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Table 8 Flowering time related lost genes in three B. rapa genotypes

From: Beyond genomic variation - comparison and functional annotation of three Brassica rapagenomes: a turnip, a rapid cycling and a Chinese cabbage

Genotype Ara ID Gene name Pathway Gene full name Protein function
Rapid cycling AT2G32950 COP1 Photoperiod CONSTITUTIVE PHOTOMORPHOGENIC 1 E3 ubiquitin ligase
Rapid cycling AT3G11440 MYB65 Gibberellin MYB65 MYB transcription factor
Rapid cycling AT3G20740 FIS3 Vernalization FERTILIZATION-INDEPENDENT ENDOSPERM Encodes a protein similar to the transcriptional regular of the animal Polycomb group
Rapid cycling AT5G03790 LMI1 Flower development LATE MERISTEM IDENTITY 1 HD-Zip transcription factor
Rapid cycling AT5G47010 LBA1 Metabolic process LOW-LEVEL BETA-AMYLASE 1 Required for nonsense-mediated mRNA decay
Chiifu AT1G04440 CKL13 Vernalization CASEIN KINASE LIKE 13 Protein serine/threonine kinase activity
Chiifu AT4G25470 CBF2 Vernalization C-REPEAT/DRE BINDING FACTOR 2 Encodes a member of the DREB subfamily A-1 of ERF/AP2 transcription factor family
Chiifu AT5G59710 VIP2 Vernalization VIRE2 INTERACTING PROTEIN 2 Encodes a nuclear-localized NOT (negative on TATA-less) domain-containing
Turnip AT1G53090 SPA4 Photoperiod SPA1-RELATED 4 WD-40 and protein kinase-like domain
Turnip AT4G27430 CIP7 Photoperiod COP1-INTERACTING PROTEIN 7 -
Turnip AT5G64813 LIP1 Photoperiod LIGHT INSENSITIVE PERIOD 1 GTPase
  1. Five lost genes are related to flowering time in Rapid cycling, covering all five categories of lowering time genes. In the other genomes just three genes are found, related only to photoperiod in turnip and vernalization in Chiifu.