Adjunct Associate Professor of Biological Sciences
Research Geneticist & Lead Scientist, USDA-ARS
PhD, 2001 University of Missouri
The genetics and consequences of maize domestication and breeding
Research descriptionMaize is an extremely diverse species, both genetically and phenotypically. My lab is interested in understanding this diversity, linking genotype to phenotype, and applying this information to maize improvement. We develop germplasm resources and use quantitative genetics and genomics approaches to create new varieties with the desired characteristics. In particular, we are focused on adaptation and kernel traits, especially as these traits relate to the domestication and breeding history of corn.
Selection has impacted maize diversity during domestication from teosinte (Zea mays ssp. parviglumis) to landraces (locally adapted populations) , and during plant breeding from landraces to modern inbred lines and hybrids. The seed was certainly a target during domestication to make an edible foodstuff during the shift from hunter-gathers to early farmer societies, as well as breeding to make the high yielding commodity of today. Selection acted on a small number of master regulators and a cascade of hundreds of genes involved in domestication and breeding traits. My lab uses this historical background to study the process of section on the seed and the consequences of selection for modern corn.
My lab uses germplasm resources such as the maize nested association mapping (NAM) population of 5000 recombinant inbred lines (RILs), the ~900 near isogenic lines (NILs) comprising the ten teoNIL populations, a set of 2000 doubled haploid (DH) lines derived from the Zea Synthetic (containing the NAM founders and 11 teosinte accessions), and landraces from around the world to conduct QTL mapping, association mapping, and selection/breeding.
Current projects investigate the genetic nature of photoperiod (daylength) response, response to elevation (highland adaptation), response to inbreeding (inbreeding depression). Using this information, we are beginning a new breeding project to create novel food corn varieties from landraces, a primary source for interesting food characteristics.
Alkhalifah, N., et al. Maize genomes to fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets (2018) BMC Research Notes, 11 (1), art. no. 452.
Vanous, A., Gardner, C., Blanco, M., Martin-Schwarze, A., Lipka, A.E., Flint-Garcia, S., Bohn, M., Edwards, J., Lübberstedt, T. Association mapping of flowering and height traits in germplasm enhancement of maize doubled haploid (GEM-DH) lines (2018) Plant Genome, 11 (2), art. no. 170083.
Bohn, M.O., Marroquin, J.J., Flint-Garcia, S., Dashiell, K., Willmot, D.B., Hibbard, B.E. 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.) (2018) Journal of Economic Entomology, 111 (1), pp. 435-444.
Gage, J.L., et al. The effect of artificial selection on phenotypic plasticity in maize (2017) Nature Communications, 8 (1), art. no. 1348.
Karn, A., Gillman, J.D., Flint-Garcia, S.A. Genetic analysis of teosinte alleles for kernel composition traits in maize (2017) G3: Genes, Genomes, Genetics, 7 (4), pp. 1157-1164.
Gu, X., Lee, T., Geng, T., Liu, K., Thoma, R., Crowley, K., Edrington, T., Ward, J.M., Wang, Y., Flint-Garcia, S., Bell, E., Glenn, K.C. Assessment of natural variability of maize lipid transfer protein using a validated sandwich ELISA (2017) Journal of Agricultural and Food Chemistry, 65 (8), pp. 1740-1749.
Flint-Garcia, S.A. Kernel evolution: From teosinte to maize (2017) Maize Kernel Development, pp. 1-16.
Lennon, J.R., Krakowsky, M., Goodman, M., Flint-Garcia, S., Balint-Kurti, P.J. Identification of teosinte alleles for resistance to southern leaf blight in near isogenic maize lines (2017) Crop Science, 57 (4), pp. 1973-1983.
Karn, A., Heim, C., Flint-Garcia, S., Bilyeu, K., Gillman, J. Development of rigorous fatty acid near-infrared spectroscopy quantitation methods in support of soybean oil improvement (2017) JAOCS, Journal of the American Oil Chemists' Society, 94 (1), pp. 69-76.
Venkatesh, T.V., Chassy, A.W., Fiehn, O., Flint-Garcia, S., Zeng, Q., Skogerson, K., Harrigan, G.G. 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 (2016) Journal of Agricultural and Food Chemistry, 64 (10), pp. 2162-2172.
Liu, Z., Cook, J., Melia-Hancock, S., Guill, K., Bottoms, C., Garcia, A., Ott, O., Nelson, R., Recker, J., Balint-Kurti, P., Larsson, S., Lepak, N., Buckler, E., Trimble, L., Tracy, W., McMullen, M.D., Flint-Garcia, S.A. Expanding Maize Genetic resources with predomestication alleles: Maize–teosinte introgression populations (2016) Plant Genome, 9 (1), 11 p.
Liu, Z., Garcia, A., McMullen, M.D., Flint-Garcia, S.A. Genetic analysis of kernel traits in maize-teosinte introgression populations (2016) G3: Genes, Genomes, Genetics, 6 (8), pp. 2523-2530.
