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ARS Home » Midwest Area » Columbia, Missouri » Plant Genetics Research » Research » Research Project #424655

Research Project: Genetics and Genomics of Complex Traits in Grain Crops

Location: Plant Genetics Research

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

The genomic basis for short-term evolution of environmental adaptation in maize Reprint Icon - (Peer Reviewed Journal)
Wisser, R.J., Fang, Z., Holland, J.B., Teixeira, J.E., Dougherty, J., Weldekidan, T., De Leon, N., Flint-Garcia, S.A., Lauter, N.C., Murray, S.C., Xu, W., Hallauer, A. 2019. The genomic basis for short-term evolution of environmental adaptation in maize. Genetics. 213(4):1479-1494. https://doi.org/10.1534/genetics.119.302780.

Optimal designs for genomic selection in hybrid crops Reprint Icon - (Peer Reviewed Journal)
Guo, T., Yu, X., Li, X., Zhang, H., Zhu, C., Flint-Garcia, S.A., McMullen, M.D., Holland, J.B., Szalma, S.J., Wisser, R., Yu, J. 2019. Optimal designs for genomic selection in hybrid crops. Molecular Plant. 12(3):390-401. https://doi.org/10.1016/j.molp.2018.12.022.

Evolution by duplication: paleopolyploidy events in plants reconstructed by deciphering the evolutionary history of VOZ transcription factors Reprint Icon - (Peer Reviewed Journal)
Gao, B., Chen, M., Li, X., Liang, Y., Zhu, F., Liu, T., Zhang, D., Wood, A.J., Oliver, M.J., Zhang, J. 2018. Evolution by duplication: paleopolyploidy events in plants reconstructed by deciphering the evolutionary history of VOZ transcription factors. Biomed Central (BMC) Plant Biology. 18:256. https://doi.org/10.1186/s12870-018-1437-8.

Sugar preferences of western corn rootworm larvae in a feeding stimulant blend Reprint Icon - (Peer Reviewed Journal)
Bernklau, E.J., Hibbard, B.E., Bjostad, L.B. 2018. Sugar preferences of western corn rootworm larvae in a feeding stimulant blend. Journal of Applied Entomology. 142(10):947-958. https://doi.org/10.1111/jen.12540.

Influence of drought on plant performance through changes in belowground tritrophic interactions Reprint Icon - (Peer Reviewed Journal)
Guyer, A., Hibbard, B.E., Holzkamper, A., Erb, M., Robert, C.A. 2018. Influence of drought on plant performance through changes in belowground tritrophic interactions. Ecology and Evolution. 8:6756-6765. http://doi.org/10.1002/ece3.4183.

The Physcomitrella patens gene atlas project: large scale RNA-seq based expression data Reprint Icon - (Peer Reviewed Journal)
Perroud, P., Hass, F., Hiss, M., Ullrich, K., Alboresi, A., Amirebrahimi, M., Barry, K., Bassi, R., Bonhomme, S., Chen, H., Coates, J., Fujita, T., Guyon-Debast, A., Lang, D., Lin, J., Lipzen, A., Nogue, F., Oliver, M.J., Ponce De Leon, I., Quatrano, R.S., Rameau, C., Reiss, B., Reski, R., Ricca, M., Saidi, Y., Sun, N., Szovenyi, P., Sreedasyam, A., Grimwood, J., Stacey, G., Schmutz, J., Rensing, S.A. 2018. The Physcomitrella patens gene atlas project: large scale RNA-seq based expression data. Plant Journal. 95:168-182. https://doi.org/10.1111/tpj.13940.

A new artificial diet for western corn rootworm larvae is compatible with and detects resistance to all current Bt toxins - (Peer Reviewed Journal)
Ludwick, D.C., Meihls, L.N., Huynh, M.P., Pereira, A.E., French, B.W., Coudron, T.A., Hibbard, B.E. 2018. A new artificial diet for western corn rootworm larvae is compatible with and detects resistance to all current Bt toxins. Scientific Reports. 8:5379. https://doi.org/10.1038/s41598-018-23738-z.

Protandry of western corn rootworm (Coleoptera: Chrysomelidae) beetle emergence partially due to earlier egg hatch of males - (Peer Reviewed Journal)
Ludwick, D.C., Zukoff, A.L., Higdon, M.L., Hibbard, B.E. 2018. Protandry of western corn rootworm (Coleoptera: Chrysomelidae) beetle emergence partially due to earlier egg hatch of males. Journal of Kansas Entomological Society. 90(2):94-99. https://doi.org/10.2317/17-14.1.

