Research Project: SoyBase and the Legume Clade Database

Location: Corn Insects and Crop Genetics Research

Publications (Clicking on the reprint icon will take you to the publication reprint.)

CAPG: comprehensive allopolyploid genotyper - (Peer Reviewed Journal)
Kulkarni, R., Zhang, Y., Cannon, S.B., Dorman, K.S. 2022. CAPG: comprehensive allopolyploid genotyper. Bioinformatics. 39(1).Article btac729. https://doi.org/10.1093/bioinformatics/btac729.

Phylogenomics of the genus Glycine sheds light on polyploid evolution and life-strategy transition - (Peer Reviewed Journal)
Zhuang, Y., Wang, X., Li, X., Hu, J., Fan, L., Landis, J.B., Cannon, S.B., Grimwood, J., Schmutz, J., Jackson, S.A., Doyle, J.J., Zhang, X., Zhang, D., Ma, J. 2022. Phylogenomics of the genus Glycine sheds light on polyploid evolution and life-strategy transition. Nature Plants. 8: 233-244. https://doi.org/10.1038/s41477-022-01102-4.

Dissecting the root phenotypic and genotypic variability of the Iowa mung bean diversity panel - (Peer Reviewed Journal)
Chiteri, K.O., Zaki Jubery, T., Dutta, S., Ganapathysubramanian, B., Cannon, S.B., Singh, A. 2022. Dissecting the root phenotypic and genotypic variability of the Iowa mung bean diversity panel. Frontiers in Plant Science. 12:808001. https://doi.org/10.3389/fpls.2021.808001.

Foster thy young: enhanced prediction of orphan genes in assembled genomes - (Peer Reviewed Journal)
Li, J., Singh, U., Bhandary, P., Campbell, J.D., Arendsee, Z., Seetharam, A., Wurtele, E. 2021. Foster thy young: enhanced prediction of orphan genes in assembled genomes. Nucleic Acids Research. 50(7):e37. https://doi.org/10.1093/nar/gkab1238.

Using crop databases to explore phenotypes: from QTL to candidate genes - (Peer Reviewed Journal)
Brown, A.V., Grant, D.M., Nelson, R. 2021. Using crop databases to explore phenotypes: from QTL to candidate genes. Plants. 10(11). Article 2494. https://doi.org/10.3390/plants10112494.

Doing genetic and genomic biology using the Legume Information System and associated resources - (Book / Chapter)
Redsun, S., Hokin, S., Cameron, C.T., Cleary, A.M., Berendzen, J., Dash, S., Brown, A.V., Wilkey, A., Campbell, J.D., Huang, W., Kalberer, S.R., Weeks, N.T., Cannon, S.B., Farmer, A.D. 2022. Doing genetic and genomic biology using the Legume Information System and associated resources. Methods in Molecular Biology. 2443. https://doi.org/10.1007/978-1-0716-2067-0_4.

Legacy genetics of arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange - (Peer Reviewed Journal)
Bertioli, D.J., Clevenger, J., Godoy, I., Stalker, T., Wood, S., Santos, J., Ballen-Taborda, C., Abernathy, B., Azevedo, V., Campbell, J.D., Chavarro, C., Chu, Y., Farmer, A.D., Fonceka, D., Gao, D., Grimwood, J., Halpin, N., Korani, W., Michelotto, M.D., Ozias-Akins, P., Vaughn, J.N., Youngblood, R., Moretzsohn, M.C., Wright, G.C., Jackson, S.A., Cannon, S.B., Scheffler, B.E., Leal-Bertioli, S.M. 2021. Legacy genetics of Arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange. Proceedings of the National Academy of Sciences(PNAS). 118(38). Article e2104899118. https://doi.org/10.1073/pnas.2104899118.

An accumulation of genetic variation and selection across the disease-related genes during apple domestication - (Peer Reviewed Journal)
Singh, J., Sun, M., Cannon, S.B., Wu, J., Khan, A. 2021. An accumulation of genetic variation and selection across the disease-related genes during apple domestication. Tree Genetics and Genomes. 17. Article 29. https://doi.org/10.1007/s11295-021-01510-1.

A better mousetrap to guard against anthracnose disease in bean - (Review Article)
Cannon, S.B., Innes, R.W. 2021. A better mousetrap to guard against anthracnose disease in bean. Journal of Experimental Botany. 72(10):3487-3488. https://doi.org/10.1093/jxb/erab146.

