Variation in the flowering time orthologs BrFLC and BrSOC1 in a natural population of Brassica 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.

Genome-Wide Characterization of the MADS-Box Gene Family in Radish (Raphanus sativus L.) and Assessment of Its Roles in Flowering and Floral Organogenesis

“…Flowering-related genes were affected by multiple flowering signals converging on the regulation of floral organ identity genes including SEP3 , AP1 , AG and AP3 , leading to flower formation eventually ( Posé et al, 2012 ; Sun et al, 2013 ; Zhou et al, 2013 ; Khan et al, 2014 ). Considerable reports have indicated that FLC and SOC1 as floral pathway integrators which were regulated by numerous genes and flowering pathways, played important roles in the flowering process ( Lee et al, 2007 ; Franks et al, 2015 ). Genetic studies showed that FLC could block the transcriptional activation of SOC1 and required SVP and FRI to delay flowering strongly ( Helliwell et al, 2006 ; Lee et al, 2007 ; Geraldo et al, 2009 ; Franks et al, 2015 ).…”

“…Considerable reports have indicated that FLC and SOC1 as floral pathway integrators which were regulated by numerous genes and flowering pathways, played important roles in the flowering process ( Lee et al, 2007 ; Franks et al, 2015 ). Genetic studies showed that FLC could block the transcriptional activation of SOC1 and required SVP and FRI to delay flowering strongly ( Helliwell et al, 2006 ; Lee et al, 2007 ; Geraldo et al, 2009 ; Franks et al, 2015 ). AGL16 , a target gene of miR824, can help to repress flowering time by interacting indirectly with FLC and directly with SVP in A. thaliana ( Hu et al, 2014 ).…”

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.…”

“…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., 2007, 2015, 2016; Franks & Weis, 2008; Hamann, Weis, & Franks, 2018). 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).…”

“…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.…”