Lennon, J.R., Krakowsky, M., Goodman, M., Flint-Garcia, S., Balint-Kurti, P.J. Identification of alleles conferring resistance to gray leaf spot in maize derived from its wild progenitor species teosinte (2016) Crop Science, 56 (1), pp. 209-218.
Venkatesh, T.V., Harrigan, G.G., Perez, T., Flint-Garcia, S. Compositional assessments of key maize populations: B73 hybrids of the nested association mapping founder lines and diverse landrace inbred lines (2015) Journal of Agricultural and Food Chemistry, 63 (21), pp. 5282-5295.
Teixeira, J.E.C., Weldekidan, T., De Leon, N., Flint-Garcia, S., Holland, J.B., Lauter, N., Murray, S.C., Xu, W., Hessel, D.A., Kleintop, A.E., Hawk, J.A., Hallauer, A., Wisser, R.J. Hallauer's Tusón: A decade of selection for tropical-to-temperate phenological adaptation in maize (2015) Heredity, 114 (2), pp. 229-240.
Hirsch, C.N., Flint-Garcia, S.A., Beissinger, T.M., Eichten, S.R., Deshpande, S., Barry, K., McMullen, M.D., Holland, J.B., Buckler, E.S., Springer, N., Robin Buell, C., de Leon, N., Kaeppler, S.M. Insights into the effects of long-term artificial selection on seed size in maize (2014) Genetics, 198 (1).
Sood, S., Flint-Garcia, S., Willcox, M.C., Holland, J.B. Mining natural variation for maize improvement: Selection on phenotypes and genes (2014) Genomics of Plant Genetic Resources: Volume 1. Managing, Sequencing and Mining Genetic Resources, pp. 615-649.
Peiffer, J.A., Romay, M.C., Gore, M.A., Flint-Garcia, S.A., Zhang, Z., Millard, M.J., Gardner, C.A.C., McMullen, M.D., Holland, J.B., Bradbury, P.J., Buckler, E.S. The genetic architecture of maize height (2014) Genetics, 196 (4), pp. 1337-1356.
Flint-Garcia, S.A. Genetics and consequences of crop domestication (2013) Journal of Agricultural and Food Chemistry, 61 (35), pp. 8267-8276.
Peiffer, J.A., Flint-Garcia, S.A., De Leon, N., McMullen, M.D., Kaeppler, S.M., Buckler, E.S. The genetic architecture of maize stalk strength (2013) PLoS ONE, 8 (6), art. no. e67066.
Romay, M.C., Millard, M.J., Glaubitz, J.C., Peiffer, J.A., Swarts, K.L., Casstevens, T.M., Elshire, R.J., Acharya, C.B., Mitchell, S.E., Flint-Garcia, S.A., McMullen, M.D., Holland, J.B., Buckler, E.S., Gardner, C.A. Comprehensive genotyping of the USA national maize inbred seed bank (2013) Genome Biology, 14 (6), art. no. R55, .
Voothuluru, P., Thompson, H.J., Flint-Garcia, S.A., Sharp, R.E. Genetic variability of oxidase oxalate activity and elongation in water-stressed primary roots of diverse maize and rice lines (2013) Plant Signaling and Behavior, 8 (3), pp. e23454.1-e23454.4.
Hung, H.-Y., Shannon, L.M., Tian, F., Bradbury, P.J., Chen, C., Flint-Garcia, S.A., McMullen, M.D., Ware, D., Buckler, E.S., Doebley, J.F., Holland, J.B. ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize (2012) Proceedings of the National Academy of Sciences of the United States of America, 109 (28), pp. E1913-E1921.
Donald, P.A., Heinz, R., Bernard, E., Hershman, D., Hensley, D., Flint-Garcia, S., Joost, R. Distribution, host status and potential sources of resistance to vittatidera zeaphila (2012) Nematropica, 42 (1), pp. 91-95.
Hung, H.-Y., Browne, C., Guill, K., Coles, N., Eller, M., Garcia, A., Lepak, N., Melia-Hancock, S., Oropeza-Rosas, M., Salvo, S., Upadyayula, N., Buckler, E.S., Flint-Garcia, S., McMullen, M.D., Rocheford, T.R., Holland, J.B. The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population (2012) Heredity, 108 (5), pp. 490-499.
Cook, J.P., McMullen, M.D., Holland, J.B., Tian, F., Bradbury, P., Ross-Ibarra, J., Buckler, E.S., Flint-Garcia, S.A. Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels (2012) Plant Physiology, 158 (2), pp. 824-834.
Brown, P.J., Upadyayula, N., Mahone, G.S., Tian, F., Bradbury, P.J., Myles, S., Holland, J.B., Flint-Garcia, S., McMullen, M.D., Buckler, E.S., Rocheford, T.R. Distinct genetic architectures for male and female inflorescence traits of maize (2011) PLoS Genetics, 7 (11), art. no. e1002383.
