Transposon insertions within alleles of BnaFLC.A10 and BnaFLC.A2 are associated with seasonal crop type in rapeseed

Abstract

In Brassicaceae, the requirement for vernalization is conferred by high expression of FLOWERING LOCUS C (FLC). The expression of FLC is known to be repressed by prolonged exposure to cold. Rapeseed (Brassica napus L.) cultivars can be classified into spring, winter, and semi-winter crop types, depending on their respective vernalization requirements. In addition to two known distinct transposon insertion events, here we identified a 4.422 kb hAT and a 5.625 kb long interspersed nuclear element transposon insertion within BnaFLC.A10, and a 810 bp miniature inverted-repeat transposable element (MITE) in BnaFLC.A2. Quantitative PCR demonstrated that these insertions lead to distinct gene expression patterns and contribute differentially to the vernalization response. Transgenic and haplotype analysis indicated that the known 621 bp MITE in the promoter region of BnaFLC.A10 is a transcriptional enhancer that appears to be the main determinant of rapeseed vernalization, and has contributed to the adaptation of rapeseed in winter cultivation environments. In the absence of this transposon insertion, the functional allele of BnaFLC.A2 is a major determinant of vernalization demand. Thus, the combination of BnaFLC.A10 carrying the 621 bp MITE insertion and a functional BnaFLC.A2 appears necessary to establish the winter rapeseed crop phenotype.

The transition to flowering in winter rapeseed during vernalization

“…The transcript levels of these Bna.FLC paralogs decreased significantly in the first 4 weeks of vernalization and remained below detection levels until the end of the vernalization period (Figure 3a). Interestingly, Bna.FLC.A10 and Bna.FLC.A02 were proposed to be the main genes that contribute to the vernalization requirement in winter rapeseed (Long et al, 2007; Raman et al, 2016; Schiessl, Quezada‐Martinez, Tebartz, Snowdon, & Qian, 2019; Wu et al, 2019; Yin et al, 2020). By looking at all Bna.FLC expression profiles, we found that Bna.FLC.C02 , Bna.FLC.C03 and Bna.FLC.C09a were not expressed in any of the stages of vernalization we analysed.…”

The replicative amplification of MITEs and their impact on rice trait variability

“…Our data confirms that MITEs are closely associated to rice genes, concentrating in gene proximal upstream and downstream regions. Many examples of MITE insertions in 5’ and 3’ of genes that alter gene expression in different plants have accumulated over the years, including insertions in promoters enhancing (Zheng et al ., 2019; Shimada et al ., 2018; Yin et al ., 2020; Xu et al ., 2020) or repressing (Mao et al ., 2015; Xu et al ., 2020) transcription, or repressing translation (Shen et al ., 2017). MITEs have been shown to frequently contain transcription factor binding sites in plants, including rice (Morata et al ., 2018), suggesting a potential impact on promoter evolution.…”

“…The apparent contradiction between a conservative cut-and-paste mechanism of transposition and MITEs high copy number was highlighted short after MITE discovery (Feschotte et al ., 2002; Casacuberta and Santiago, 2003), but the mechanism by which MITEs amplify is still obscure. MITEs are tightly associated with plant genes (Santiago et al ., 2002; Lu et al ., 2012; Benjak et al ., 2009), and examples of these elements potentially altering gene expression have accumulated over the years (Santiago et al ., 2002; Lu et al ., 2012; Naito et al ., 2009; Yang et al ., 2005; Xu et al ., 2020; Zheng et al ., 2019; Yin et al ., 2020). Moreover, it has recently been shown that MITEs frequently contain Transcription Factor Binding Sites (TFBS) in plants, which may allow their mobilization to alter transcriptional networks by rewiring new genes (Morata et al ., 2018), and that they can induce structural variability through aberrant transposition events (Chen et al ., 2020).…”

Regulation and Subfunctionalization of Flowering Time Genes in the Allotetraploid Oil Crop Brassica napus

“…The data indicate that Bna.FLC.A10 is not only responsible for the high vernalization dependency of winter types, but also for the moderate vernalization dependency of semi-winter types. A recent study identified additional transposon insertions influencing expression in the promoters of Bna.FLC.A10 and Bna.FLC.A02 and concluded that Bna.FLC.A10 determines growth type in combination with Bna.FLC.A02 (Yin et al, 2020). Interestingly, swedes (ssp.…”