Elimination of an unfavorable allele conferring pod shattering in an elite soybean cultivar by CRISPR/Cas9.

Pod shattering can lead to devastating yield loss of soybean and has been a negatively selected trait in soybean domestication and breeding. Nevertheless, a significant portion of soybean cultivars are still pod shattering-susceptible, limiting their regional and climatic adaptabilities. Here we performed genetic diagnosis on the shattering-susceptible trait of a national registered cultivar, Huachun6 (HC6), and found that HC6 carries the susceptible genotype of a candidate () gene, which exists in a significant portion of soybean cultivars. We next performed genome editing on gene by clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9). In T progenies, several transgene-free lines with mutations were characterized without affecting major agronomic traits. The mutation significantly improved the pod shattering resistance which is associated with aberrant lignin distribution in inner sclerenchyma. Our work demonstrated that precision breeding by genome editing on holds great potential for precisely improving pod shattering resistance and adaptability of soybean cultivars.