to explain contemporary patterns of polymorphisms in rice, including a (i) selectively neutral population bottleneck model, (ii) bottleneck plus migration model, (iii) multiple selective sweeps model, and (iv) bottleneck plus selective sweeps model. We find that a simple bottleneck model, which has been the dominant demographic model for domesticated species, cannot explain the derived nucleotide polymorphism site frequency spectrum in rice. Instead, a bottleneck model that incorporates selective sweeps, or a more complex demographic model that includes subdivision and gene flow, are more plausible explanations for patterns of variation in domesticated rice varieties. If selective sweeps are indeed the explanation for the observed nucleotide data of domesticated rice, it suggests that strong selection can leave its imprint on genome-wide polymorphism patterns, contrary to expectations that selection results only in a local signature of variation.

AB - Domesticated Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild ancestor, O. rufipogon, across 111 randomly chosen gene fragments, and use these to infer the evolutionary dynamics that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide polymorphisms (SNPs) in O. sativa varieties, a pattern that has not been reported for other crop species. We developed several alternative models to explain contemporary patterns of polymorphisms in rice, including a (i) selectively neutral population bottleneck model, (ii) bottleneck plus migration model, (iii) multiple selective sweeps model, and (iv) bottleneck plus selective sweeps model. We find that a simple bottleneck model, which has been the dominant demographic model for domesticated species, cannot explain the derived nucleotide polymorphism site frequency spectrum in rice. Instead, a bottleneck model that incorporates selective sweeps, or a more complex demographic model that includes subdivision and gene flow, are more plausible explanations for patterns of variation in domesticated rice varieties. If selective sweeps are indeed the explanation for the observed nucleotide data of domesticated rice, it suggests that strong selection can leave its imprint on genome-wide polymorphism patterns, contrary to expectations that selection results only in a local signature of variation.

U2 - 10.1371/journal.pgen.0030163

DO - 10.1371/journal.pgen.0030163

M3 - Journal article

C2 - 17907810

VL - 3

SP - 1745

EP - 1756

JO - P L o S Genetics

JF - P L o S Genetics

SN - 1553-7390

IS - 9

ER -