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Publications

2018

Zhu, X., Sun, L., Kuppu, S., Hu, R., Mishra, N., Smith, J., Esmaeili, N., Gore, M. A., Auld, D., Payton, P., Shen, G., and Zhang, H. 2018. The yield difference between wild-type cotton and IPT-transgenic cotton depends on when water-deficit stress is applied. Scientific Reports 8:2538. doi:10.1038/s41598-018-20944-7

Pauli, D., Ziegler, G. Ren, M., Jenks, M. A., Hunsaker, D. J., Zhang, M., Baxter, I. and Gore, M. A. 2018. Multivariate analysis of the cotton seed ionome reveals a shared genetic architecture. G3: Genes| Genomes| Genetics doi:

Byrne, P. F., Volk, G. M., Gardner, C., Gore, M. A., Simon, P. W., and Smith, S. 2018. Sustaining the future of plant breeding: The Critical role of the USDA-ARS National Plant Germplasm System. Crop Science 58:1-18. doi:10.2135/cropsci2017.05.0303

2017

Diepenbrock, C. H., Kandianis, C. B., Lipka, A. E., Magallanes-Lundback, M., Vaillancourt, B., Góngora-Castillo, E., Wallace, J. G., Cepela, J., Mesberg, A., Bradbury, P. J., Ilut, D. C., Mateos-Hernandez, M., Hamilton, J., Owens, B. F., Tiede, T., Buckler, E. S., Rocheford, T., Buell, C. R., Gore, M. A., and DellaPenna, D. 2017. Novel loci underlie natural variation of vitamin E levels in maize grain. The Plant Cell 29:2374-2392.

Pauli, D., White, J. W., Andrade-Sanchez, P., Conley, M., Heun, J., Thorp, K. R., French, A. N., Hunsaker, D. J., Carmo-Silva, E. A., Wang, G., and Gore, M. A. 2017. Investigation of the influence of leaf thickness on canopy reflectance and physiological traits in upland and Pima cotton populations. Frontiers in Plant Science 8:1405. doi:10.3389/fpls.2017.01405

DeChant, C., Wiesner-Hanks, T., Chen, S., Stewart, E., Yosinski, J., Gore, M. A., Nelson, R., Lipson, H. 2017. Automated identification of northern leaf blight-infected maize plants from field imagery using deep learning. Phytopathology 107:1426-1432. doi:10.1094/PHYTO-11-16-0417-R

Ilut, D. C., Sanchez, P. L., Coffelt, T. A., Dyer, J. M., Jenks, M. A., and Gore, M. A. 2017. A century of guayule: Comprehensive genetic characterization of the US national guayule (Parthenium argentatum A. Gray) germplasm collection. Industrial Crops and Products 109:300-309. doi:10.1016/j.indcrop.2017.08.029

Ariga, H., Katori, T., Tsuchimatsu, T., Hirase, T., Tajima, Y., Parker, J. E., Alcázar, R., Koornneef, M., Hoekenga, O., Lipka, A. E., Gore, M. A., Sakakibara, H., Kojima, M., Kobayashi, Y., Iuchi, S., Kobayashi, M., Shinozaki, K., Sakata, Y., Hayashi, T., Saijo, Y., and Taji, T. 2017. NLR locus-mediated trade-off between abiotic and biotic stress adaptation in Arabidopsis. Nature Plants 3:17072. doi:10.1038/nplants.2017.72

Holdsworth, W. L., Gazave, E., Cheng, P., Myers, J. R., Gore, M. A., Coyne, C. J., McGee, R. J., and Mazourek, M. 2017. A community resource for exploring and utilizing genetic diversity in the USDA pea single plant plus collection. Horticulture Research 4:17017. doi:10.1038/hortres.2017.17

Grover, C. E., Gallagher, J. P., Szadkowski, E. P., Page, J. T., Gore, M. A., Udall, J. A., and Wendel, J. F. 2017. Nucleotide diversity in the two co-resident genomes of allopolyploid cotton. Plant Systematics and Evolution 303:1–22. doi:10.1007/s00606-017-1411-1

Dabbert, T. A., Pauli, D., and Gore, M. A. 2017. Influences of the combination of high temperature and water deficit on the heritabilities and correlations of agronomic and fiber quality traits in upland cotton. Euphytica 213:6. doi:10.1007/s10681-016-1798-8

Angelovici, R., Batushansky, A., Deason, N., Gonzalez-Jorge, S., Gore, M. A., Fait, A., and DellaPenna, D. 2017. Network-guided GWAS improves identification of genes affecting free amino acids. Plant Physiology 173:872-886. doi:10.1104/pp.16.01287

Carlson, M. O., Gazave, E., Gore, M. A., and Smart, C. D. 2017. Temporal genetic dynamics of an experimental, biparental field population of Phytophthora capsici. Frontiers in Genetics 8:26. doi:10.3389/fgene.2017.00026.

