Targeted deletions of large syntenic regions in Arabidopsis thaliana
Plant genomes have undergone multiple rounds of whole genome duplication and polyploidy over time. As a result, many plant species, including Arabidopsis thaliana, have numerous retained duplicate blocks or syntenic regions within their genomes, resulting in the retention of paralogous genes. We deleted four large duplicated blocks, ranging from ~115 kb to ~684 kb using Staphylococcus aureus Cas9 (SaCas9) to explore the effects of knocking out these retained blocks in Arabidopsis. Deletions were subsequently verified using whole genome sequencing, which revealed that there were limited off-target effects. The number of deleted genes ranged from 16 to 60, and deleted transposable element (TE) genes ranged from 4 to 112 among the four deleted retained blocks. Two deletion lines showed distinct phenotypes resulting from the loss of many genes, while two other deletions displayed no obvious defects for flowering time or hypocotyl elongation. Moreover, RNA sequencing (RNA-seq) analysis of the deleted lines revealed that expression compensation was not a general response to the deleted regions. Thus, it is possible to obtain viable plants when deleting large genomic regions that may be redundant or regions that contain non-essential genes. These results demonstrate that large chromosomal deletions can be used as a tool for various genome engineering approaches, such as genome minimization in plants and allele replacement using homology-directed repair mechanisms and other precision editing methods. Targeted deletions of large chromosome fragments will be a valuable tool for research and biotechnology applications.