Cotton Science

Screening of highly efficient sgRNA for gene editing marker genes GhOMT1 and GhPGF in cotton

Guo Haomeng, Dai Peihong, Zhang Jin’en, Zhang Guoshuai, Lei Jianfeng, Liu Xiaodong

Cotton Science, 2025, 37(2): 153-164. DOI: 10.11963/cs20250005

基因ID Gene ID	区域 Region	潜在脱靶位点的序列 Sequence of the putative off-target site	匹配碱基数量（包括PAM） Number of the matched bases (include PAM)	样本读取数量 Number of sample reads
Gh_A09G1911	CDS	GAACCAAGTGGAACTTCCAAGGG	18	1 092
Gh_D03G1692	CDS	GAAAGCTGTGGAACTTGCAATGG	19	889
Gh_A02G1362	CDS	GAAAGCTGTGGAACATGCAATGG	18	970

Table 4 Detection and analysis of the potential off-target sites for GhOMT1-sgRNA2

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Fig. 1 Sequencing chromatogram of target sites of GhOMT1 and GhPGF A: Comparison of sequencing chromatogram of target sites of GhOMT1-sgRNA2 in wild type (WT) and Cas9-OE plants transformed with CLCrV-AtU6-26::GhOMT1-sgRNA viral vectors. B: Comparison of sequencing chromatogram of target sites of GhPGF-sgRNA in wild type (WT) and Cas9-OE plants transformed with CLCrV-AtU6-26::GhPGF-sgRNA viral vectors.
Table 1 Analysis of mutation patterns in plants with high editing efficiency of GhOMT1
Table 2 Analysis of mutation patterns in plants with high and low editing efficiency of GhPGF
Table 3 Relationship between viral accumulation and gene editing efficiency
Fig. 2 Analysis of the predicted secondary structures of GhOMT1-sgRNAs and GhPGF-sgRNA A-H: Secondary structures of GhOMT1-sgRNA1 to GhOMT1-sgRNA8. I: Secondary structure of GhPGF-sgRNA. RAR: retinoic acid receptors.
Fig. 3 Sequence alignment analysis of the 3 potential off-target sites for GhOMT1-sgRNA2 PAM: protospacer adjacent motif. Off-score: off-target effect score. Consensus: consistent base sequence.