Variation in the flowering time orthologsBrFLCandBrSOC1in a natural population ofBrassica rapa

Rebecca Lalchan,Kevin P Jordan,Maya Strahl,Amy Litt,Jennifer J Weber,Beatriz Perez-Sweeney,Steven J Franks,Anna Nowogrodzki

doi:10.7717/peerj.1339

Abstract

Understanding the genetic basis of natural phenotypic variation is of great importance, particularly since selection can act on this variation to cause evolution. We examined expression and allelic variation in candidate flowering time loci in Brassica rapa plants derived from a natural population and showing a broad range in the timing of first flowering. The loci of interest were orthologs of the Arabidopsis genes FLC and SOC1 (BrFLC and BrSOC1, respectively), which in Arabidopsis play a central role in the flowering time regulatory network, with FLC repressing and SOC1 promoting flowering. In B. rapa, there are four copies of FLC and three of SOC1. Plants were grown in controlled conditions in the lab. Comparisons were made between plants that flowered the earliest and latest, with the difference in average flowering time between these groups ∼30 days. As expected, we found that total expression of BrSOC1 paralogs was significantly greater in early than in late flowering plants. Paralog-specific primers showed that expression was greater in early flowering plants in the BrSOC1 paralogs Br004928, Br00393 and Br009324, although the difference was not significant in Br009324. Thus expression of at least 2 of the 3 BrSOC1 orthologs is consistent with their predicted role in flowering time in this natural population. Sequences of the promoter regions of the BrSOC1 orthologs were variable, but there was no association between allelic variation at these loci and flowering time variation. For the BrFLC orthologs, expression varied over time, but did not differ between the early and late flowering plants. The coding regions, promoter regions and introns of these genes were generally invariant. Thus the BrFLC orthologs do not appear to influence flowering time in this population. Overall, the results suggest that even for a trait like flowering time that is controlled by a very well described genetic regulatory network, understanding the underlying genetic basis of natural variation in such a quantitative trait is challenging.

Highlights

Genetic variation contributes to phenotypic variation and provides the raw material that natural selection acts upon to produce adaptive evolution
We focused on sequence and expression variation in orthologs of the key Arabidopsis flowering time regulatory genes FLC and SOC1, testing the hypothesis that such variation underlies the natural variation observed in flowering time
We found that combined BrSOC1 expression was significantly greater in early compared to late flowering plants (F1,18 = 49.2, p < 0.0001; Fig. 4), consistent with experiments in Arabidopsis showing that SOC1 promotes flowering (Immink et al, 2012)

Summary

Introduction

Genetic variation contributes to phenotypic variation and provides the raw material that natural selection acts upon to produce adaptive evolution. Despite a burgeoning amount of genetic and genomic information, we still know little about genetic variation in ecologically important traits in natural populations. One such trait in plant populations is the timing of first flowering. To predict the ability of populations to evolve in response to climate change, it is useful to understand the relationship between genetic variation and phenotypic variation in the traits of interest, since selection can act on this variation to produce evolutionary change (Hoffmann & Sgro, 2011). The genetic basis of phenotypic variation and evolutionary responses to climate change is rarely known, this is an emerging area of investigation, with the genetic basis of variation in flowering time amenable to study (Franks & Hoffmann, 2012)

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Conclusion