Bird, K. A., An, H., Gazave, E., Gore, M. A., Pires, J. C., Robertson, L. D., and Labate, J. A. 2017. Population structure and phylogenetic relationships in a diverse panel of Brassica rapa L. Frontiers in Plant Science 8:321. doi:10.3389/fpls.2017.00321

Thompson, A. L., Pauli, D., Tomasi, P., Yurchenko, O., Jenks, M. A., Dyer, J. M., and Gore, M. A. 2017. Chemical variation for fiber cuticular wax levels in upland cotton (Gossypium hirsutum L.) evaluated under contrasting irrigation regimes. Industrial Crops and Products 100:153-162. doi:10.1016/j.indcrop.2017.02.030

2016

Buckler, E. S., Ilut, D. C., Wang, X., Kretzschmar, T., Gore, M. A., and Mitchell, S. E. 2016. rAmpSeq: Using repetitive sequences for robust genotyping. PrePrint at bioRxiv. doi:10.1101/096628

Pauli, D., Chapman, S. C., Bart, R., Topp, C. N., Lawrence-Dill, C. J., Poland, J., and Gore, M. A. 2016. The quest for understanding phenotypic variation via integrated approaches in the field environment. Plant Physiology 172:622-634. doi:10.1104/pp.16.00592

Gonzalez-Jorge, S., Mehrshahi, P., Magallanes-Lundback, M., Lipka, A. E., Angelovici, R., Gore, M. A., and DellaPenna, D. 2016. ZEAXANTHIN EPOXIDASE activity potentiates carotenoid degradation in maturing Arabidopsis seed. Plant Physiology 171:1837-1851. doi:10.1104/pp.16.00604

French, A. N., Gore, M. A., and Thompson, A. 2016. Cotton phenotyping with lidar from a track-mounted platform. Proceedings of SPIE 9866, Autonomous air and ground sensing systems for agricultural optimization and phenotyping, SPIE Proceedings 9866. doi:10.1117/12.2224423

Gazave, E., Tassone E. E., Ilut, D. C., Wingerson, M., Datema, E., Witsenboer, H., Davis, J. B., Grant, D., Dyer, J. M., Jenks, M. A., Brown, J., and Gore, M. A. 2016. Population genomic analysis reveals differential evolutionary histories and patterns of diversity across subgenomes and subpopulations of Brassica napus L. Frontiers in Plant Science 7:525. doi:10.3389/fpls.2016.00525

Pauli, D., Andrade-Sanchez, P., Carmo-Silva, A. E., Gazave, E., French, A. N., Heun, J., Hunsaker, D. J., Lipka, A. E., Setter, T. L., Strand, R. J., Thorp, K. R., Wang, S., White, J. W., and Gore, M. A. 2016. Field-based high-throughput plant phenotyping reveals the temporal patterns of quantitative trait loci associated with stress-responsive traits in cotton. G3: Genes| Genomes| Genetics 6:865-879. doi:10.1534/g3.115.023515

Hinze, L. L., Gazave, E., Gore, M. A., Fang, D. D., Scheffler, B. E., Yu, J. Z., Jones, D. C., Frelichowski, J., and Percy, R. G. 2016. Genetic diversity of the two commercial tetraploid cotton species in the Gossypium Diversity Reference Set. Journal of Heredity 107:274-286. doi:10.1093/jhered/esw004

Ilut, D. C., Lipka, A. E., Jeong, N., Bae, D. N., Kim, D. H., Kim, J. H., Redekar, N., Yang, K., Park, W., Kang, S.-T., Kim, N., Moon, J.-K., Saghai Maroof, M. A., Gore, M. A., and Jeong, S.-C. 2016. Identification of haplotypes at the Rsv4 genomic region in soybean associated with durable resistance to soybean mosaic virus. Theoretical and Applied Genetics 129:453-468. doi:10.1007/s00122-015-2640-8

