Reference "Genome-wide patterns of nucleotide polymorphism in domesticated rice"

Reference ID

11650

Title

Genome-wide patterns of nucleotide polymorphism in domesticated rice

Source

PLoS Genet, 2007, vol. 3, pp. 1745-1756

Authors (12)

Caicedo-A-L	Williamson-S-H	Hernandez-R-D	Boyko-A
Fledel-Alon-A	York-T-L	Polato-N-R	Olsen-K-M
Nielsen-R	McCouch-S-R	Bustamante-C-D	Purugganan-M-D

Abstract

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.