The demographic history, genomic variation, and transcontinental genotype-phenotype-environment map of mungbean

Lin, Y.-P.; Chen, H.-W.; Chien, C.-C.; Lien, Y.-H.; Ong, P.-W.; Yeh, C.-M.; Yeh, P.-M.; Chai, M.-W.; Douglas, C. A.; Alam, A. M.; Win, M. M.; Pratap, A.; Boddepalli, V. N.; Karimi, R.; Zohoungbogbo, H. P. F.; Tignegre, J. B. D. L. S.; Asibuo, J. Y.; Binagwa, P. H.; Mbeyagala, E. K.; Malik, S. R.; Samsonova, M. G.; Chu, J. H.; Yen, J.-Y.; von Wettberg, E. B.; Naito, K.; Schafleitner, R.; Nair, R. M.; Lee, C.-R.

doi:10.1101/2025.10.16.682767

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bioRxiv · 10.1101/2025.10.16.682767

The demographic history, genomic variation, and transcontinental genotype-phenotype-environment map of mungbean

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Abstract

The breeding of mungbean, a crucial Asian legume, has been hampered by the lack of genomic resources. The International Mungbean Improvement Network (IMIN) aims to ensure global access to diverse germplasms and genomic resources. Using 780 worldwide wild and cultivated accessions, we report this species most comprehensive (pan)genomic variation, demographic history, and genotype-phenotype-environment map. Despite archaeological evidence of the earliest cultivation in South Asia, present-day wild populations only possess relict traces of shared polymorphisms with cultivars. We showed that parallel losses of black seed coats in two Vigna species were caused by the same mutational mechanism in the same gene. In large-scale cross-continent field trials, we found accessions from distant environments from the trial sites have lower performance, especially in high-heritability and high-yield sites, suggesting future breeding priority in benign conditions on accessions from similar environments. Our comprehensive genomic and trial resources facilitate future breeding success of this essential crop.

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Lin, Y.-P., Chen, H.-W., Chien, C.-C., Lien, Y.-H., Ong, P.-W., Yeh, C.-M., Yeh, P.-M., Chai, M.-W., Douglas, C. A., Alam, A. M., Win, M. M., Pratap, A., Boddepalli, V. N., Karimi, R., Zohoungbogbo, H. P. F., Tignegre, J. B. D. L. S., Asibuo, J. Y., Binagwa, P. H., Mbeyagala, E. K., Malik, S. R., Samsonova, M. G., Chu, J. H., Yen, J.-Y., von Wettberg, E. B., Naito, K., Schafleitner, R., Nair, R. M., Lee, C.-R.. 2025-10-16. The demographic history, genomic variation, and transcontinental genotype-phenotype-environment map of mungbean. https://doi.org/10.1101/2025.10.16.682767

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