Tassone, E. E., Lipka, A. E., Tomasi, P., Lohrey, G. T., Dyer, J. M., Gore, M. A., and Jenks, M. A. 2016. Chemical variation for leaf cuticular wax levels revealed in a diverse panel of Brassica napus L. Industrial Crops and Products 79:77-83. doi:10.1016/j.indcrop.2015.10.047

2015

Thorp, K. R., Gore, M. A., Andrade-Sanchez, P., Carmo-Silva, E., Welch, S. M., White, J. W., and French, A. N. 2015. Proximal hyperspectral sensing and data analysis approaches for field-based plant phenomics. Computers and Electronics in Agriculture 118:225-236. doi:10.1016/j.compag.2015.09.005

Ilut, D. C., Sanchez, P. L., Costich, D. E., Friebe, B., Coffelt, T. A., Dyer, J. M., Jenks, M. A., and Gore, M. A. 2015. Genomic diversity and phylogenetic relationships in the genus Parthenium (Asteraceae). Industrial Crops and Products 76:920-929. doi:10.1016/j.indcrop.2015.07.035

Grover, C. E., Gallagher, J. P., Jareczek, J. J., Page, J. T., Udall, J. A., Gore, M. A., and Wendel, J. F. 2015. Re-evaluating the phylogeny of allopolyploid Gossypium L. Molecular Phylogenetics and Evolution 92:45-52. doi:10.1016/j.ympev.2015.05.023

Hulse-Kemp, A. M., Lemm, J., Plieske, J., Ashrafi, H., Buyyarapu, R., Fang, D. D., Frelichowski, J., Giband, M., Hague, S., Hinze, L. L., Kochan, K., Riggs, P., Scheffler, J. A., Udall, J. A., Ulloa, M., Wang, S. S., Zhu, Q.-H., Bag, S. K., Bhardwaj, A., Burke, J. J., Byers, R. L., Claverie, M., Gore, M. A., et al. and Stelly, D. M. 2015. Development of a 63K SNP array for Gossypium and high-density mapping of intra- and inter-specific populations of cotton (G. hirsutum L.). G3: Genes| Genomes| Genetics 5:1187-1209. doi:10.1534/g3.115.018416

Diepenbrock, C. H. and Gore, M. A. 2015. Closing the divide between human nutrition and plant breeding. Crop Science 55:1437-1448. doi:10.2135/cropsci2014.08.0555

Lipka, A. E., Kandianis, C. B., Hudson, M. E., Yu, J., Drnevich, J., Bradbury, P. J., and Gore, M. A. 2015. From association to prediction: statistical methods for the dissection and selection of complex traits in plants. Current Opinion in Plant Biology 24:110-118. doi:10.1016/j.pbi.2015.02.010

Hinze, L. L., Fang, D. D., Gore, M. A., Scheffler, B. E., Yu, J. Z., Frelichowski, J., and Percy, R. G. 2015. Molecular characterization of the Gossypium diversity reference set of the US national cotton germplasm collection. Theoretical and Applied Genetics 128:313-327. doi:10.1007/s00122-014-2431-7

2014

Dabbert, T. A. and Gore, M. A. 2014. Challenges and perspectives on improving heat and drought stress resilience in cotton. The Journal of Cotton Science 18:393-409.

Owens, B. F., Lipka, A. E., Magallanes-Lundback, M., Tiede, T., Diepenbrock, C. H., Kandianis, C. B., Kim, E., Cepela, J., Mateos Hernandez, M., Buell, C. R., Buckler, E. S., DellaPenna, D., Gore, M. A., and Rocheford, T. 2014. A foundation for provitamin A biofortification of maize: Genome-wide association and genomic prediction models of carotenoid levels. Genetics 198:1699–1716. doi:10.1534/genetics.114.169979

Yurchenko, O. P., Park, S., Ilut, D. C., Inmon, J. J., Millhollon, J. C., Liechty, Z., Page, J. T., Jenks, M. A., Chapman, K. D., Udall, J. A., Gore, M. A., and Dyer, J. M. 2014. Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium. BMC Plant Biology 14:312.

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., and Buckler, E. S. 2014. The genetic architecture of maize height. Genetics 196:1337-1356.

Gore, M. A., Fang, D. D., Poland, J. A., Zhang, J., Percy, R. G., Cantrell, R. G., Thyssen, G., and Lipka, A. E. 2014. Linkage map construction and quantitative trait locus analysis of agronomic and fiber quality traits in cotton. The Plant Genome 7:1-10.