The legume information system and associated online genomic resources - (Peer Reviewed Journal)
Berendzen, J., Brown, A.V., Cameron, C.T., Campbell, J.D., Cleary, A.M., Dash, S., Hokin, S., Huang, W., Kalberer, S.R., Nelson, R., Redsun, S., Weeks, N.T., Wilkey, A., Farmer, A.D., Cannon, S.B. 2021. The legume information system and associated online genomic resources. Legume Science. Article e74. https://doi.org/10.1002/leg3.74.

A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database - (Peer Reviewed Journal)
Brown, A.V., Connors, S., Huang, W., Wilkey, A., Grant, D.M., Weeks, N.T., Cannon, S.B., Graham, M.A., Nelson, R. 2020. A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Research. 49(D1):D1496-D1501. https://doi.org/10.1093/nar/gkaa1107.

GCViT: a method for interactive, genome-wide visualization of resequencing and SNP array data - (Peer Reviewed Journal)
Wilkey, A., Brown, A.V., Cannon, S.B., Cannon, E.K. 2020. GCViT: a method for interactive, genome-wide visualization of resequencing and SNP array data. Biomed Central (BMC) Genomics. 21. Article 822. https://doi.org/10.1186/s12864-020-07217-2.

Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing - (Peer Reviewed Journal)
Valliyodan, B., Brown, A.V., Wang, J., Patil, G., Liu, Y., Otyama, P.I., Nelson, R., Vuong, T., Song, Q., Musket, T.A., Wagner, R., Marri, P., Reddy, S., Sessions, A., Wu, X., Grant, D.M., Bayer, P., Roorkiwal, M., Varshney, R.K., Liu, X., Edwards, D., Xu, D., Joshi, T., Cannon, S.B., Nguyen, H.T. 2020. Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing. Scientific Data. 8. Article 50. https://doi.org/10.1038/s41597-021-00834-w.

Which came first: the tuber or the vine? A taxonomic overview of underground storage in the legumes - (Review Article)
Stai, J.S., Von Wettberg, E.B, Smykal, P., Cannon, S.B. 2020. Which came first: the tuber or the vine? A taxonomic overview of underground storage in the legumes. Legume Perspectives. (19):5-7.

Apios americana – natural history and ethnobotany - (Review Article)
Kalberer, S.R., Belamkar, V., Singh, J., Cannon, S.B. 2020. Apios americana: natural history and ethnobotany. Legume Perspectives. (19):29-32.

The first genetic map for a psoraleoid legume (Bituminaria bituminosa)reveals highly conserved synteny with phaseoloid legumes - (Peer Reviewed Journal)
Nelson, M.N., Jabbari, J.S., Turakulov, R., Pradhan, A., Pazos-Navarro, M., Stai, J.S., Cannon, S.B., Real, D. 2020. The first genetic map for a psoraleoid legume (Bituminaria bituminosa)reveals highly conserved synteny with phaseoloid legumes. Plants. 9(8). Article 973. https://doi.org/10.3390/plants9080973.

Family-specific gains and losses of protein domains in the legume and grass plant families - (Peer Reviewed Journal)
Yadav, A., Fernandez-Baca, D., Cannon, S.B. 2020. Family-specific gains and losses of protein domains in the legume and grass plant families. Evolutionary Bioinformatics. 16. https://doi.org/10.1177/1176934320939943.

Evaluating two different models of peanut’s origin - (Other)
Bertioli, D.J., Abernathy, B., Seijo, G., Clevenger, J., Cannon, S.B. 2020. Evaluating two different models of peanut’s origin. Nature Genetics. https://doi.org/10.1038/s41588-020-0626-1.

The future of legume genetic data resources: Challenges, opportunities, and priorities - (Peer Reviewed Journal)
Bauchet, G., Bett, K.E., Cameron, C.T., Campbell, J.D., Cannon, E., Cannon, S.B., Carlson, J., Chan, A., Cleary, A., Close, T., Cook, D., Cooksey, A., Coyne, C.J., Dash, S., Dickstein, R., Farmer, A., Fernandez-Baca, D., Hokin, S., Jones, E., Kang, Y., Monteros, M., Munoz-Amatriain, M., Mysore, K., Pislariu, C., Richards, C.M., Shi, A., Town, C., Udvardi, M., Wettberg, E., Young, N., Zhao, P. 2019. The future of legume genetic data resources: Challenges, opportunities, and priorities. Legume Science. 1(1):e16. https://doi.org/10.1002/leg3.16.

