Novel genetic tools to accelerate the breeding of new resilient crop varieties for sustainable agriculture: characterization of CRF transcription factors for crop genetic improvement

Biotic and abiotic stressors resulting from climate change induce stress responses in plants, negatively impacting their development and causing significant damage to agriculture. This has led to a growing need for the development of stress-resilient crops. While considerable knowledge exists about plant stress responses, the interplay between stress and development—referred to as stress-development crosstalk—remains poorly understood. This area of study holds significant potential for advancing crop improvement. Cytokinin Response Factors (CRFs), recognised for their roles in both stress responses and plant development, are promising candidates in this crosstalk as part of a side branch of the classical cytokinin (CK) two-component signalling pathway. These transcription factors have been well-characterised in species such as Arabidopsis and tomato, but have been largely neglected in the Asteraceae family, which includes many economically important leafy crops, such as Lactuca sativa and Cichorium species. To bridge this gap, we conducted an in-depth characterization of CRFs in lettuce (LsCRFs) and evaluated CRFs potential as targets for crop genetic improvement in both lettuce and tomato. Dedicated bioinformatic pipelines were developed, along with manually-curated genome annotations for lettuce. Transcriptomic meta-analyses under abiotic stress, combined with in-house RNAseq transcript profiling under CK and oxidative stress treatments, were used to characterize the transcriptional responses of LsCRFs and cytokinin pathway genes. Gene Coexpression Networks (GCNs) identified specific LsCRF members as key hubs in the regulatory networks underlying the stress-development trade-off. Furthermore, an exploration of natural and domestication-related genetic diversity in germplasm collections of lettuce and tomato identified allelic variants of CRF genes that may confer stress tolerance, contributing to breeding for stress-resilient crops with improved pathogen response and photosynthetic traits.