Comparative Genomics of Flowering Time Pathways Using Brachypodium distachyon as a Model for the Temperate Grasses
Open accessAbstract
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.
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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).”
From Breeding crop plants with deep roots: their role in sustainable carbon, nutrient and water sequestration (2011) · cites this paper as Higgins et al., 2010
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- Authors
- Higgins, J. A., Bailey, P. C., & Laurie, D. A.
- Affiliations
- John Innes Centre (GB)
- Corresponding author
- Higgins, Janet A.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2010-04-19
- Volume
- 5
- Issue
- 4
- Pages
- e10065
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC2856676
- 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
- gold
- doi.org
- 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
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