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Leguminous plants, such as soybeans, peas, and chickpeas, typically contain two to three times more protein than cereals like wheat and rice, with low fat content (primarily unsaturated fats) and no cholesterol, making them essential for cardiovascular health and blood sugar management. Since the release of the soybean genome in 2010, genomic research in Fabaceae has advanced dramatically. High-quality reference genomes have been assembled for key species, including soybeans (Glycine max), common beans (Phaseolus vulgaris), chickpeas (Cicer arietinum), and model legumes like Medicago truncatula and Lotus japonicus, leveraging long-read sequencing, single-cell technologies, and improved assembly algorithms. These advancements have enabled telomere-to-telomere (T2T) assemblies, pan-genome constructions, and the identification of structural variants (SVs) and presence\/absence variations (PAVs), enriching our understanding of genetic diversity and domestication history. Functional genomic tools, such as CRISPR-Cas9 gene editing, mutagenesis, and high-throughput omics (transcriptomics, metabolomics), have elucidated regulatory networks controlling critical traits like photoperiod sensitivity (e.g., E1 and Tof16 genes in soybeans), seed development (GmSWEET39 for oil\/protein transport), nitrogen fixation efficiency, and stress resilience (e.g., Rpp3 for rust resistance). Genome-wide association studies (GWAS) and comparative genomics have further linked genetic variants to agronomic traits, such as pod size in peanuts (PSW1) and flowering time in common beans (COL2). This review synthesizes recent breakthroughs in legume genomics, highlighting the integration of multi-omic approaches to accelerate gene cloning and functional confirmation of the genes cloned.<\/jats:p>","DOI":"10.3390\/ijms26136323","type":"journal-article","created":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T06:56:54Z","timestamp":1751353014000},"page":"6323","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Functional Genomics: From Soybean to Legume"],"prefix":"10.3390","volume":"26","author":[{"given":"Can","family":"Zhou","sequence":"first","affiliation":[{"name":"College of Agriculture, Northeast Agricultural University, Harbin 150030, China"},{"name":"State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haiyan","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Agriculture, Northeast Agricultural University, Harbin 150030, China"},{"name":"State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaobin","family":"Zhu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuqiu","family":"Li","sequence":"additional","affiliation":[{"name":"Jilin Academy Agricultural of Sciences (Northeast Agricultural Research Center of China), Changchun 130033, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Million","family":"Tadege","sequence":"additional","affiliation":[{"name":"Institute for Agricultural Biosciences, Oklahoma State University, Stillwater, OK 74078, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shihao","family":"Wu","sequence":"additional","affiliation":[{"name":"Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhaoming","family":"Qi","sequence":"additional","affiliation":[{"name":"College of Agriculture, Northeast Agricultural University, Harbin 150030, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhengjun","family":"Xia","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,6,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"44","DOI":"10.12705\/661.3","article-title":"A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny","volume":"66","author":"Azani","year":"2017","journal-title":"Taxon"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"R323","DOI":"10.1016\/j.cub.2025.03.049","article-title":"Legumes","volume":"35","author":"Hughes","year":"2025","journal-title":"Curr. 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