Abstract
Flowering time genes have a strong influence on successful reproduction and life cycle adaptation. However, their regulation is highly complex and only well understood in diploid model systems. For crops with a polyploid background from the genus Brassica, data on flowering time gene variation are scarce, although indispensable for modern breeding techniques like marker-assisted breeding. We have deep-sequenced all paralogs of 35 Arabidopsis thaliana flowering regulators using Sequence Capture followed by Illumina sequencing in two selected accessions of the vegetable species Brassica rapa and Brassica oleracea, respectively. Using these data, we were able to call SNPs, InDels and copy number variations (CNVs) for genes from the total flowering time network including central flowering regulators, but also genes from the vernalisation pathway, the photoperiod pathway, temperature regulation, the circadian clock and the downstream effectors. Comparing the results to a complementary data set from the allotetraploid species Brassica napus, we detected rearrangements in B. napus which probably occurred early after the allopolyploidisation event. Those data are both a valuable resource for flowering time research in those vegetable species, as well as a contribution to speciation genetics.
Highlights
105 regions had a BLAST hit to a target gene of B. napus as analyzed in (Schiessl et al, 2017b), while 95 regions of those with a BLAST hit co-localized with an annotated B. rapa gene
For the two B. oleracea accessions we found 3010 regions with a normalized coverage of at least 10, with 365 regions co-localizing with an annotated B. oleracea gene and 111 regions showing a BLAST hit to a target B. napus region
When mapping the sequencing reads from B. rapa and B. oleracea onto the B. napus reference genome, we found that BnaA02g16710D (Bna.ZTL.A02) had a strongly reduced normalized coverage in both B. rapa lines (2 and 13% of the mean B. napus coverage), while both B.oleracea lines had significant coverage at this locus (169 and 159% of the mean B. napus coverage)
Summary
It contains many phenotypically extremely different vegetable, turnip and oil crops, among them garden turnip, Chinese cabbage and Pak Choi (Brassica rapa) and cabbage, broccoli, cauliflower, Brussels sprouts, kale, kohlrabi and savoy (Brassica oleracea) (Paterson et al, 2001). Both species are diploid progenitors of B. napus, which comprises rapeseed/ canola and rutabagas (Chalhoub et al, 2014). Adequate regulation of flowering and flowering time is crucial for crop production especially for leafy vegetable crops as in B. rapa and B. oleracea. The expression of FT is negatively regulated by the transcriptional repressor FLOWERING LOCUS C (FLC) in interaction with other genetic factors from the vernalisation pathway, and positively regulated via the transcriptional
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