Tian, F., Bradbury, P.J., Brown, P.J., Hung, H., Sun, Q., Flint-Garcia, S., Rocheford, T.R., McMullen, M.D., Holland, J.B., Buckler, E.S. Genome-wide association study of leaf architecture in the maize nested association mapping population (2011) Nature Genetics, 43 (2), pp. 159-162.
Bottoms, C.A., Flint-Garcia, S., McMullen, M.D. IView: Introgression library visualization and query tool (2010) BMC Bioinformatics, 11 (SUPPL. 6), art. no. 28, .
Zhang, N., Gur, A., Gibon, Y., Sulpice, R., Flint-Garcia, S., McMullen, M.D., Stitt, M., Buckler, E.S. Genetic analysis of central carbon metabolism unveils an amino acid substitution that alters maize NAD-Dependent isocitrate dehydrogenase activity (2010) PLoS ONE, 5 (4), art. no. e9991.
Dubois, P.G., Olsefski, G.T., Flint-Garcia, S., Setter, T.L., Hoekenga, O.A., Brutnell, T.P. Physiological and genetic characterization of end-of-day far-red light response in maize seedlings (2010) Plant Physiology, 154 (1), pp. 173-186.
Flint-Garcia, S.A., Guill, K.E., Sanchez-Villeda, H., Schroeder, S.G., McMullen, M.D. Maize amino acid pathways maintain high levels of genetic diversity (2009) Maydica, 54 (4), pp. 375-386.
Flint-Garcia, S.A., Buckler, E.S., Tiffin, P., Ersoz, E., Springer, N.M. Heterosis is prevalent for multiple traits in diverse maize germplasm (2009) PLoS ONE, 4 (10), art. no. e0007433.
Flint-Garcia, S.A., Bodnar, A.L., Scott, M.P. Wide variability in kernel composition, seed characteristics, and zein profiles among diverse maize inbreds, landraces, and teosinte (2009) Theoretical and Applied Genetics, 119 (6), pp. 1129-1142.
McMullen, M.D., et al. Genetic properties of the maize nested association mapping population (2009) Science, 325 (5941), pp. 737-740.
Buckler, E.S., et al. The genetic architecture of maize flowering time (2009) Science, 325 (5941), pp. 714-718.
Flint-Garcia, S.A., Dashiell, K.E., Prischmann, D.A., Bohn, M.O., Hibbard, B.E. Conventional screening overlooks resistance sources: Rootworm damage of diverse inbred lines and their R73 hybrids is unrelated (2009) Journal of Economic Entomology, 102 (3), pp. 1317-1324.
Sanchez-Villeda, H., Schroeder, S., Flint-Garcia, S., Guill, K.E., Yamasaki, M., McMullen, M.D. DNAAlignEditor: DNA alignment editor tool (2008) BMC Bioinformatics, 9, art. no. 154.
Hibbard, B.E., Willmot, D., Flint-Garcia, S.A., Darrah, L. Registration of the maize germplasm CRW3(S1)C6 with resistance to western corn rootworm (2007) Journal of Plant Registrations, 1, pp 151-152.
Flint-Garcia, S.A., Thuillet, A.-C., Yu, J., Pressoir, G., Romero, S.M., Mitchell, S.E., Doebley, J., Kresovich, S., Goodman, M.M., Buckler, E.S. Maize association population: A high-resolution platform for quantitative trait locus dissection (2005) Plant Journal, 44 (6), pp. 1054-1064.
Flint-Garcia, S.A., Thornsberry, J.M., Edward IV, S.B. Structure of linkage disequilibrium in plants (2003) Annual Review of Plant Biology, 54, pp. 357-374.
Flint-Garcia, S.A., Darrah, L.L., McMullen, M.D., Hibbard, B.E. Phenotypic versus marker-assisted selection for stalk strength and second-generation European corn borer resistance in maize (2003) Theoretical and Applied Genetics, 107 (7), pp. 1331-1336.
Flint-Garcia, S.A., McMullen, M.D., Darrah, L.L. Genetic relationship of stalk strength and ear height in maize (2003) Crop Science, 43 (1), pp. 23-31.
Flint-Garcia, S.A., Jampatong, C., Darrah, L.L., McMullen, M.D. Quantitative trait locus analysis of stalk strength in four maize populations (2003) Crop Science, 43 (1), pp. 13-22.
Cocciolone, S.M., Chopra, S., Flint-Garcia, S.A., McMullen, M.D., Peterson, T. Tissue-specific patterns of a maize Myb transcription factor are epigenetically regulated (2001) Plant Journal, 27 (5), pp. 467-478.
Byrne, P., McMullen, M., Snook, M., Musket, T., Xu, G., Lee, E., Flint, S., Widstrom, N., Wiseman, B., Coe, E. Metabolic channeling suggested by QTL analysis of silk maysin and apimaysin concentration (1997) Maize Genetics Cooperation Newsletter, 71, pp. 26-27.
Honors & Awards
Selected honors and awards
Secretary’s Honor Award, U.S. Department of Agriculture 2012