Cited by 280Plant Molecular Biology ResearchChromosomal and Genetic VariationsGenetic Mapping and Diversity in Plants and Animals

Comparative Genomics of Flowering Time Pathways Using Brachypodium distachyon as a Model for the Temperate Grasses

Open access
Higgins, Janet A., Bailey, Paul C., Laurie, David A.·2010·PLoS ONE

Abstract

Brachypodium distachyon (Brachypodium) is a model for the temperate grasses which include important cereals such as barley, wheat and oats. Comparison of the Brachypodium genome (accession Bd21) with those of the model dicot Arabidopsis thaliana and the tropical cereal rice (Oryza sativa) provides an opportunity to compare and contrast genetic pathways controlling important traits. We analysed the homologies of genes controlling the induction of flowering using pathways curated in Arabidopsis Reactome as a starting point. Pathways include those detecting and responding to the environmental cues of day length (photoperiod) and extended periods of low temperature (vernalization). Variation in these responses has been selected during cereal domestication, providing an interesting comparison with the wild genome of Brachypodium. Brachypodium Bd21 has well conserved homologues of circadian clock, photoperiod pathway and autonomous pathway genes defined in Arabidopsis and homologues of vernalization pathway genes defined in cereals with the exception of VRN2 which was absent. Bd21 also lacked a member of the CO family (CO3). In both cases flanking genes were conserved showing that these genes are deleted in at least this accession. Segmental duplication explains the presence of two CO-like genes in temperate cereals, of which one (Hd1) is retained in rice, and explains many differences in gene family structure between grasses and Arabidopsis. The conserved fine structure of duplications shows that they largely evolved to their present structure before the divergence of the rice and Brachypodium. Of four flowering-time genes found in rice but absent in Arabidopsis, two were found in Bd21 (Id1, OsMADS51) and two were absent (Ghd7, Ehd1). Overall, results suggest that an ancient core photoperiod pathway promoting flowering via the induction of FT has been modified by the recruitment of additional lineage specific pathways that promote or repress FT expression.

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.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1371/journal.pone.0010065

Cites

139 of 139 references verified0 citation errors · 0 not checkable

Statistics

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.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Some flowering time genes that contribute to perenniality seem to be conserved between monocots and dicots, in a way that root architecture is not.

    “though at least some flowering time genes that contribute to perenniality seem to be conserved between monocots and dicots (Wang et al., 2009;Higgins et al., 2010), in a way that root architecture is not (see above).”

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Higgins, J. A., Bailey, P. C., & Laurie, D. A.
Affiliations
John Innes Centre (GB)
Corresponding author
Higgins, Janet A.
Venue
PLoS ONE
Published
2010-04-19
Volume
5
Issue
4
Pages
e10065
ISSN
1932-6203 (ISSN-L)
OpenAlex
W1988145565
Cited by
280
References
139
Citations by year
2026: 6 · 2025: 4 · 2024: 5 · 2023: 7 · 2022: 18 · 2021: 12 · 2020: 17 · 2019: 14 · 2018: 22 · 2017: 15 · 2016: 28 · 2015: 15 · 2014: 18 · 2013: 38 · 2012: 32
FWCI
38.11
Type
journal article
Language
en
Open access
Locations
  • PLoS ONE (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Figshare (submittedVersion, cc-by)
Funders
  • Gatsby Charitable Foundation
  • Biotechnology and Biological Sciences Research Council (BBS/E/J/000CA286)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Keywords
flowering time, Brachypodium distachyon, temperate grass, photoperiod pathway, vernalization pathway, autonomous pathway, circadian clock, CONSTANS, segmental duplication, gene family evolution, cereal domestication, Arabidopsis thaliana, rice, gene homology, MADS-box genes
MeSH terms
Poaceae, Temperature, Genes, Plant, Photoperiod, Genome, Plant, Genomics, Flowers, Metabolic Networks and Pathways

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