The evolution of Brassica napus FLOWERING LOCUST paralogues in the context of inverted chromosomal duplication blocks

Abstract

BackgroundThe gene FLOWERING LOCUS T (FT) and its orthologues play a central role in the integration of flowering signals within Arabidopsis and other diverse species. Multiple copies of FT, with different cis-intronic sequence, exist and appear to operate harmoniously within polyploid crop species such as Brassica napus (AACC), a member of the same plant family as Arabidopsis.ResultsWe have identified six BnFT paralogues from the genome of B. napus and mapped them to six distinct regions, each of which is homologous to a common ancestral block (E) of Arabidopsis chromosome 1. Four of the six regions were present within inverted duplicated regions of chromosomes A7 and C6. The coding sequences of BnFT paralogues showed 92-99% identities to each other and 85-87% identity with that of Arabidopsis. However, two of the paralogues on chromosomes A2 and C2, BnA2.FT and BnC2.FT, were found to lack the distinctive CArG box that is located within intron 1 that has been shown in Arabidopsis to be the binding site for theFLC protein. Three BnFT paralogues (BnA2.FT, BnC6.FT.a and BnC6.FT.b) were associated with two major QTL clusters for flowering time. One of the QTLs encompassing two BnFT paralogues (BnC6.FT.a and BnC6.FT.b) on chromosome C6 was resolved further using near isogenic lines, specific alleles of which were both shown to promote flowering. Association analysis of the three BnFT paralogues across 55 cultivars of B. napus showed that the alleles detected in the original parents of the mapping population used to detect QTL (NY7 and Tapidor) were ubiquitous amongst spring and winter type cultivars of rapeseed. It was inferred that the ancestral FT homologues in Brassica evolved from two distinct copies, one of which was duplicated along with inversion of the associated chromosomal segment prior to the divergence of B. rapa (AA) and B. oleracea (CC). At least ten such inverted duplicated blocks (IDBs) were identified covering a quarter of the whole B. napus genome.ConclusionSix orthologues of Arabidopsis FT were identified and mapped in the genome of B. napus which sheds new light on the evolution of paralogues in polyploidy species. The allelic variation of BnFT paralogues results in functional differences affecting flowering time between winter and spring type cultivars of oilseed Brassica. The prevalent inverted duplicated blocks, two of which were located by four of the six BnFT paralogues, contributed to gene duplications and might represent predominant pathway of evolution in Brassica.

BnaC9.SMG7b functions as a positive regulator of number of seeds per silique in rapeseed (Brassica napus L.) by regulating the formation of functional female gametophytes

“…SMG7b and BnaC9.SMG7c may specifically function in female and male meiotic cell cycle progression, respectively, whereas other homologous BnSMG7 copies may be mainly involved in NMD decay, although they can complement the function of BnaC9.SMG7b to some extent. In polyploid crops, the functional divergence of duplicated genes may be an important source of quantitative trait variation, such as the flowering time regulation in B. napus (Wang et al, 2009).…”

Expression divergence of FRUITFULL homeologs enhanced pod shatter resistance in Brassica napus

“…nlm.nih.gov) and a standard BLAST search, some paralogs with very high sequence identity were found. Because homeologs were derived from the same ancestral gene, they are typically highly conserved, as observed for many genes in polyploid species (Wang et al, 2009;Huang and Brûlé-Babel, 2010).…”

Identification of quantitative trait loci controlling late bolting in Chinese cabbage (Brassica rapa L.) parental line Nou 6 gou

“…Similarly, Okazaki et al (2007) reported that BoFLC2 plays a central role in the repression of flowering in B. oleracea (Okazaki et al 2007). Wang et al (2009) reported that BnC6FTa, the orthologous gene of BrFTa, was associated with the major QTL for flowering time in B. napus. Furthermore, our QTL analysis showed that BrFTa was located near QTL for bolting time in B. rapa (Fig.…”