Variation in the flowering time orthologsBrFLCandBrSOC1in a natural population ofBrassica rapa

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.

Rapid evolutionary changes in gene expression in response to climate fluctuations

“…At this time point, all of the plants had started flowering, so they were at the same developmental stage. The tissue type and collection time was previously identified as optimal for comparative analysis of gene expression in B. rapa (Franks et al, 2015). Fresh leaf material was sampled from fully developed basal leaves, and the leaves collected were similar among all plants.…”

“…Previous studies in this system demonstrated that variation in flowering time has a genetic basis and is heritable (Franks et al, 2007), is under directional selection by drought (Weis, Wadgymar, Sekor, & Franks, 2014), and evolves rapidly following dry (Franks, 2011;Franks et al, 2007) and wet periods (Hamann et al, 2018). Individual flowering time candidate genes differed in expression levels between early and late flowering individuals (Franks et al, 2015). At the genome scale, many genes showed evolutionary shifts in frequencies between ancestral and descendant lines.…”

“…One particularly well-studied case of evolutionary responses to fluctuations in climatic conditions in natural populations is the evolution of Californian Brassica rapa populations in response to drought (Franks, 2011;Franks et al, 2007Franks et al, , 2015Franks et al, , 2016. Previous studies in this system demonstrated that variation in flowering time has a genetic basis and is heritable (Franks et al, 2007), is under directional selection by drought (Weis, Wadgymar, Sekor, & Franks, 2014), and evolves rapidly following dry (Franks, 2011;Franks et al, 2007) and wet periods (Hamann et al, 2018).…”

FLC expression is down-regulated by cold treatment in Diplotaxis tenuifolia (wild rocket), but flowering time is unaffected

“…This could be due to its origins in the Mediterranean where a vernalization response would be a disadvantage as has been found in B.napus varieties grown in Mediterranean climates where the lack of a vernalization requirement is important for its early flowering phenotype ( Dahanayake and Galwey, 1999 ). Other studies in B.rapa have also shown that vernalization isn’t a requirement for plants bred in warmer climates ( Franks et al, 2015 ).…”

Translating Flowering Time From Arabidopsis thaliana to Brassicaceae and Asteraceae Crop Species

“…Overexpression of a B. rapa SOC1 ortholog ( BrAGL20 ) in B. napus causes early flowering [55], suggesting that the function of this gene may be conserved in Brassicaceae. Moreover, association between flowering time and expression of the two SOC1 paralogs Br004928 and Br000393 was found in a natural population of B. rapa [56].…”