CRISPR/Cas genome editing strategies to enhance abiotic stress tolerance in sugar crops

Abstract

Sugar crops including sugarcane, sugar beets, and sweet sorghum, are fundamental for global sucrose supply and crucial feedstocks for bioethanol production and industrial bioproducts. However, yield and sucrose accumulation are significantly influenced by abiotic stresses, including drought, salinity/alkalinity, heat, chilling/freezing, and heavy metal toxicity. The polygenic complexity of stress tolerance, particularly in sugarcane with its large, polyploid, and haplotype-diverse genome, presents significant challenges for conventional breeding, rendering it slow and imprecise. This review combines advances in genome-editing technologies, including CRISPR/Cas systems (Cas9 and Cas12a), along with transcriptional techniques (CRISPRa/i), base editors, and prime editors. These tools, combined with the progress in reference genomes, haplotype-resolved assemblies, and pangenomes, have facilitated precise gene discovery, genomic selection, and targeted editing. CRISPR-based approaches offer promising avenues for enhancing key stress-responsive pathways governing oxidative homeostasis, membrane integrity, osmotic regulation, hormone signaling, and ion-homeostasis in sugar crops. Prominent candidate targets include transcription factors (TF), signaling components, raffinose biosynthesis genes implicated in freezing tolerance, regulators of salt and alkaline stress, and determinants of heavy metal tolerance and sequestration. Translational challenges, such as off-target effects, low transformation efficiencies, and editing multiple homologues or haplotypes, are being addressed such as DNA-free ribonucleoprotein (RNP) delivery, high-throughput screening, haplotype-specific target design, and haplotype-aware guide RNA engineering based on unique genetic variation sites across different gene haplotypes. Collectively, the integration of advanced CRISPR toolkits with enhanced genomic information resources and phenotyping capabilities holds significant potential for accelerating the development of precision-bred, multi-stress-resilient sugar crops that sustain yield, quality, and industrial value under abiotic stress conditions.