Abstract
Flax (Linum usitatissimum) is a cool season crop commercially cultivated for seed oil and stem fibre production. A comprehensive characterization of the heat shock factor (HSF) candidate genes in flax can accelerate genetic improvement and adaptive breeding for high temperature stress tolerance. We report the genome-wide identification of 34 putative HSF genes from the flax genome, which we mapped on 14 of the 15 chromosomes. Through comparative homology analysis, we classified these genes into three broad groups, and sub-groups. The arrangement of HSF-specific protein motifs, DNA-binding domain (DBD) and hydrophobic heptad repeat (HR-A/B), and exon-intron boundaries substantiated the phylogenetic separation of these genes. Orthologous relationships and evolutionary analysis revealed that the co-evolution of the LusHSF genes was due to recent genome duplication events. Digital and RT-qPCR analyses provided significant evidence of the differential expression of the LusHSF genes in various tissues, at various developmental stages, and in response to high-temperature stress. The co-localization of diverse cis-acting elements in the promoters of the LusHSF genes further emphasized their regulatory roles in the abiotic stress response. We further confirmed DNA-binding sites on the LusHSF proteins and designed guide RNA sequences for gene editing with minimal off-target effects. These results will hasten functional investigations of LusHSFs or assist in devising genome engineering strategies to develop high-temperature stress tolerant flax cultivars.
Highlights
The impact of global warming on crop productivity is alarming and presumed to decrease global crop yield by 1.5% per decade
We identified guide RNA sequences from the LusHSFs to be used in functional studies and genetic improvement through gene editing with the aim of obtaining minimal off-target genomic effects
The individual heat shock factor (HSF) protein sequences were further supported by scanning against the Pfam-A database at the E-value threshold of 10−3 and the Simple Modular Architecture Research Tool (SMART) web server for the presence of the characteristic HSF-DNA-binding domain (DBD) and coiled-coil structures
Summary
The impact of global warming on crop productivity is alarming and presumed to decrease global crop yield by 1.5% per decade. These proteins respond by the folding, accumulation, and degradation of other protective proteins when cells are exposed to HT stress[2] The expression of these HSP-coding genes is regulated by a group of DNA-binding transcription factors, known as heat shock factors (HSFs). Upon HT stress, several proteins in the cell misfold, to which HSPs interact and become dissociated from HSFA This dissociation allows HSFA to form trimers, expose the NLS sequence and translocate to the nucleus to trigger transcription. The genome-wide analysis of HSF genes in various plants has revealed their regulatory roles in HT stress and in other abiotic stress responses. The genetically variable superior alleles of HSPs and HSFs can be harnessed to breed flax varieties with an enhanced capacity to adapt to warm climatic conditions. We identified guide RNA (gRNA) sequences from the LusHSFs to be used in functional studies and genetic improvement through gene editing with the aim of obtaining minimal off-target genomic effects
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