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Coffea arabica  is an allotetraploid of high economic importance.  C .  arabica  transcriptome is a combination of the transcripts of two parental genomes ( C .  eugenioides  and  C .  canephora ) that gave rise to the homeologous genes of the species. Previous studies have reported the transcriptional dynamics of  C .  arabica . In these reports, the ancestry of homeologous genes was identified and the overall regulation of homeologous differential expression (HDE) was explored. One of these genes is part of the  FRIGIDA -like family ( FRL ), which includes the  Arabidopsis thaliana  flowering-time regulation protein,  FRIGIDA  ( FRI ). As nonfunctional  FRI  proteins give rise to rapid-cycling summer annual ecotypes instead of vernalization-responsive winter-annuals, allelic variation in  FRI  can modulate flowering time in  A .  thaliana . Using bioinformatics, genomic analysis, and the evaluation of gene expression of homeologs, we characterized the  FRL  gene family in  C .  arabica . Our findings indicate that  C .  arabica  expresses 10  FRL  homeologs, and that, throughout flower and fruit development, these genes are differentially transcribed. Strikingly, in addition to confirming the expression of  FRL  genes during zygotic embryogenesis, we detected  FRL  expression during direct somatic embryogenesis, a novel finding regarding the  FRL  gene family. The HDE profile of  FRL  genes suggests an intertwined homeologous gene regulation. Furthermore, we observed that  FLC  gene of  C .  arabica  has an expression profile similar to that of  CaFRL  genes.

scientific reports

Homeologous regulation of Frigida-like genes provides insights on reproductive development and somatic embryogenesis in the allotetraploid Coffea arabica