Engineering quantitative trait variation for crop improvement by genome editing

Traditional plant breeding is limited by incremental improvements in quantitative traits that often rely on rare naturally occurring mutations in gene regulatory regions. We use CRISPR/Cas9 genome-editing of promoters to engineer quantitative variation for breeding. Using a simple genetic scheme exploiting trans-generational heritability of Cas9, multiple promoter variants for SlCLV3 were rapidly produced and evaluated for phenotypic impact. In addition to simple indel lesions, this approach also generated several larger order promoter variants that were assayed by Illumina sequencing. These promoter alleles provide a quantitative range of SlCLV3 activity for fine manipulation of yield components.