The Brassica rapa FLC homologue FLC2 is a key regulator of flowering time, identified through transcriptional co-expression networks

Abstract

The role of many genes and interactions among genes involved in flowering time have been studied extensively in Arabidopsis, and the purpose of this study was to investigate how effectively results obtained with the model species Arabidopsis can be applied to the Brassicacea with often larger and more complex genomes. Brassica rapa represents a very close relative, with its triplicated genome, with subgenomes having evolved by genome fractionation. The question of whether this genome fractionation is a random process, or whether specific genes are preferentially retained, such as flowering time (Ft) genes that play a role in the extreme morphological variation within the B. rapa species (displayed by the diverse morphotypes), is addressed. Data are presented showing that indeed Ft genes are preferentially retained, so the next intriguing question is whether these different orthologues of Arabidopsis Ft genes play similar roles compared with Arabidopsis, and what is the role of these different orthologues in B. rapa. Using a genetical–genomics approach, co-location of flowering quantitative trait loci (QTLs) and expression QTLs (eQTLs) resulted in identification of candidate genes for flowering QTLs and visualization of co-expression networks of Ft genes and flowering time. A major flowering QTL on A02 at the BrFLC2 locus co-localized with cis eQTLs for BrFLC2, BrSSR1, and BrTCP11, and trans eQTLs for the photoperiod gene BrCO and two paralogues of the floral integrator genes BrSOC1 and BrFT. It is concluded that the BrFLC2 Ft gene is a major regulator of flowering time in the studied doubled haploid population.

Genetic Dissection of Leaf Development in Brassica rapa Using a Genetical Genomics Approach

“…In this study, 61 out of 91 leaf genes from Arabidopsis have two or more paralogs in the B. rapa genome, while 22 have retained a single copy. Similar to this observation, genes related to flowering were maintained in higher numbers than expected when gene loss was random (Xiao et al, 2013;Supplemental Table S1). According to the "gene balance hypothesis" (Birchler and Veitia, 2010), dosage-sensitive genes duplicated by polyploidy are those with products that function in multisubunit complexes.…”

“…Similarly, five copQTLs for three traits colocalized with BRASSICA RAPA HASTY1 (BrHST1) on A01, BrGA20OX3 on A02, BRASSICA RAPA LEAFY PETIOLE on A03, BRASSICA Figure 4. The data on the regulation of the Ft genes cis-BRASSICA RAPA MADS AFFECTING FLOWERING4 (BrMAF4) and trans-BRASSICA RAPA PHYTOCHROME A are according to our previous study (Xiao et al, 2013).…”

“…Twelve Ft candidate genes associated with Ft as a positive control were added in the analysis (Xiao et al, 2013). A total of 118 probes/genes representing 110 B. rapa genes orthologous to 72 Arabidopsis genes revealed a total of 173 eQTLs (marker probe associations) against all 509 genetic markers, with at least one to five eQTLs per probe (log of the odds [LOD] $ 3; Fig.…”

“…Gene loss was certainly not random. For example, circadian clock genes and flowering genes were preferentially retained in the evolution in B. rapa (Lou et al, 2012;Tang et al, 2012;Xiao et al, 2013).…”

“…Duplicated genes are of major importance for evolutionary novelty, since they can contribute to functional innovation by mutation of their coding sequences, expression divergence, and rewiring regulatory networks through variation in interactions among different orthologs (Gaeta et al, 2007;Liu and Adams, 2007;De Smet and Van de Peer, 2012). Several studies have correlated variation in gene expression or the fate of duplicated genes to phenotypic diversity, such as flowering time (Ft) variation, leaf shape, size, and numbers, pest resistance, and stress tolerance in eukaryotes (Gaeta et al, 2007;Hovav et al, 2008;Feng et al, 2009;Whittle and Krochko, 2009;Combes et al, 2012;Costa et al, 2012;Xiao et al, 2013).…”