Target Gene Identification and sgRNA Design for Waterlogging Tolerance in Foxtail Millet via CRISPR-based Transcriptional Activation
Background: CRISPR activation (CRISPRa) uses non-functional Cas9 endonuclease (dCas9) but retains the genome targeting ability through its single guide RNAs (sgRNAs). CRISPRa is widely utilized as a gene activation system exploiting its ability to recruit various transcriptional activation domains (TADs) to enhance the expression of the target gene(s). Drought tolerant and resource-efficient crops like millets can mitigate the effects of climate change and strengthen food security. Objective: This study aimed to use the Setaria italica (foxtail millet) genome sequence to identify a target gene and the subsequent generation of sgRNAs for use in CRISPRa for conferring waterlogging tolerance that will benefit the future expansion of its cultivation area. Methods and Results: Leveraging existing RNA-seq data and information on functional studies in model plants and from other cereal species, maize and barley, have enabled the identification of candidate ERFVII from the foxtail millet genome sequence in the attempt to engineer waterlogging tolerance. The study provides a step-by-step example for using publicly accessible databases and bioinformatics tools from NCBI and Phytozome to identify and characterize the ortholog from Setaria italica. Softberry was used for promoter annotation to obtain the transcription start site (TSS). Subsequently, CRISP-P 2.0 design tools were employed to generate and select a few efficient sgRNAs for CRISPRa that minimize potentially deleterious off-target binding. Conclusion: The study is a helpful example of how to advance in genomics research, including the revolutionizing CRISPR technology in Setaria italica, which can be adopted in other plant species by utilizing the available genome sequence.