Legume Genomics and Genetics 2024, Vol.15, No.4, 199-209 http://cropscipublisher.com/index.php/lgg 199 Review and Progress Open Access CRISPR/Cas9 Genome Editing in Legumes: Opportunities for Functional Genomics and Breeding Dandan Huang Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China Corresponding email: dandan.huang@cuixi.org Legume Genomics and Genetics, 2024 Vol.15, No.4 doi: 10.5376/lgg.2024.15.0020 Received: 10 Jul., 2024 Accepted: 11 Aug., 2024 Published: 22 Aug., 2024 Copyright © 2024 Huang, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Huang D.D., 2024, CRISPR/Cas9 genome editing in legumes: opportunities for functional genomics and breeding, Legume Genomics and Genetics, 15(4): 199-209 (doi: 10.5376/lgg.2024.15.0020) Abstract Legumes play a crucial role in global agriculture and food security, yet they face significant challenges in breeding for improved traits. This study explores the potential of CRISPR/Cas9 genome editing as a transformative tool in legume functional genomics and breeding. It begins by outlining the importance of legumes and the limitations of traditional breeding methods. The study then delves into the mechanisms and advantages of CRISPR/Cas9, highlighting its application in functional genomics, such as gene knockout and activation studies. A case study on drought tolerance in soybeans demonstrates the practical application of CRISPR/Cas9 in identifying and enhancing key traits. Furthermore, the study discusses the broad applications of this technology in improving biotic and abiotic stress resistance, enhancing quality traits, and accelerating the breeding process, including a detailed case study on disease resistance in chickpeas. The study also addresses the challenges and ethical considerations associated with CRISPR/Cas9, such as off-target effects and regulatory issues. Looking forward, the study explores future innovations and the integration of CRISPR/Cas9 into legume breeding programs, emphasizing its potential for sustainable agriculture and global food security. This study underscores the vast opportunities that CRISPR/Cas9 presents for advancing legume breeding and anticipates its growing impact on agricultural practices. Keywords CRISPR/Cas9; Legume breeding; Functional genomics; Drought tolerance; Disease resistance 1 Introduction Legume crops, including chickpea, pigeonpea, cowpea, and groundnut, are vital for global nutrition and food security. They are a major source of proteins and health-promoting phytochemicals, particularly in Asia and Sub-Saharan Africa, where they are often grown in marginal environments (Varshney, 2016; Bhowmik et al., 2021). These crops also play a crucial role in sustainable agricultural production through their ability to fix atmospheric nitrogen, thereby improving soil quality and reducing the need for synthetic fertilizers (Pandey et al., 2016; Corte et al., 2019). The nutritional benefits and environmental sustainability of legumes underscore their importance in addressing global food security challenges. Despite their significance, legume crops face several breeding challenges. Low productivity due to biotic and abiotic stresses is a major issue, particularly in marginal environments (Varshney, 2016). Traditional breeding methods have had limited success in overcoming these challenges due to the complex genetic architecture of traits such as drought tolerance, disease resistance, and nutritional quality (Pandey et al., 2016; Bhowmik et al., 2021). Additionally, the recalcitrance of some legumes to in vitro gene transfer and regeneration poses a significant hurdle to genetic improvement efforts. These challenges necessitate the adoption of advanced breeding technologies to accelerate genetic gains in legume crops (Abdelrahman et al., 2018; Chen et al., 2019). CRISPR/Cas9 is a revolutionary genome-editing technology derived from the bacterial adaptive immune system. It involves the use of an endonuclease, Cas9, guided by a single-guide RNA (sgRNA) to introduce double-strand breaks at specific genomic locations. These breaks are then repaired by the cell's natural repair mechanisms, leading to targeted genetic modifications (Corte et al., 2019). This precise editing capability allows for the disruption, modification, or regulation of target genes, making CRISPR/Cas9 a powerful tool for functional genomics and crop improvement (Chen et al., 2019). CRISPR/Cas9 offers several advantages over traditional
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