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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Research Project #425040

Research Project: SoyBase and the Legume Clade Database

Location: Corn Insects and Crop Genetics Research

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

Molecular tools for detecting Pdh1 can improve soybean breeding efficiency by reducing yield losses due to pod shatter - (Peer Reviewed Journal)
Miranda, C., Culp, C., Skrabisova, M., Joshi, T., Belzile, F., Grant, D.M., Bilyeu, K.D. 2019. Molecular tools for detecting Pdh1 can improve soybean breeding efficiency by reducing yield losses due to pod shatter. Molecular Breeding. 39:27. https://doi.org/10.1007/s11032-019-0935-1.

A review of breeding objectives, genomic resources, and marker-assisted methods in common bean (Phaseolus vulgaris L.) - (Peer Reviewed Journal)
Assefa, T., Rubyogo, J., Mahama, A.A., Brown, A.V., Cannon, E., Blair, M.W., Cannon, S.B. 2019. A review of breeding objectives, genomic resources, and marker-assisted methods in common bean (Phaseolus vulgaris L.). Molecular Breeding. 39:20. https://doi.org/10.1007/s11032-018-0920-0.

Ten quick tips for sharing genomic data - (Peer Reviewed Journal)
Brown, A.V., Campbell, J.D., Assefa, T., Grant, D.M., Nelson, R., Weeks, N.T., Cannon, S.B. 2018. Ten quick tips for sharing genomic data. PLoS Computational Biology. https://doi.org/10.1371/journal.pcbi.1006472.

Uneven recombination and linkage disequilibrium across a reference SNP map for common bean (Phaseolus vulgaris L.) - (Peer Reviewed Journal)
Blair, M.W., Cortes, A.J., Farmer, A.D., Huang, W., Penmetsa, V., Cannon, S.B. 2018. Uneven recombination and linkage disequilibrium across a reference SNP map for common bean (Phaseolus vulgaris L.). PLoS One. 13(3):e0189597. https://doi.org/10.1371/journal.pone.0189597.

A transcriptome-SNP-derived linkage map of Apios americana (potato bean) provides insights about genome re-organization and synteny conservation in the phaseoloid legumes - (Peer Reviewed Journal)
Singh, J., Kalberer, S.R., Belamkar, V., Assefa, T., Nelson, M.N., Farmer, A.D., Blackmon, W.J., Cannon, S.B. 2017. A transcriptome-SNP-derived linkage map of Apios americana (potato bean) provides insights about genome re-organization and synteny conservation in the phaseoloid legumes. Theoretical and Applied Genetics. 131(2):333-351. https://doi.org/10.1007/s00122-017-3004-3.

Improving adaptation to drought stress in white pea bean (Phaseolus vulgaris L): genotypic effects on grain yield, yield components and pod harvest index - (Peer Reviewed Journal)
Assefa, T., Rao, I.M., Cannon, S.B., Wu, J., Gutema, Z., Blair, M., Otyama, P., Alemayehu, F., Dagne, B. 2017. Improving adaptation to drought stress in white pea bean (Phaseolus vulgaris L): genotypic effects on grain yield, yield components and pod harvest index. Plant Breeding. 136(4):548-561. doi:10.1111/pbr.12496.

Genomics-assisted characterization of a breeding collection of Apios americana, an edible tuberous legume - (Peer Reviewed Journal)
Belamkar, V., Farmer, A.D., Weeks, N.T., Kalberer, S.R., Blackmon, W.J., Cannon, S.B. 2016. Genomics-assisted characterization of a breeding collection of Apios americana, an edible tuberous legume. Nature Scientific Reports. 6:34908. doi: 10.1038/srep34908.

A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: Insights into plant-microbe interactions and legume evolution - (Peer Reviewed Journal)
Hane, J.K., Yao, M., Kamphuis, L.G., Nelson, M.N., Atkins, C.A., Bravo, A., Bringans, S., Cannon, S.B., Huang, W., Cullerne, D., Foley, R., Garg, G., Gao, L., Harrison, M., Li, S., Mcgrath, A., Morahan, G., Taylor, J., Weller, J., Jianbo, J., Singh, K.B. 2016. A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: Insights into plant-microbe interactions and legume evolution. Plant Biotechnology Journal. doi: 10.1111/pbi.12615.

Dynamic transcriptome profiling of Bean Common Mosaic Virus (BCMV) infection in Common Bean (Phaseolus vulgaris L.) - (Peer Reviewed Journal)
Martin, K., Jugpreet, S., Hill, J.H., Whitham, S., Cannon, S.B. 2016. Dynamic transcriptome profiling of Bean Common Mosaic Virus (BCMV) infection in Common Bean (Phaseolus vulgaris L.). Biomed Central (BMC) Genomics. 17:613. doi:10.1186/s12864-016-2976-8.

Characterization and development mechanism of Apios americana tuber starch - (Peer Reviewed Journal)
Yangcheng, H., Belamkar, V., Cannon, S.B., Jane, J. 2016. Characterization and development mechanism of Apios americana tuber starch. Carbohydrate Polymers. 151:198-205. doi:10.1016/j.carbpol.2016.05.062.