Diet improvement for western corn rootworm (Coleoptera: Chrysomelidae) larvae Reprint Icon - (Peer Reviewed Journal)
Huynh, M.P., Meihls, L.N., Hibbard, B.E., Lapointe, S.L., Niedz, R.P., Ludwick, D.C., Coudron, T.A. 2017. Diet improvement for western corn rootworm (Coleoptera: Chrysomelidae) larvae. PLoS One. 12(11):e0187997. https://doi.org/10.1371/journal.pone.0187997.

The interplay of demography and selection during maize domestication and expansion Reprint Icon - (Peer Reviewed Journal)
Wang, L., Beissinger, T.M., Lorant, A., Ross-Ibarra, C., Ross-Ibarra, J., Hufford, M.B. 2017. The interplay of demography and selection during maize domestication and expansion. Genome Biology. 18:215. https://doi.org/10.1186/s13059-017-1346-4.

Desiccation tolerance in Physcomitrella patens: Rate of dehydration and the involvement of endogenous abscisic acid (ABA) Reprint Icon - (Peer Reviewed Journal)
Xiao, L., Yobi, A., Koster, K., He, Y., Oliver, M.J. 2017. Desiccation tolerance in Physcomitrella patens: Rate of dehydration and the involvement of endogenous abscisic acid (ABA). Plant Cell and Environment. 41:275-284. https://doi.org/10.1111/pce.13096.

Response of maize hybrids with and without rootworm-and drought-tolerance to rootworm infestation under well-watered and drought conditions Reprint Icon - (Peer Reviewed Journal)
Mahmoud, M.A., Sharp, R.E., Oliver, M.J., Finke, D.L., Bohn, M., Ellersieck, M.R., Hibbard, B.E. 2018. Response of maize hybrids with and without rootworm-and drought-tolerance to rootworm infestation under well-watered and drought conditions. Journal of Economic Entomology. 111(1): 193-208. https://doi.org/10.1093/jee/tox309.

Quantitative trait loci mapping of western corn rootworm (Coleoptera: Chrysomelidae) host plant resistance in two populations of doubled haploid lines in maize (Zea mays L.) Reprint Icon - (Peer Reviewed Journal)
Bohn, M.O., Marroquin, J.J., Flint Garcia, S.A., Dashiell, K.E., Wilmot, D.B., Hibbard, B.E. 2018. Quantitative trait loci mapping of western corn rootworm (Coleoptera: Chrysomelidae) host plant resistance in two populations of doubled haploid lines in maize (Zea mays L.). Journal of Economic Entomology. 111(1):435-444. https://doi.org/10.1093/jee/tox310.

Maize kernel evolution: From teosinte to maize - (Book / Chapter)
Flint Garcia, S.A. 2017. Maize kernel evolution: From teosinte to maize. CAB International United Kingdom. In: Larkins, B., editor. Maize Kernel Development. Oxfordshire, UK. CAB International United Kingdom. p. 1-15.

A soil-plate based pipeline for assessing cereal root growth in response to polyethylene glycol (PEG)-induced water deficit stress Reprint Icon - (Peer Reviewed Journal)
Nelson, S.K., Oliver, M.J. 2017. A soil-plate based pipeline for assessing cereal root growth in response to polyethylene glycol (PEG)-induced water deficit stress. Frontiers in Plant Science. 8:1272. https://doi.org/10.3389/fpls.2017.01272.

Sporobolus stapfianus: Insights into desiccation tolerance in the resurrection grasses from linking transcriptomics to metabolomics Reprint Icon - (Peer Reviewed Journal)
Yobi, A., Schlauch, K.A., Tillet, R.L., Yim, W.C., Espinoza, C., Wone, B.W., Cushman, J.C., Oliver, M.J. 2017. Sporobolus stapfianus: Insights into desiccation tolerance in the resurrection grasses from linking transcriptomics to metabolomics. Biomed Central (BMC) Plant Biology. 17:67. https://doi.org/10.1186/s12870-017-1013-7.

Medical subject heading (MeSH) annotations illuminate maize genetics and evolution Reprint Icon - (Peer Reviewed Journal)
Beissinger, T.M., Morota, G. 2017. Medical subject heading (MeSH) annotations illuminate maize genetics and evolution. Plant Methods. 13:8. doi: 10.1186/s13007-017-0159-5.

Genetic analysis of teosinte alleles for kernel composition traits in maize Reprint Icon - (Peer Reviewed Journal)
Karn, A., Gillman, J.D., Flint Garcia, S.A. 2017. Genetic analysis of teosinte alleles for kernel composition traits in maize. G3, Genes/Genomes/Genetics. 7(4):1157-1164. doi:org/10.1534/g3.117.039529.

