Genome-wide identification and expression analysis of the CBF/DREB1 gene family in lettuce

Authors: Park, Sunchung - Sun; SHI, AINONG - University Of Arkansas; Mou, Beiquan

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/12/2020
Publication Date: 3/31/2020
Citation: Park, S., Shi, A., Mou, B. 2020. Genome-wide identification and expression analysis of the CBF/DREB1 gene family in lettuce. Scientific Reports. 10:5733. https://doi.org/10.1038/s41598-020-62458-1.
DOI: https://doi.org/10.1038/s41598-020-62458-1

Interpretive Summary: Lettuce grows poorly under cold temperatures, consequently limiting its distribution to regions with mild winters such as the lower deserts of California and Arizona, where brief periods of freezing temperatures occur in mid-winter. Brief exposures to frost can drastically reduce quality of the lettuce. Freezing temperatures can cause blisters and peeling of lettuce leaves that may lead to decay and rot. Damaged leaves also provide entrance for plant pathogens. Thus, improvement of freezing tolerance is an important long-term lettuce breeding goal for mid-winter production. The C-repeat binding factor (CBF)/dehydration-responsive element binding (DREB1) transcription factors have been known for their prominent role in freezing tolerance in many crops. We identified 14 CBF transcription factors in lettuce through a bioinformatic search of lettuce genome that was released in 2017. The lettuce CBFs are responsive not only to cold stress but also to heat or salt stress, suggesting their roles in protection against a wide range of abiotic stresses.

Technical Abstract: The C-repeat binding factor (CBF)/dehydration-responsive element binding (DREB1) proteins play a prominent role in freezing tolerance and are highly conserved in higher plants. Here we performed a genome-wide search of the CBF/DREB1 gene family in lettuce (Lactuca sativa L.) and identified 14 members of the family with one member gene containing a non-sense mutation within the AP2 DNA-binding domain. A comprehensive phylogenetic analysis of the CBF/DREB1 family members in 20 plant species from the Asterid or Rosid clade provided evidence that tandem duplication played an important role in the expansion of the CBF/DREB1 family. Expression analysis showed that twelve of the lettuce CBF genes were responsive to low temperature (4'°C), and that three and six of them could also be responsive to salt and heat stresses, respectively. Unlike Arabidopsis thaliana whose members of the CBF/DREB1 family respond only to a particular stress, lettuce CBFs provide wider protection from combinations of abiotic stresses. A global transcriptome analysis revealed distinctive temporal expression patterns among the cold-regulated genes in lettuce plants exposed to low temperature. Genes induced throughout the cold treatment are enriched in functions associated with protection from UV and high-light intensity and the genes suppressed after 7 days of cold exposure are enriched in photosynthesis-associated functions. These results provide insight into the molecular evolutionary properties of the CBF/DREB1 gene family in lettuce and a reference for genetic improvement of the lettuce response to cold acclimation.