Differential Expression of Genes Important for Adaptation inCapsella bursa-pastoris(Brassicaceae)

Abstract

Understanding the genetic basis of natural variation is of primary interest for evolutionary studies of adaptation. In Capsella bursa-pastoris, a close relative of Arabidopsis (Arabidopsis thaliana), variation in flowering time is correlated with latitude, suggestive of an adaptation to photoperiod. To identify pathways regulating natural flowering time variation in C. bursapastoris, we have studied gene expression differences between two pairs of early-and late-flowering C. bursa-pastoris accessions and compared their response to vernalization. Using Arabidopsis microarrays, we found a large number of significant differences in gene expression between flowering ecotypes. The key flowering time gene FLOWERING LOCUS C (FLC) was not differentially expressed prior to vernalization. This result is in contrast to those in Arabidopsis, where most natural flowering time variation acts through FLC. However, the gibberellin and photoperiodic flowering pathways were significantly enriched for gene expression differences between early-and late-flowering C. bursa-pastoris. Gibberellin biosynthesis genes were downregulated in late-flowering accessions, whereas circadian core genes in the photoperiodic pathway were differentially expressed between early-and late-flowering accessions. Detailed time-series experiments clearly demonstrated that the diurnal rhythm of CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) and TIMING OF CAB EXPRESSION1 (TOC1) expression differed between flowering ecotypes, both under constant light and long-day conditions. Differential expression of flowering time genes was biologically validated in an independent pair of flowering ecotypes, suggesting a shared genetic basis or parallel evolution of similar regulatory differences. We conclude that genes involved in regulation of the circadian clock, such as CCA1 and TOC1, are strong candidates for the evolution of adaptive flowering time variation in C. bursa-pastoris.

Natural diversity in daily rhythms of gene expression contributes to phenotypic variation

“…S5). Previous studies had reported natural variation of daily transcriptional rhythms in the range of hours (14,17), but our experiments reveal that natural alleles can cause significant variation of a higher level of precision.…”

“…Natural diversity in daily transcriptional rhythms has mostly been analyzed by comparing gene expression between limited numbers of selected genotypes and by using temporal resolutions of relatively low precision (14,17). To date, there has been no extensive survey describing how rhythms of expression vary at the intraspecies level, at more informative temporal resolutions, and during biologically relevant day/night cycles.…”

Long‐term acclimation to reciprocal light conditions suggests depth‐related selection in the marine foundation speciesPosidonia oceanica

“…Both phytochromes and cryptochromes mediate several morphological, physiological, and developmental responses to red, far‐red, and blue light in plants and algae (Li & Yang, 2007; Maloof, Borevitz, Weigel, & Chory, 2000; Schmitt, Stinchcombe, Heschel, & Huber, 2003; Smith, 2000). They have also a key role in controlling photoperiod in plants (Balasubramanian et al., 2006; Hall et al., 2007; Mendez‐Vigo, Pico, Ramiro, & Martı, 2011; Slotte, Holm, Mcintyre, Lagercrantz, & Lascoux, 2007). Indeed, the down‐regulation of cryptochrome 1 (during the whole exposure period) and phytochrome A (in T2 and T3) is noteworthy because these two photoreceptors are intimately involved in promoting several light acclimation responses in higher plants (see, e.g., Walters, Rogers, Shephard, & Horton, 1999).…”

Local Selection Across a Latitudinal Gradient Shapes Nucleotide Diversity in Balsam Poplar, Populus balsamifera L

“…Surveys of natural allelic variation among A. thaliana accessions sampled from diverse latitudes have identified two flowering-time genes, FRIGIDA (FRI) and FLOWERING LOCUS C (FLC), that show evidence of local adaptation with latitude (Caicedo et al 2004;Stinchcombe et al 2004;Le Corre 2005). In other species, local selection has targeted members of the phytochrome gene family (PHYE) in Cardamine japonica (Ikeda et al 2009) and PHYB2 in Populus tremula (Ingvarsson et al 2006;Ingvarsson et al 2008) and components of the circadian clock (Böhlenius et al 2006;Slotte et al 2007;Brachi et al 2010;Ma et al 2010). These studies suggest that homologs of the A. thaliana flowering-time gene network underlie ecologically important adaptive variation in phenological responses in other species, making them promising candidates for studying the molecular basis of local adaptation, as well as testing the repeatability of evolution across taxa in genes that influence quantitative traits.…”