A naturally occurring InDel variation in BraA.FLC.b (BrFLC2) associated with flowering time variation in Brassica rapa

Abstract

BackgroundFlowering time is an important trait in Brassica rapa crops. FLOWERING LOCUS C (FLC) is a MADS-box transcription factor that acts as a potent repressor of flowering. Expression of FLC is silenced when plants are exposed to low temperature, which activates flowering. There are four copies of FLC in B. rapa. Analyses of different segregating populations have suggested that BraA.FLC.a (BrFLC1) and BraA.FLC.b (BrFLC2) play major roles in controlling flowering time in B. rapa.ResultsWe analyzed the BrFLC2 sequence in nine B. rapa accessions, and identified a 57-bp insertion/deletion (InDel) across exon 4 and intron 4 resulting in a non-functional allele. In total, three types of transcripts were identified for this mutated BrFLC2 allele. The InDel was used to develop a PCR-based marker, which was used to screen a collection of 159 B. rapa accessions. The deletion genotype was present only in oil-type B. rapa, including ssp. oleifera and ssp. tricolaris, and not in other subspecies. The deletion genotype was significantly correlated with variation in flowering time. In contrast, the reported splicing site variation in BrFLC1, which also leads to a non-functional locus, was detected but not correlated with variation in flowering time in oil-type B. rapa, although it was correlated with variation in flowering time in vegetable-type B. rapa.ConclusionsOur results suggest that the naturally occurring deletion mutation across exon 4 and intron 4 in BrFLC2 gene contributes greatly to variation in flowering time in oil-type B. rapa. The observed different relationship between BrFLC1 or BrFLC2 and flowering time variation indicates that the control of flowering time has evolved separately between oil-type and vegetable-type B. rapa groups.

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

“…The PC-175 sequence did not have this deletion and was identical to the reference Chinese cabbage sequence in this region. Wu et al (2012) sequenced BrFLC2 alleles from Yellow sarson (accession L143), three Chinese cabbage genotypes, Rapid cycling (accession L144), Mizuna, Neep greens, Turnip, and Caixin, and identified a discontinuous 57bp insertion/deletion (InDel) across exon 4 and intron 4 in Yellow sarson resulting in a non-functional allele (Wu et al , 2012). This deletion was absent in all other vegetable accessions they tested and present in many of the tested oil types, and homozygous in the three Yellow sarson accessions tested, but absent in the other accessions they tested.…”

An allotetraploid Brassica napus early‐flowering mutant has BnaFLC2‐regulated flowering

“…In B. oleracea , only BolFLC2 contributes to the control of flowering time . In B. rapa , BraFLC1 and BraFLC2 are candidate genes for the flowering time and vernalization response QTL in B. rapa …”

“…In B. rapa , BraFLC1 and BraFLC2 are candidate genes for the flowering time and vernalization response QTL in B. rapa . Deletion mutation across exon 4 and intron 4 in BrFLC2 gene contributes greatly to variation in flowering time in oil‐type B. rapa …”

Differential Expression of Flowering Genes between Rapid- and Slow-Cycling Brassica rapa

“…Schranz et al (2002) and Franks et al (2015) reported presence of four FLC paralogues in B. rapa (BrFLC1,BrFLC2,BrFLC3,and BrFLC5). A genetic-genomics approach revealed that BrFLC2 is a major regulator of flowering time in B. rapa (Wu et al 2012;Xiao et al 2013;2014). Recently, Li et al (2016) reported that early flowering phenotypes of B. rapa is related to be nonfunctional BrFLCs which are truncated form by premature termination, but slow or late flowering types contain functional or intact forms of BrFLC1, BrFLC2, and BrFLC3.…”