Recent advances in the improvement of soybean seed traits by genome editing

Simultaneous site-directed mutagenesis for soybean ß-amyrin synthase genes via DNA-free CRISPR/Cas9 system using a single gRNA

KEY MESSAGE

We generated soybean mutants related to two ß-amyrin synthase genes using DNA-free site-directed mutagenesis system. Our results suggested that one of the genes is predominant in the soyasaponin biosynthesis. Soyasaponins, which are triterpenoid saponins contained in soybean [Glycine max (L.) Merril], are responsible for the astringent aftertaste of soyfood, and their complete elimination from soybean seeds is a key challenge in the development of cultivars with improved taste. While the loss of function in the ß-amyrin synthase genes (GmBAS1 and GmBAS2) has proven effective in reducing soyasaponin content in soybean seeds, the specific functional roles of these genes remain unclear. In this study, site-directed mutagenesis was performed on two GmBAS loci using a DNA-free clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated endonuclease 9 (Cas9) system. A complex of sgRNA targeting sequences conserved in the two loci and Cas9 protein was introduced into the shoot apical meristems of soybean embryonic axes via bombardment. Cleaved amplified polymorphic sequences (CAPS) analysis conducted 1 month post-bombardment revealed that 138 seedlings out of 1,467 screened exhibited mutations at one or both GmBAS loci. CAPS and sequencing analysis in the subsequent generation identified a total of 16 plants with inheritable mutations ranging from one to ten nucleotides. High-performance liquid chromatography (HPLC) analysis showed that site-directed mutagenesis in the GmBAS1 locus resulted in the absence of soyasaponins in mature seeds, as well as in young roots, stems, and leaves. These findings demonstrate that GmBAS1 is the predominant ß-amyrin synthase gene in soybean plants. In addition, the DNA-free CRISPR/Cas9 system was shown to be highly efficient in inducing simultaneous mutagenesis at two target loci using a single gRNA.

A fast and genotype-independent in planta Agrobacterium-mediated transformation method for soybean

Efficient genotype-independent transformation and genome editing are highly desirable for plant biotechnology research and product development efforts. We have developed a novel approach to enable fast, high-throughput, and genotype-flexible Agrobacterium-mediated transformation using the important crop soybean as a test system. This new method is called GiFT (genotype-independent fast transformation) and involves only a few simple steps. The method uses germinated seeds as explants, and DNA delivery is achieved through Agrobacterium infection of wounded explants as in conventional in vitro-based methods. Following infection, the wounded explants are incubated in liquid medium with a sublethal level of selection and then transplanted directly into soil. The transplanted seedlings are then selected with herbicide spray for 3 weeks. The time required from initiation to fully established healthy T0 transgenic events is about 35 days. The GiFT method requires minimal in vitro manipulation or use of tissue culture media. Because the regeneration occurs in planta, the GiFT method is highly flexible with respect to genotype, which we demonstrate via successful transformation of elite germplasms from diverse genetic backgrounds. We also show that the soybean GiFT method can be applied to both conventional binary vectors and CRISPR-Cas12a vectors for genome editing applications. Analyses of T1 progeny demonstrate that the events have a high inheritance rate and can be used for genome engineering applications. By minimizing the need for tissue culture, the novel approach described here significantly improves operational efficiency while greatly reducing personnel and supply costs. It is the first industry-scale transformation method to utilize in planta selection in a major field crop.