Sanchez, P. L., Chen, M.-K., Pessarakli, M., Hill, H. J., Gore, M. A., and Jenks, M. A. 2014. Effects of temperature and salinity on germination of non-pelleted and pelleted guayule (Parthenium argentatum A. Gray) seeds. Industrial Crops and Products 55:90-96.

Sanchez, P. L., Costich, D. E., Friebe, B., Coffelt, T. A., Jenks, M. A., and Gore, M. A. 2014. Genome size variation in guayule and mariola: Fundamental descriptors for polyploid plant taxa. Industrial Crops and Products 54:1-5.

Fang, H., Zhou, H., Sanogo, S., Lipka, A. E., Fang, D. D., Percy, R. G., Hughs, S. E., Jones, D. C., Gore, M. A., and Zhang, J. 2014. Quantitative trait locus analysis of Verticillium wilt resistance in an introgressed recombinant inbred population of Upland cotton. Molecular Breeding 33:709-720.

Tyagi, P., Gore, M. A., Bowman, D. T., Campbell, B. T., Udall, J. A., and Kuraparthy, V. 2014. Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.). Theoretical and Applied Genetics 127:283-295.

Andrade-Sanchez, P., Gore, M. A., Heun, J. T., Thorp, K. R., Carmo-Silva, A. E., French, A. N., Salvucci, M. E., and White, J. W. 2014. Development and evaluation of a field-based high-throughput phenotyping platform. Functional Plant Biology 41:68-79.

2013

Angelovici, R., Lipka, A. E., Deason, N., Gonzalez–Jorge, S., Lin, H., Cepela, J., Buell, R., Gore, M. A., and DellaPenna, D. 2013. Genome-wide analysis of branched-chain amino acid levels in Arabidopsis seed. The Plant Cell 25:4827-4843.

Gonzalez-Jorge, S., Ha, S.-H., Gilliland, L. U., Little, H., Zhou, A., Magallanes-Lundback, M., Lipka, A. E., Cepela, J., Buell, R., Gore, M. A., and DellaPenna, D. 2013. CAROTENOID CLEAVAGE DIOXYGENASE4 is a negative regulator of β-carotene content in Arabidopsis seed. The Plant Cell 25:4812-4826.

Lipka, A. E., Gore, M. A., Magallanes-Lundback, M., Mesberg, A., Lin, H., Tiede, T., Chen, C., Buell, C. R., Buckler, E. S., Rocheford, T., and DellaPenna, D. 2013. Genome-wide association study and pathway level analysis of tocochromanol levels in maize grain. G3: Genes| Genomes| Genetics 3:1287-1299.

Chandler, K., Lipka, A. E., Owens, B. F., Li, H., Buckler, E. S., Rocheford, T., and Gore, M. A. 2013. Genetic analysis of visually scored orange kernel color in maize. Crop Science 53:189-200.

Yu, J., Yu, S., Gore, M., Wu, M., Zhai, H., Li, X., Shuli, F., Song, M., and Zhang, J. 2013. Identification of quantitative trait loci across interspecific F2, F2:3 and testcross populations for agronomic and fiber traits in tetraploid cotton. Euphytica 191:375-389.

2012

Lipka, A. E., Tian, F., Wang Q., Peiffer, J., Li, M., Bradbury, P. J., Gore, M. A., Buckler, E. S., and Zhang, Z. 2012. GAPIT: genome association and prediction integrated tool. Bioinformatics 28:2397-2399.

Thorp, K., Andrade-Sanchez, P., Gore, M., White, J., and French, A. 2012. Information technologies for field-based high-throughput phenotyping. Resource-Engineering and Technology for a Sustainable World 19:8-9.

Chia, J., Song, C., Bradbury, P., Costich, D., De Leon, N., Doebley, J., Elshire, R., Gaut, B., Geller, L., Glaubitz, J., Gore, M., Guill, K., Holland, J., Hufford, M., Lai, J., Li, M., Liu, X., Lu, Y., McCombie, R., Nelson, R., Poland, J.A., Prasanna, B. M., Phyäjärvi, T., Rong, T., Sekhon, R., Sun, Q., Tenaillon, M., Tian, F., Wang, J., Xu, X., Zhang, Z., Kaeppler, S. M., Ross-Ibarra, J., McMullen, M. D., Buckler, E. S., Zhang, G., Xu, Y., and Ware, D. 2012. Maize HapMap2 identifies extant variation from a genome in flux. Nature Genetics 44:803-807.

