Production of novel beneficial alleles of a rice yield-related QTL by CRISPR/Cas9.

In crop plants, many beneficial alleles of yield-related quantitative trait loci involve changes in transcription, rather than changes in protein coding sequence. However, these alleles have multiple mutations and discerning the causal mutation and then recapitulating this mutation in elite crop cultivars has remained challenging. Now, CRISPR-Cas9 approaches allow researchers to address both issues. Our study of a locus involved in resistance to lodging demonstrated that saturation editing of the qSCSA3-1/OsTB1/SCM3 region led to loss-of-function, normal-like, and gain-of-function plant types, based on OsTB1 expression and stem cross-section area. One gain-of-function allele recapitulated a previously described beneficial allele of OsTB1 carrying a TGTG insertion in the 5' region of OsTB1 and enhanced OsTB1 expression at the inflorescence formation stage. These studies indicate that genome editing technology, combined with information on agronomically important genes, can accelerate genetic improvement of crops.