Natural variation in phytochrome signaling

Maloof, Julin N.; Borevitz, Justin O.; Weigel, Detlef; Chory, Joanne

doi:10.1006/scdb.2000.0198

Cited by 34 publications

(23 citation statements)

References 70 publications

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“…Notably, the proper response to light depends on whether or not the plant is native to that environment. For example, the ability of low R/FR to induce shade-avoidance responses is reduced in species and populations normally growing under shady conditions (11), an example of adaptive variation in phytochromemediated responses (12, 13).…”

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confidence: 99%

Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light

Filiault¹,

Wessinger²,

Dinneny

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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101

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Plants have a sophisticated system for sensing and responding to their light environment. The light responses of populations and species native to different habitats show adaptive variation; understanding the mechanisms underlying photomorphogenic variation is therefore of significant interest. In Arabidopsis thaliana , phytochrome B (PHYB) is the dominant photoreceptor for red light and plays a major role in white light. Because PHYB has been proposed as a candidate gene for several quantitative trait loci (QTLs) affecting light response, we have investigated sequence and functional variation in Arabidopsis PHYB . We examined PHYB sequences in 33 A. thaliana individuals and in the close relative Arabidopsis lyrata . From 14 nonsynonymous polymorphisms, we chose 5 for further study based on previous QTL studies. In a larger collection of A. thaliana accessions, one of these five polymorphisms, I143L, was associated with variation in red light response. We used transgenic analysis to test this association and confirmed experimentally that natural PHYB polymorphisms cause differential plant responses to light. Furthermore, our results show that allelic variation of PHYB activity is due to amino acid rather than regulatory changes. Together with earlier studies linking variation in light sensitivity to photoreceptor genes, our work suggests that photoreceptors may be a common target of natural selection.

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confidence: 99%

Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light

Filiault¹,

Wessinger²,

Dinneny

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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101

102

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“…Several recent studies of candidate genes from multiple accessions have linked PHYC or PHYD variation to flowering time and/or morphological variation in Arabidopsis and millet Pennistum glaucum (Balasubramanian et al, 2006;Samis et al, 2008;Ehrenreich et al, 2009;Saïdou et al, 2009) and have identified geographic structuring at PHYA and PHYE in Cardamine nipponica (Ikeda et al, 2008(Ikeda et al, , 2009). The ultimate goal of most of these studies is to link traits to genes, and they provide insight into how light signaling works in natural environments (Maloof et al, 2000). Additionally, they contribute to our understanding of phytochrome structural-functional models (e.g., Maloof et al, 2001;Filiault et al, 2008).…”

Section: Insights From Comparative Sequence Analysesmentioning

confidence: 99%

Evolutionary Studies Illuminate the Structural-Functional Model of Plant Phytochromes

Mathews

2010

The Plant Cell

107

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A synthesis of insights from functional and evolutionary studies reveals how the phytochrome photoreceptor system has evolved to impart both stability and flexibility. Phytochromes in seed plants diverged into three major forms, phyA, phyB, and phyC, very early in the history of seed plants. Two additional forms, phyE and phyD, are restricted to flowering plants and Brassicaceae, respectively. While phyC, D, and E are absent from at least some taxa, phyA and phyB are present in all sampled seed plants and are the principal mediators of red/far-red-induced responses. Conversely, phyC-E apparently function in concert with phyB and, where present, expand the repertoire of phyB activities. Despite major advances, aspects of the structural-functional models for these photoreceptors remain elusive. Comparative sequence analyses expand the array of locus-specific mutant alleles for analysis by revealing historic mutations that occurred during gene lineage splitting and divergence. With insights from crystallographic data, a subset of these mutants can be chosen for functional studies to test their importance and determine the molecular mechanism by which they might impact light perception and signaling. In

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“…The photosensory activity of the phytochrome protein stems from its ability to convert between a biologically inactive form, Pr, absorbing light at red wavelengths and a biologically active form, Pfr, absorbing light at far-red wavelengths (Smith 2000;Quail 2002). The conversion between the Pr and Pfr forms involves conformational changes of the molecule that allows for changes in signaling activity of the phytochrome protein (Maloof et al 2000). The ratio of red to far-red light changes over both short (a single day) and long (over a season) timescales and phytochromes can thus provide a plant with temporal signals that are used to synchronize developmental changes, such as the initiation or release of dormancy, with changing environmental conditions across a growing season (Smith 2000).…”

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“…The ratio of red to far-red light changes over both short (a single day) and long (over a season) timescales and phytochromes can thus provide a plant with temporal signals that are used to synchronize developmental changes, such as the initiation or release of dormancy, with changing environmental conditions across a growing season (Smith 2000). Phytochromes are thus ideal candidate genes for mediating ecologically important variation in the timing of developmental processes such as dormancy or flowering (Maloof et al 2000). Incidentally, mutations in two members of the phytochrome gene family, PHYA and PHYC have been shown to be responsible for natural variation in light sensitivity, seedling growth, and flowering time in Arabidopsis thaliana (Maloof et al 2001;Balasubramanian et al 2006).…”

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Nucleotide Polymorphism and Phenotypic Associations Within and Around the phytochrome B2 Locus in European Aspen (Populus tremula, Salicaceae)

Ingvarsson¹,

García²,

et al. 2008

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We investigated the utility of association mapping to dissect the genetic basis of naturally occurring variation in bud phenology in European aspen (Populus tremula). With this aim, we surveyed nucleotide polymorphism in 13 fragments spanning an 80-kb region surrounding the phytochrome B2 (phyB2) locus. Although polymorphism varies substantially across the phyB2 region, we detected no signs for deviations from neutral expectations. We also identified a total of 41 single nucleotide polymorphisms (SNPs) that were subsequently scored in a mapping population consisting of 120 trees. We identified two nonsynonymous SNPs in the phytochrome B2 gene that were independently associated with variation in the timing of bud set and that explained between 1.5 and 5% of the observed phenotypic variation in bud set. Earlier studies have shown that the frequencies of both these SNPs vary clinally with latitude. Linkage disequilibrium across the region was low, suggesting that the SNPs we identified are strong candidates for being causally linked to variation in bud set in our mapping populations. One of the SNPs (T608N) is located in the ''hinge region,'' close to the chromophore binding site of the phyB2 protein. The other SNP (L1078P) is located in a region supposed to mediate downstream signaling from the phyB2 locus. The lack of population structure, combined with low levels of linkage disequilibrium, suggests that association mapping is a fruitful method for dissecting naturally occurring variation in Populus tremula.

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Natural variation in phytochrome signaling

Cited by 34 publications

References 70 publications

Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light

Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light

Evolutionary Studies Illuminate the Structural-Functional Model of Plant Phytochromes

Nucleotide Polymorphism and Phenotypic Associations Within and Around the phytochrome B2 Locus in European Aspen (Populus tremula, Salicaceae)

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