Mung bean, an ancient Asian legume, plays an essential role in global agriculture due to its high nutritional value, nitrogen-fixation ability, and adaptability to diverse environments. Despite its long domestication history from wild V. radiata var. sublobata, the genetic mechanisms driving its morphological and physiological evolution remain unclear. Previous genome assemblies have improved our understanding of single-nucleotide polymorphisms (SNPs), but structural variations (SVs)—large-scale genomic rearrangements that can alter gene dosage and expression—have been underexplored. These SVs are increasingly recognized as major forces in crop domestication. Based on these challenges, it is necessary to conduct an in-depth investigation of structural variation in mung bean domestication.
Researchers from the Shandong Academy of Agricultural Sciences and their collaborators have published a study (DOI: 10.1093/hr/uhae337) in Horticulture Research on March 1, 2025, detailing the first gap-free, telomere-to-telomere (T2T) genome assembly of mung bean cultivar ‘Weilv-9’. The 500-megabase assembly covers 11 chromosomes and contains 28,740 protein-coding genes. Integrating genomic resequencing of 113 mung bean accessions, the team uncovered how transposable element expansion, structural variants, and selective pressures have driven the crop’s transition from wild to cultivated forms, offering unprecedented insights into its domestication process.
Using a combination of PacBio HiFi, Oxford Nanopore, and Hi-C sequencing, the researchers achieved an exceptionally complete genome with an N50 of 46 Mb and 98.8% completeness, surpassing all previous versions. Nearly half of the genome (49.17%) consists of repetitive elements, mainly long terminal repeats (LTRs). The study revealed that recent amplification of Ty1/copia and Ty3/gypsy retrotransposons significantly altered expression of neighboring genes involved in salinity response and ion transport.
Comprehensive analysis of 36 wild and 78 cultivated accessions identified over 13 million SNPs and 115,000 SVs, highlighting the divergence in genetic variation between wild and cultivated populations. Notably, genes affected by major allele frequency SVs exhibited lower expression levels, suggesting selection-induced regulation. Cross-population tests further revealed strong selection on genes linked to fatty acid, suberin, and phenylpropanoid biosynthetic processes—pathways essential for strengthening cell walls and enhancing stress resistance. These findings suggest that structural variants played a key role in the shift from prostrate to erect plant architecture during mung bean domestication.
“Our research provides a complete genomic blueprint of mung bean for the first time,” said lead author Dr. Guan Li. “By combining high-precision long-read sequencing with comparative population genomics, we could trace the footprints of domestication embedded in SVs. These results not only reveal how wild mung beans evolved into modern cultivars but also offer new molecular targets for improving yield, nutrition, and environmental resilience. The T2T reference genome now serves as a cornerstone for genetic innovation in legume breeding.”
The gap-free genome opens a new era for mung bean genetic improvement. The identified structural variants and domestication-related genes can be leveraged to enhance resistance to drought, salinity, and pathogens through precise breeding and genome editing. Insights into fatty acid and phenylpropanoid metabolism may also guide efforts to increase nutritional quality and optimize seed composition. Beyond mung bean, the study provides a genomic framework for exploring domestication in related legumes such as cowpea and black gram, accelerating crop improvement across diverse agricultural systems.
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References
DOI
10.1093/hr/uhae337
Original Source URL
https://doi.org/10.1093/hr/uhae337
Funding information
This research was supported by the Key R&D Program of Shandong Province (2022LZGC022, 2021LZGC025, and 2023LZGC001), the National Natural Science Foundation of China (32201736), the Natural Science Foundation of Shandong Province for Young Scholars (ZR2023QC153), and the Agricultural Science and Technology Innovation Project of SAAS (CXGC2023F13, CXGC2024F13, and CXGC2023C02).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.