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

Abstract

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.

Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis

“…In Arabidopsis, genetic variations from SNPs to CNVs could affect gene functions; for example, SNPs can change amino acids in phytochrome A (PHYA) and B (PHYB), affecting light responses and flowering time (Maloof et al 2001;Filiault et al 2008). A SNP also created a new splicing site that altered gene function (GuyonDebast et al 2010).…”

Regulatory change at Physalis Organ Size 1 correlates to natural variation in tomatillo reproductive organ size

“…However, few were proven to be involved in the natural variation of the size of certain organs. Several of the resolved loci alter the encoded protein sequence, thus, either the protein is functionally altered, or it becomes non-functional, and the resulting allelic polymorphisms can explain the origin of natural variation [34][35][36][37][38][39][40][41] . Nonetheless, substantial natural variation exists in gene expression within and among natural populations, and this quantitative variation is also important in the evolution of natural variation 36,42 .…”

Evolutionary Studies Illuminate the Structural-Functional Model of Plant Phytochromes

“…Natural populations of most species harbor extensive variation, and particularly where genomic and genetic resources are also available, they offer a useful set of genetic polymorphisms for study (e.g., AlonsoBlanco and Koornneef, 2000;Shindo et al, 2005;Buckler et al, 2009;McMullen et al, 2009). Studies of natural variation have been used to map quantitative trait loci controlling responses to light, dark, and cold in Arabidopsis Borevitz et al, 2002;Meng et al, 2008), to identify accessions that vary in responses to R or FR light (Maloof et al, 2001;Botto and Smith, 2002;Filiault et al, 2008) or in phytochrome activities (Eichenberg et al, 2000b), to infer a role for phyB in chromatin compaction (Tessadori et al, 2009), and to investigate the basis of plastic responses to shifts in the R:FR ratio (Brock et al, 2007). Natural variation in phytochrome responses has been detected in other species, including barley (Hordeum vulgare; Biyashev et al, 1997), oat (Avena sativa; Hou and Simpson, 1993), and Plantago lanceolata (Van Hinsberg, 1998), and single nucleotide polymorphisms at PHYB are candidates for causal linkage with clinal variation in bud set in Populus tremula (Ingvarsson et al, 2006).…”

“…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). For example, a polymorphism discovered in a sequence screen of natural PHYB alleles is associated with variation in response to R (Filiault et al, 2008), and the PHYA sequence in a natural mutant with reduced sensitivity to FR, Lm-2, has a single amino acid polymorphism at position 548 that leads to greater stability of the phyA holoprotein (Maloof et al, 2001).…”

“…Additionally, they contribute to our understanding of phytochrome structural-functional models (e.g., Maloof et al, 2001;Filiault et al, 2008). For example, a polymorphism discovered in a sequence screen of natural PHYB alleles is associated with variation in response to R (Filiault et al, 2008), and the PHYA sequence in a natural mutant with reduced sensitivity to FR, Lm-2, has a single amino acid polymorphism at position 548 that leads to greater stability of the phyA holoprotein (Maloof et al, 2001). The change in FR sensitivity results from a M548T mis-sense mutation in the tongue region of the PHY domain, a region of Synechocystis Cph1 that seals the chromophore pocket and stabilizes Pfr (Essen et al, 2008).…”