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

Abstract

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 <i>Pod dehiscence 1</i> (<i>PDH1</i>) gene, which exists in a significant portion of soybean cultivars. We next performed genome editing on <i>PDH1</i> gene by clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9). In T₂ progenies, several transgene-free lines with <i>pdh1</i> mutations were characterized without affecting major agronomic traits. The <i>pdh1</i> 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 <i>PDH1</i> holds great potential for precisely improving pod shattering resistance and adaptability of soybean cultivars.