Genome-wide patterns of nucleotide polymorphism in domesticated rice

Ana L. Caicedo, Scott H. Williamson, Ryan D. Hernandez, Adam Boyko, Adi Fledel-Alon, Thomas L. York, Nicholas R. Polato, Kenneth M. Olsen, Rasmus Nielsen, Susan R. McCouch, Carlos D. Bustamante, Michael D. Purugganan

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)1745-1756
Number of pages12
JournalPLoS Genetics
Volume3
Issue number9
DOIs
StatePublished - Sep 2007

Fingerprint

polymorphism
rice
Nucleotides
genome
nucleotides
genetic polymorphism
Genome
Oryza sativa
demographic statistics
Demography
Oryza
population bottleneck
crop
Gene Flow
crops
ancestry
single nucleotide polymorphism
gene flow
Single Nucleotide Polymorphism
History

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics
  • Cancer Research
  • Genetics(clinical)

Cite this

Caicedo, A. L., Williamson, S. H., Hernandez, R. D., Boyko, A., Fledel-Alon, A., York, T. L., ... Purugganan, M. D. (2007). Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genetics, 3(9), 1745-1756. https://doi.org/10.1371/journal.pgen.0030163

Genome-wide patterns of nucleotide polymorphism in domesticated rice. / Caicedo, Ana L.; Williamson, Scott H.; Hernandez, Ryan D.; Boyko, Adam; Fledel-Alon, Adi; York, Thomas L.; Polato, Nicholas R.; Olsen, Kenneth M.; Nielsen, Rasmus; McCouch, Susan R.; Bustamante, Carlos D.; Purugganan, Michael D.

In: PLoS Genetics, Vol. 3, No. 9, 09.2007, p. 1745-1756.

Research output: Contribution to journalArticle

Caicedo, AL, Williamson, SH, Hernandez, RD, Boyko, A, Fledel-Alon, A, York, TL, Polato, NR, Olsen, KM, Nielsen, R, McCouch, SR, Bustamante, CD & Purugganan, MD 2007, 'Genome-wide patterns of nucleotide polymorphism in domesticated rice', PLoS Genetics, vol. 3, no. 9, pp. 1745-1756. https://doi.org/10.1371/journal.pgen.0030163
Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, York TL et al. Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genetics. 2007 Sep;3(9):1745-1756. https://doi.org/10.1371/journal.pgen.0030163
Caicedo, Ana L. ; Williamson, Scott H. ; Hernandez, Ryan D. ; Boyko, Adam ; Fledel-Alon, Adi ; York, Thomas L. ; Polato, Nicholas R. ; Olsen, Kenneth M. ; Nielsen, Rasmus ; McCouch, Susan R. ; Bustamante, Carlos D. ; Purugganan, Michael D. / Genome-wide patterns of nucleotide polymorphism in domesticated rice. In: PLoS Genetics. 2007 ; Vol. 3, No. 9. pp. 1745-1756.
@article{c33ba992f50144149560b1ed8872f83e,
title = "Genome-wide patterns of nucleotide polymorphism in domesticated rice",
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.",
author = "Caicedo, {Ana L.} and Williamson, {Scott H.} and Hernandez, {Ryan D.} and Adam Boyko and Adi Fledel-Alon and York, {Thomas L.} and Polato, {Nicholas R.} and Olsen, {Kenneth M.} and Rasmus Nielsen and McCouch, {Susan R.} and Bustamante, {Carlos D.} and Purugganan, {Michael D.}",
year = "2007",
month = "9",
doi = "10.1371/journal.pgen.0030163",
language = "English (US)",
volume = "3",
pages = "1745--1756",
journal = "PLoS Genetics",
issn = "1553-7390",
publisher = "Public Library of Science",
number = "9",

}

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.

PY - 2007/9

Y1 - 2007/9

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.

UR - http://www.scopus.com/inward/record.url?scp=34848916049&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=34848916049&partnerID=8YFLogxK

U2 - 10.1371/journal.pgen.0030163

DO - 10.1371/journal.pgen.0030163

M3 - Article

C2 - 17907810

AN - SCOPUS:34848916049

VL - 3

SP - 1745

EP - 1756

JO - PLoS Genetics

JF - PLoS Genetics

SN - 1553-7390

IS - 9

ER -