Assessment of natural variability of maize lipid transfer protein using a validated sandwich ELISA - (Peer Reviewed Journal)
Gu, X., Lee, T., Geng, T., Liu, K., Thoma, R., Crowley, K., Edrington, T., Ward, J., Wang, Y., Flint Garcia, S.A., Bell, E., Glenn, K. 2017. Assessment of natural variability of maize lipid transfer protein using a validated sandwich ELISA. Journal of Agricultural and Food Chemistry. 65:1740-1749. doi: 10.1021/acs.jafc.6b03583.

A footprint of desiccation tolerance in the genome of Xerophyta viscosa Reprint Icon - (Peer Reviewed Journal)
Costa, M.D., Artur, M.S., Maia, J., Jonkheer, E., Derks, M.F., Nijveen, H., Williams, B., Mundree, S.G., Jimenez-Gomez, J.M., Hesselink, T., Schijlen, E.G., Ligterink, W., Oliver, M.J., Farrant, J.M., Hilhorst, H.W. 2017. A footprint of desiccation tolerance in the genome of Xerophyta viscosa. Nature Plants. 3:17038. Available: http://www.nature.com/articles/nplants201738.

Water deficit-induced changes in transcription factor expression in maize seedlings Reprint Icon - (Peer Reviewed Journal)
Seeve, C.M., Cho, I., Hearne, L.B., Srivastava, G.P., Joshi, T., Smith, D., Sharp, R.E., Oliver, M.J. 2017. Water deficit-induced changes in transcription factor expression in maize seedlings. Plant Cell and Environment. 40:686-701. doi: 10.1111/pce.12891.

Rootworm management: status of GM traits, insecticides, and potential new tools - (Literature Review)
Ludwick, D.C., Hibbard, B.E. 2017. Rootworm management: status of GM traits, insecticides, and potential new tools. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources. 11(2016). Available: http://www.cabi.org/cabreviews/abstract/20173027030.

The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize Reprint Icon - (Peer Reviewed Journal)
Walsh, J.R., Schaeffer, M.L., Zhang, P., Rhee, S.Y., Dickerson, J.A., Sen, T.Z. 2016. The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize. BMC Systems Biology. 10:129. doi: 10.1186/s12918-016-0369-x.

Genetic analysis of kernel traits in maize-teosinte introgression populations Reprint Icon - (Peer Reviewed Journal)
Liu, Z., Garcia, A., McMullen, M., Flint Garcia, S.A. 2016. Genetic analysis of kernel traits in maize-teosinte introgression populations. G3, Genes/Genomes/Genetics. 6(8):2523-2530. doi: 10.1534/g3.116.030155/-/DC1.

MeSH-informed enrichment analysis and MeSH-guided semantic similarity among functional terms and gene products in chicken Reprint Icon - (Peer Reviewed Journal)
Morota, G., Beissinger, T.M., Penagaricano, F. 2016. MeSH-informed enrichment analysis and MeSH-guided semantic similarity among functional terms and gene products in chicken. G3, Genes/Genomes/Genetics. 6(8):2447-2453. doi: 10.1534/g3.116.031096.

Metabolomic assessment of key maize resources: GC-MS and NMR profiling of grain from B73 hybrids of the nested association mapping (NAM) founders and of geographically diverse landraces Reprint Icon - (Peer Reviewed Journal)
Venkatesh, T.V., Chassy, A., Fiehn, O., Flint Garcia, S.A., Zeng, Q., Skogerson, K., Harrigan, G.G. 2016. Metabolomic assessment of key maize resources: GC-MS and NMR profiling of grain from B73 hybrids of the nested association mapping (NAM) founders and of geographically diverse landraces. Journal of Agricultural and Food Chemistry. 64(10):2162-2172. doi: 10.1021/acs.jafc.5b04901.

Key genes involved in desiccation tolerance and dormancy across life forms Reprint Icon - (Peer Reviewed Journal)
Costa, M.C., Farrant, J.M., Oliver, M.J., Ligterink, W., Buitink, J., Hilhorst, H.M. 2016. Key genes involved in desiccation tolerance and dormancy across life forms. Plant Science. 251:162-168. doi: 10.1016/j.plantsci.2016.02.001.

Recent demography drives changes in linked selection across the maize genome Reprint Icon - (Peer Reviewed Journal)
Beissinger, T.M., Wang, L., Crosby, K., Durvasula, A., Hufford, M.B., Ross-Ibarra, J. 2016. Recent demography drives changes in linked selection across the maize genome. Nature Plants. doi:10.1038/nplants.2016.84.