The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut - (Peer Reviewed Journal)
Bertioli, D., Cannon, S.B., Froenicke, L., Huang, G., Farmer, A.D., Cannon, E., Dash, S., Liu, X., Barkley, N.L., Guo, B., Scheffler, B.E., et al. 2016. The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nature Genetics. 48:438-446. doi: 10.1038/ng.3517.

Legume Information System (LegumeInfo.org): a key component of a set of federated data resources for the legume family - (Peer Reviewed Journal)
Dash, S., Campbell, J.D., Cannon, E., Cleary, A.M., Huang, W., Kalberer, S.R., Karingula, V., Rice, A.G., Singh, J., Umale, P.E., Weeks, N.T., Wilkey, A.P., Farmer, A.D., Cannon, S.B. 2015. Legume Information System (LegumeInfo.org): a key component of a set of federated data resources for the legume family. 2016. Nucleic Acids Research. 44 (D1):D1181-D1188. doi: 10.1093/nar/gkv1159.

An ontology approach to comparative phenomics in plants - (Peer Reviewed Journal)
Oellrich, A., Walls, R.L., Cannon, E., Cannon, S.B., Cooper, L., Gardiner, J., Gkoutos, G.V., Harper, E.C., He, M., Hoehndorf, R., Jaiswal, P., Kalberer, S.R., Lloyd, J., Meinke, D., Menda, N., Moore, L., Nelson, R., Pujar, A., Lawrence, C.J., Huala, E. 2015. An ontology approach to comparative phenomics in plants. Plant Methods. 11:10. DOI: 10.1186/s13007-015-0053-y.

PeanutBase and other bioinformatic resources for peanut - (Book / Chapter)
Dash, S., Cannon, E., Kalberer, S.R., Farmer, A.D., Cannon, S.B. 2016. PeanutBase and other bioinformatic resources for peanut. In: Stalker, T.H., Wilson, R.F., editors. Peanuts: Genetidcs, Processing, and Utilization (AOCS Monograph Series on Oilseeds). Waltham, MA: Academic Press and AOCS Press. p. 241-252.

Multiple polyploidy events in the early radiation of nodulating and non-nodulating legumes - (Peer Reviewed Journal)
Cannon, S.B., McKain, M.R., Harkess, A., Nelson, M.N., Dash, S., Deyholos, M.K., Peng, Y., Joyce, B., Stewart, C.N., Rolf, M., Kutchan, T., Xuemei, T., Chen, C., Zhang, Y., Carpenter, E., Wong, G., Doyle, J., Leebens-Mack, J. 2014. Multiple polyploidy events in the early radiation of nodulating and non-nodulating legumes. Molecular Biology and Evolution. 32(1):193-210. DOI: 10.1093/molbev/msu296.

Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress - (Peer Reviewed Journal)
Belamkar, V., Weeks, N.T., Bharti, A.K., Farmer, A.D., Graham, M.A., Cannon, S.B. 2014. Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress. Biomed Central (BMC) Genomics. 15:950. DOI:10.1186/1471-2164-15-950.

Genome resilience and prevalence of segmental duplications following fast neutron irradiation of soybean - (Abstract Only)
Bolon, Y., Stec, A.O., Michno, J., Roessler, J., Bhaskar, P.B., Ries, L., Dobbels, A.A., Campbell, B.W., Young, N.P., Anderson, J.E., Grant, D.M., Orf, J.H., Naeve, S.L., Muehlbauer, G.J., Vance, C.P., Stupar, R.M. 2014. Genome resilience and prevalence of segmental duplications following fast neutron irradiation of soybean. Genetics. DOI:10.1534/genetics.114.170340.

Occurrence and characterization of Bean common mosaic virus strain NL1 in Iowa - (Peer Reviewed Journal)
Martin, K.M., Hill, J.H., Cannon, S.B. 2014. Occurrence and characterization of Bean common mosaic virus strain NL1 in Iowa. Plant Disease. 98(11):1593. DOI: 10.1094/PDIS-07-14-0673-PDN.

Comprehensive transcriptome assembly of chickpea (Cicer arietinum L.) using Sanger and next generation sequencing platforms: development and applications - (Peer Reviewed Journal)
Kudapa, H., Azam, S., Sharpe, A.G., Taran, B., Li, R., Deonovic, B., Cameron, C., Farmer, A.D., Cannon, S.B., Varshney, R.K. 2014. Comprehensive transcriptome assembly of chickpea (Cicer arietinum L.) using Sanger and next generation sequencing platforms: development and applications. PLoS One. 9(1):e86039. DOI: 10.1371/journal.pone.0086039.

De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity - (Peer Reviewed Journal)
Haas, B.J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P.D., Bowden, J., Couger, M.B., Eccles, D., Li, B., Lieber, M., Weeks, N.T. 2013. De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity. Nature Protocols. 8(8):1494-1512.