Carmo-Silva, E. A., Gore, M. A., Andrade-Sanchez, P., French, A. N., Hunsaker, D. J., and Salvucci, M. E. 2012. Decreased CO2 availability and inactivation of Rubisco limit photosynthesis in cotton plants under heat and drought stress in the field. Environmental and Experimental Botany 83:1-11.

White, J. W., Andrade-Sanchez, P., Gore, M. A., Bronson, K. F., Coffelt, T. A., Conley, M. M., Feldmann, K. A., French, A. N., Heun, J. T., Hunsaker, D. J., Jenks, M. A, Kimball, B. A., Roth, R. L., Strand, R. J., Thorp, K. R., Wall, G. W., and Wang, G. 2012. Field-based phenomics for plant genetics research. Field Crops Research 133:101-112.

Gore, M. A., Percy, R. G., Zhang, J., Fang, D. D., and Cantrell, R. G. 2012. Registration of the TM-1/NM24016 cotton recombinant inbred mapping population. Journal of Plant Registrations 6:124-127.

2011

Gore, M. A., Coyle, G., Friebe, B., Coffelt, T. A., and Salvucci, M. E. 2011. Complex ploidy level variation in guayule breeding programs. Crop Science 51:210-216.

Setter, T. L., Yan, J., Warburton, M., Ribaut, J.-M., Xu, Y., Sawkins, M., Buckler, E. S., Zhang, Z., and Gore, M. A. 2011. Genetic association mapping identifies single nucleotide polymorphisms in genes that affect abscisic acid levels in maize floral tissues during drought. Journal of Experimental Botany 62:701-716.

Gore, M. 2011. Molecular plant breeding. Field Crops Research 123:183-184.

2010

Zhang, Z., Ersoz, E., Lai, C.-Q., Todhunter, R. J., Tiwari, H. K., Gore, M. A., Bradbury, P. J., Yu, J., Arnett, D. K., Ordovas, J. M., and Buckler, E. S. 2010. Mixed linear model approach adapted for genome-wide association studies. Nature Genetics 42:355-360.

Li, Q., Yang, X., Bai, G., Warburton, M., Mahuku, G., Gore, M., Dai, J., Li, J., and Yan, J. 2010. Cloning and characterization of a putative GS3 ortholog involved in maize kernel development. Theoretical and Applied Genetics 120:753-763.

2009

Gore, M. A., Chia, J.-M., Elshire, R. J., Sun, Q., Ersoz, E. S., Hurwitz, B. L., Peiffer, J. A., McMullen, M. D., Grills, G. S., Ross-Ibarra, J., Ware, D. H., and Buckler, E. S. 2009. A first generation haplotype map of maize. Science 326:1115-1117.

Gore, M. A., Wright, M. H., Ersoz, E. S., Bouffard, P., Szekeres, E. S., Jarvie, T. P., Hurwitz, B. L., Narechania, A., Harkins, T. T., Grills, G. S., Ware, D. H., and Buckler, E. S. 2009. Large-scale discovery of gene-enriched SNPs. The Plant Genome 2:121-133.

2008

Zhu, C., Gore, M., Buckler, E. S., and Yu, J. 2008. Status and prospects of association mapping in plants. The Plant Genome 1:5-20.

2007

Buckler, E., and Gore, M. 2007. An Arabidopsis haplotype map takes root. Nature Genetics 39: 1056-1057.

Gore, M., Bradbury, P., Hogers, R., Kirst, M., Verstege, E., van Oeveren, J., Peleman, J., Buckler, E., and van Eijk, M. 2007. Evaluation of target preparation methods for single-feature polymorphism detection in large complex plant genomes. Crop Science 47: S135–S148.

2004

Hayes, A. J., Jeong, S. C., Gore, M. A., Yu, Y. G., Buss, G. R., Tolin, S. A., and Saghai Maroof, M. A. 2004. Recombination within a nucleotide-binding-site/leucine-rich-repeat gene cluster produces new variants conditioning resistance to soybean mosaic virus in soybeans. Genetics 166: 493-503.

2003

Padidam, M., Gore, M., Lu, D. L., and Smirnova, O. 2003. Chemical-inducible, ecdysone receptor-based gene expression system for plants. Transgenic Research 12: 101-109.

2002

Gore, M. A., Hayes, A. J., Jeong, S. C., Yue, Y. G., Buss, G. R., and Saghai Maroof, M. A. 2002. Mapping tightly linked genes controlling potyvirus infection at the Rsv1 and Rpv1 region in soybean. Genome 45: 592-599.