Expanding maize genetic resources with predomestication alleles: maize-teosinte introgression populations Reprint Icon - (Peer Reviewed Journal)
Liu, Z., Cook, J., Melia-Hancock, S., Guill, K.E., Bottoms, C., Garcia, A., Ott, O., Nelson, R., Recker, J., Balint-Kurti, P.J., Larsson, S., Lepak, N.K., Buckler, E.S., Trimble, L., Tracy, W., McMullen, M.D., Flint-Garcia, S.A. 2016. Expanding maize genetic resources with predomestication alleles: maize-teosinte introgression populations. The Plant Genome. 9(1). doi:10.3835/plantgenome2015.07.0053.

The genomic impacts of drift and selection for hybrid performance in maize Reprint Icon - (Peer Reviewed Journal)
Gerke, J.P., Edwards, J.W., Guill, K.E., Ross-Ibarra, J., McMullen, M.D. 2015. The genomic impacts of drift and selection for hybrid performance in maize. Genetics. 201(1201-1211). doi: 10.1534/genetics.115.182410.

Compositional assessments of key maize populations: B73 hybrids of the nested association mapping founder lines and diverse landrace inbred lines Reprint Icon - (Peer Reviewed Journal)
Venkatesh, T.V., Harrigan, G.G., Perez, T., Flint-Garcia, S.A. 2015. Compositional assessments of key maize populations: B73 hybrids of the nested association mapping founder lines and diverse landrace inbred lines. Journal of Agricultural and Food Chemistry. 63:5282-5295.

The resurrection genome of Boea hygrometrica: A blueprint for survival of dehydration Reprint Icon - (Peer Reviewed Journal)
Xiao, L., Yang, G., Zhang, L., Yang, X., Zhao, S., Ji, Z., Zhou, Q., Hu, M., Oliver, M.J., He, Y., et.al 2015. The resurrection genome of Boea hygrometrica: A blueprint for survival of dehydration. Proceedings of the National Academy of Sciences. 112(18):5833-5837.

Why we need GMO crops in agriculture - (Review Article)
Oliver, M.J. 2014. Why we need GMO crops in agriculture. Missouri Medicine. 111.6:493-507.

Hallauer’s Tusón: a decade of selection for tropical-to-temperate phenological adaptation in maize Reprint Icon - (Peer Reviewed Journal)
Teixeira, J.E., Weldekidan, T., de Leon, N., Flint Garcia, S.A., Holland, J.B., Lauter, N.C., Murray, S.C., Xu, W., Hessel, D., Kleintop, A.E., Hawk, J., Hallauer, A.R., Wisser, R. 2015. Hallauer’s Tusón: a decade of selection for tropical-to-temperate phenological adaptation in maize. Heredity. 114:229-240.

Insights into the effects of long-term artificial selection on seed size in maize Reprint Icon - (Peer Reviewed Journal)
Hirsch, C.N., Flint Garcia, S.A., Beissinger, T.M., Eichten, S.R., Deshpande, S., Barry, K., Mcmullen, M.D., Holland, J.B., Buckler IV, E.S., Springer, N., Buell, R.C., de Leon, N., Kaeppler, S.M. 2014. Insights into the effects of long-term artificial selection on seed size in maize. Genetics. 198(1):409-421.

BC4GO: a full-text corpus for the BioCreative IV GO Task Reprint Icon - (Peer Reviewed Journal)
Van Auken, K., Schaeffer, M.L., McQuilton, P., Laulederkind, S.J., Li, D., Wang, S., Hayman, G., Tweedie, S., Arighi, C.N., Done, J., et al. 2014. BC4GO: a full-text corpus for the BioCreative IV GO Task. Database: The Journal of Biological Databases and Curation. 2014:1-9. Available: http://database.oxfordjournals.org/content/2014/bau074

Plant water relations II: how plants manage water deficit and why it matters - (Review Article)
Williams, M., Oliver, M.J., Pallardy, S.G. 2014. Plant water relations II: how plants manage water deficit and why it matters. The Plant Cell. 26(4):1-15.

Plant water relations I: uptake and transport - (Review Article)
Williams, M., Oliver, M.J., Pallardy, S.G. 2014. Plant water relations I: uptake and transport. The Plant Cell. 26:1.

Maize databases - (Book / Chapter)
Schaeffer, M.L., Sen, T.Z., Lawrence, C.J. 2014. Maize databases. In: Wusirika, R., Bohn, M., Lai, J., Kole, C., editors. Genetics, Genomics and Breeding of Maize. Boca Raton, FL: CRC Press. p. 215-235.

The genetic architecture of maize height Reprint Icon - (Peer Reviewed Journal)
Peiffer, J.A., Romay, M.C., Gore, M.A., Flint Garcia, S.A., Zhang, Z., Millard, M.J., Gardner, C.A., McMullen, M.D., Holland, J.B., Bradbury, P., Buckler IV, E.S. 2014. The genetic architecture of maize height. Genetics. 196:1337-1356.