The DOI matches its Crossref record; 35 of the 35 references it cites were found in a registry or an index.
Selection Under Domestication: Evidence for a Sweep in the Rice Waxy Genomic Region
Abstract
Rice (Oryza sativa) was cultivated by Asian Neolithic farmers >11,000 years ago, and different cultures have selected for divergent starch qualities in the rice grain during and after the domestication process. An intron 1 splice donor site mutation of the Waxy gene is responsible for the absence of amylose in glutinous rice varieties. This mutation appears to have also played an important role in the origin of low amylose, nonglutinous temperate japonica rice varieties, which form a primary component of Northeast Asian cuisines. Waxy DNA sequence analyses indicate that the splice donor mutation is prevalent in temperate japonica rice varieties, but rare or absent in tropical japonica, indica, aus, and aromatic varieties. Sequence analysis across a 500-kb genomic region centered on Waxy reveals patterns consistent with a selective sweep in the temperate japonicas associated with the mutation. The size of the selective sweep (>250 kb) indicates very strong selection in this region, with an inferred selection coefficient that is higher than similar estimates from maize domestication genes or wild species. These findings demonstrate that selection pressures associated with crop domestication regimes can exceed by one to two orders of magnitude those observed for genes under even strong selection in natural systems.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Primer3 on the WWW for General Users and for Biologist Programmers
Rozen, S., & Skaletsky, H. (2003) · Bioinformatics Methods and Protocols · doi:10.1385/1-59259-192-2:365 · Cited by 15,013
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
Tajima, F. (1989) · Genetics · doi:10.1093/genetics/123.3.585 · Cited by 13,941
Detecting recent positive selection in the human genome from haplotype structure
Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z. P., Richter, D. J., Schaffner, S. F., Gabriel, S. B., Platko, J. V., Patterson, N. J., McDonald, G. J., et al. (2002) · Nature · doi:10.1038/nature01140 · Cited by 2,106
Rozas, J., & Rozas, R. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.2.174 · Cited by 1,968
The effect of linkage on limits to artificial selection
Hill, W. G., & Robertson, A. (1966) · Genetical Research · doi:10.1017/s0016672300010156 · Cited by 1,823
The variation of animals and plants under domestication /
Darwin, C. (1905) · J. Murray eBooks · doi:10.5962/bhl.title.84435 · Cited by 1,707
RICE: Chemistry and Technology
(2004) · doi:10.1094/1891127349 · Cited by 1,565
The effect of linkage on limits to artificial selection
HILL, W. G., & ROBERTSON, A. (2007) · Genetics Research · doi:10.1017/s001667230800949x · Cited by 1,561
Simmonds, N. W. (1979) · Medical Entomology and Zoology · Cited by 1,171
Genetic Structure and Diversity in Oryza sativa L.
Garris, A. J., Tai, T. H., Coburn, J., Kresovich, S., & McCouch, S. (2005) · Genetics · doi:10.1534/genetics.104.035642 · Cited by 1,137
Self-citation
Cited by
Adaptation from standing genetic variation
BARRETT, R., & SCHLUTER, D. (2008) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2007.09.008 · Cited by 2,091
The nature of selection during plant domestication
Purugganan, M. D., & Fuller, D. Q. (2009) · Nature · doi:10.1038/nature07895 · Cited by 1,011
Self-citationComparative population genomics of maize domestication and improvement
Hufford, M. B., Xu, X., van Heerwaarden, J., Pyhäjärvi, T., Chia, J.-M., Cartwright, R. A., Elshire, R. J., Glaubitz, J. C., Guill, K. E., Kaeppler, S. M., et al. (2012) · Nature Genetics · doi:10.1038/ng.2309 · Cited by 960
Rewiring of the Fruit Metabolome in Tomato Breeding
Zhu, G., Wang, S., Huang, Z., Zhang, S., Liao, Q., Zhang, C., Lin, T., Qin, M., Peng, M., Yang, C., et al. (2018) · Cell · doi:10.1016/j.cell.2017.12.019 · Cited by 958
Deletion in a gene associated with grain size increased yields during rice domestication
Shomura, A., Izawa, T., Ebana, K., Ebitani, T., Kanegae, H., Konishi, S., & Yano, M. (2008) · Nature Genetics · doi:10.1038/ng.169 · Cited by 888
Metadata
- Authors
- Olsen, K. M., Caicedo, A. L., Polato, N., McClung, A., McCouch, S., & Purugganan, M. D.
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-06-01
- Volume
- 173
- Issue
- 2
- Pages
- 975-983
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- OpenAlex
- W2135793062
- Cited by
- 263
- References
- 35
- FWCI
- 10.78
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Selection Under Domestication: Evidence for a Sweep in the Rice Waxy Genomic Region. https://app.cochat.ai/papers/10.1534/genetics.106.056473
- The paper
- Olsen, K. M., Caicedo, A. L., Polato, N., McClung, A., McCouch, S., & Purugganan, M. D. (2006). Selection Under Domestication: Evidence for a Sweep in the Rice Waxy Genomic Region. Genetics. https://doi.org/10.1534/genetics.106.056473
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
