Although CRISPR-Cas9 technology has been rapidly applied in soybean genetic improvement, it is difficult to achieve the targeted editing of the specific loci in the soybean complex genome due to the limitations of the classical protospacer adjacent motif (PAM). Here, we developed a PAM-less genome editing system mediated by SpRY in soybean. By performing targeted editing of representative agronomic trait targets in soybean and evaluating the results, we demonstrate that the SpRY protein can achieve efficient targeted mutagenesis at relaxed PAM sites in soybean. Furthermore, the SpRY-based cytosine base editor SpRY-hA3A and the adenine base editor SpRY-ABE8e both can accurately induce C-to-T and A-to-G conversion in soybean, respectively. Thus, our data illustrate that the SpRY toolbox can edit the soybean genomic sequence in a PAM-free manner, breaking restrictive PAM barriers in the soybean genome editing technology system. More importantly, our research enriches soybean genome editing tools, which has important practical application value for precise editing and molecular design in soybean breeding.

Genome editing-mediated haploid inducer systems (HISs) present a promising strategy for enhancing breeding efficiency in legume crops, which are vital for sustainable agriculture due to their nutritional benefits and ability to fix nitrogen. Traditional legume breeding is often slow and complicated by the complexity of legumes’ genomes and the challenges associated with tissue culture. Recent advancements have broadened the applicability of HISs in legume crops, facilitating a reduction in the duration of the breeding cycle. By integrating genome editing technology with haploid breeding systems, researchers can achieve precise genetic modifications and rapidly produce homozygous lines, thereby significantly accelerating the development of desired traits. This review explores the current status and future prospects of genome editing-mediated HISs in legumes, emphasizing the mechanisms of haploid induction; recent breakthroughs; and existing technical challenges. Furthermore, we highlight the necessity for additional research to optimize these systems across various legume species, which has the potential to greatly enhance breeding efficiency and contribute to the sustainability of legume production.

Shoot branching in plants (including tillering in graminaceous crops) is a key agronomic trait affecting plant architecture, resource allocation, and final yield. Branching is a complex developmental process modulated by genetic networks regulating axillary meristem (AM) initiation and subsequent bud activation. This review summarizes the genetic regulatory networks identified in model plants, specifically Arabidopsis thaliana (a dicot) and Oryza sativa (a monocot). Building on this cross-species theoretical framework, we focus on soybean ( Glycine max ), a major economic crop, and provide a comprehensive analysis of recent progress in the functional characterization of branch number specific regulators and quantitative trait loci (QTLs). Given the bottlenecks in soybean architecture improvement resulting from its complex and highly redundant genome, recalcitrance to genetic transformation, and high environmental sensitivity, we discuss potential strategies based on multidisciplinary approaches and emerging technologies. This review aims to provide a new insight for shaping the ideal plant architecture in soybean through molecular design breeding.