Construction and comparison of three new reference-quality genome assemblies for soybean - (Peer Reviewed Journal)
Valliyodan, B., Cannon, S.B., Bayer, P.E., Shu, S., Brown, A.V., Ren, L., Jenkins, J., Chung, C.Y.L., Chan, T.F., Daum, C.G., Plott, C., Hastie, A., Baruch, K., Barry, K.W., Huang, W., Gunvant, P., Varshney, R.K., Hu, H., Batley, J., Yuan, Y., Song, Q., Stupar, R.M., Goodstein, D.M., Stacey, G., Lam, H.M., Jackson, S.A., Schmutz, J., Grimwood, J., Edwards, D., Nguyen, H.T. 2019. Construction and comparison of three new reference-quality genome assemblies for soybean. Plant Journal. 100(5):1066-1082. https://doi.org/10.1111/tpj.14500.

Genome-wide associations and epistatic interactions for internode number, plant height, seed weight and seed yield in soybean - (Peer Reviewed Journal)
Assefa, T., Otyama, P., Brown, A.V., Kalberer, S.R., Kulkarni, R.S., Cannon, S.B. 2019. Genome-wide associations and epistatic interactions for internode number, plant height, seed weight and seed yield in soybean. BMC Genomics. 20(527). https://doi.org/10.1186/s12864-019-5907-7.

Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection - (Peer Reviewed Journal)
Otyama, P.I., Wilkey, A., Kulkarni, R., Assefa, T., Chu, Y., Clevenger, J., O'Conner, D.J., Wright, G.C., Dezern, S.W., MacDonald, G.E., Anglin, N.L., Cannon, E.K.S., Ozias-Akins, P., Cannon, S.B. 2019. Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection. BMC Genomics. https://doi.org/10.1186/s12864-019-5824-9.

The genome of cowpea (Vigna unguiculata [L.] Walp.) - (Peer Reviewed Journal)
Lonardi, S., Munoz-Amatriain, M., Liang, Q., Shu, S., Wanamaker, S., Lo, S., Tanskanen, J., Zhu, T., Schulman, A.H., Luo, M., Alhakami, H., Ounit, R., Abid, H., Verdier, J., Roberts, P.A., Santos, J., Ndeve, A., Dolezel, J., Vrana, J., Hokin, S.A., Farmer, A.D., Cannon, S.B., Close, T.J. 2019. The genome of cowpea (Vigna unguiculata [L.] Walp.). Plant Journal. 98(5)767-782. https://doi.org/10.1111/tpj.14349.

Cercis: A non-polyploid genomic relic within the generally polyploid legume family - (Peer Reviewed Journal)
Stai, J.S., Yadav, A., Sinou, C., Bruneau, A., Doyle, J.J., Fernandez-Baca, D., Cannon, S.B. 2019. Cercis: A non-polyploid genomic relic within the generally polyploid legume family. Frontiers in Plant Science. 10:345. https://doi.org/10.3389/fpls.2019.00345.

Reconstruction of ancestral genome reveals chromosome evolution history for selected legume species - (Peer Reviewed Journal)
Ren, L., Huang, W., Cannon, S.B. 2019. Reconstruction of ancestral genome reveals chromosome evolution history for selected legume species. New Phytologist. https://doi.org/10.1111/nph.15770.

A reference-grade wild soybean genome - (Peer Reviewed Journal)
Min, X., Yik-Lok, C., Man-Wah, L., Fuk-Ling, W., Xin, W., Ailin, L., Zhili, W., King-Yung, A., Tin-Hang, W., Suk-Wah, I., Zhixia, X., Kejing, F., Ming-Sin, N., Linfeng, Y., Tianquan, D., Lijuan, H., Lu, C., Aisi, F., Qiong, D., Junxian, H., Gyuhwa, C., Sachiko, I., Babu, V., Nguyen, H., Cannon, S.B., Foyer, C.H., Ting-Fung, C., Hon-Ming, L. 2019. A reference-grade wild soybean genome. Nature Communications. 10:1216. https://doi.org/10.1038/s41467-019-09142-9.