In Review

D.E. Hufnagel, K. Kananen, J.C. Glaubitz, J. de Jesus Sanchez-Gonzalez, J.F. Doebley, M.B. Hufford. Evidence for Multiple Teosinte Hybrid Zones in Central Mexico. [preprint]

M.B. Hufford, A.S. Seetharam, M.R. Woodhouse, K.M. Chougule, S. Ou, J. Liu, W.A. Ricci, T. Guo, A. Olson, Y. Qiu, R.D. Coletta, S. Tittes, A.I. Hudson, A.P. Marand, S. Wei, Z. Lu, B. Wang, M.K. Tello-Ruiz, R.D. Piri, N. Wang, D. Kim, Y. Zeng, C.H. O’Connor, X. Li, A.M. Gilbert, E. Baggs, K.V. Krasileva, J.L. Portwood II, E.K.S. Cannon, C.M. Andorf, N. Manchanda, S.J. Snodgrass, D.E. Hufnagel, Q. Jiang, S. Pedersen, M.L. Syring, D.A. Kudrna, V. Llaca, K. Fengler, R.J. Schmitz, J. Ross-Ibarra, J. Yu, J.I. Gent, C.N. Hirsch, D. Ware, R.K. Dawe. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. [preprint]

F. Rodríguez-Zapata, A.C Barnes, K.A. Blöcher-Juárez, D. Gates, A. Kur, L. Wang, G.M. Janzen, S. Jensen, J.M. Estévez-Palmas, T. Crow, R. Aguilar-Rangel, E. Demesa-Arevalo, T. Skopelitis, S. Pérez-Limón, W.L. Stutts, P. Thompson, Y. Chiu, F. Jackson, O. Fiehn, D. Runcie, E.S. Buckler, J. Ross-Ibarra, M.B. Hufford, R.J.H Sawers, R. Rellán-Álvarez. Teosinte introgression modulates phosphatidylcholine levels and induces early maize flowering time. [preprint]

L. Wang, E.B. Josephs, K.M. Lee, L.M. Roberts, R. Rellán-Álvarez, J. Ross-Ibarra, M.B. Hufford. Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces. [preprint]

Gates, D.J., D. Runcie, G.M. Janzen, A. Romero-Navarro, M. Willcox, K. Sonder, S.J. Snodgrass, F. Rodríguez-Zapata, R.J.H. Sawers, R. Rellán-Álvarez, E.S. Buckler, S. Hearne, M.B. Hufford, J. Ross-Ibarra. Single-gene resolution of locally adaptive genetic variation in Mexican maize. [preprint]

Published Manuscripts

A.V. Verzegnazzi, I. Gonçalves dos Santos, M.D. Krause, M. Hufford, U.K Frei, J. Campbell, V. Costa Almeida, L.T. Zuffo, N. Boerman & T. Lübberstedt. 2021. Major locus for spontaneous haploid genome doubling detected by a case–control GWAS in exotic maize germplasm. Theoretical and Applied Genetics 58

D. Coletta, R., Qiu, Y., Ou, S., M.B. Hufford, C.N. Hirsch. 2021. How the pan-genome is changing crop genomics and improvement. Genome Biology 22: 3

Liu, J., A.S. Seetharam, K. Chougule, S. Ou, K. Swentowsky, J.I. Gent, V. Llaca, M. Woodhouse, N. Manchanda, G. Presting, D. Kudrna, M. Alabady, C.N. Hirsch, K. Fengler, D. Ware, T. Michael, M.B. Hufford, R.K. Dawe. 2020. Gapless assembly of maize chromosomes using long read technologies. Genome Biology 21: 121

Hufnagel, D.E., M.B. Hufford, A. S. Seetharam. 2020. SequelTools: A suite of tools for working with PacBio Sequel raw sequence data. BMC Bioinformatics 21: 429

Ou, S., J. Liu, K.M. Chougule, A. Fungtammasan, A.S. Seetharam, J. Stein, V. Llaca, N. Manchanda, A.M. Gilbert, X. Wei, C. Chin, D.E. Hufnagel, S. Pedersen, S. Snodgrass, K. Fengler, M. Woodhouse, B.P. Walenz, S. Koren, A.M. Phillippy, B. Hannigan, R.K. Dawe, C.N. Hirsch, M.B. Hufford, Doreen Ware. 2020. Effect of sequence depth and length in long-read assembly of the maize inbred NC358 Nature Communications 11: 2288

Manchanda., N., J.L. Portwood, II, M.R. Woodhouse, A.S. Seetharam, C.M. Andorf, M.B. Hufford. 2020. GenomeQC: A quality assessment tool for genome assemblies and gene annotations. BMC Genomics 21: 193

Wang, B., Z. Lin, X. Li, Y. Zhao,…J. Lai, M.B. Hufford, J. Ross-Ibarra, H. He, H. Wang. 2020. Genome-wide selection and genetic improvement during modern maize breeding. Nature Genetics 52: 565–571

Coffman, S.M., M.B. Hufford, C.M. Andorf, T. Lübberstedt. 2020. Haplotype structure in commercial maize breeding programs in relation to key founder lines. Theoretical and Applied Genetics 133: 547-561

Ou, S., W. Su, Y. Liao, K. Chougule, J.R.A. Agda, A.J. Hellinga, C. Santiago Blanco Lugo, D. Ware, T. Peterson, N. Jiang, C.N. Hirsch, M.B. Hufford. 2019. Benchmarking Transposable Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline. Genome Biology 20: 275

Gonzalez-Segovia, E., S. Pérez-Limon, G.C. Cíntora-Martínez, A. Guerrero-Zavala, G.M. Janzen, M.B. Hufford, J. Ross-Ibarra, R.J.H Sawers. 2019. Characterization of introgression from the teosinte Zea mays ssp. mexicana to Mexican highland maize. PeerJ e6815

Woodhouse, M.R. and M.B. Hufford. 2019. Parallelism and convergence in post-domestication adaptation in cereal grasses. Philosophical Transactions B 374: 20180245

Andorf, C., W.D. Beavis, M.B. Hufford, T. Lübberstedt, S. Smith, W. Suza, K. Wang, M. Woodhouse, J. Yu. 2019. Technological advanced in maize breeding: Past, present and future. Theoretical and Applied Genetics 132: 817-849

Hufford, M.B., J.C.B.M.y Teran, P. Gepts. 2019. Crop Biodiversity: An unfinished magnum opus of nature. Annual Review of Plant Biology 70: 727-751

Janzen, G.M., L. Wang, M.B. Hufford. 2019. The Extent of Adaptive Wild Introgression in Crops. New Phytologist 221: 1279-1288

Trujillo, J., A. Seetharam, M.B. Hufford, M. Beilstein, R. Mosher. 2018. Evidence for a unique DNA-dependent RNA polymerase in cereal crops. Molecular Biology and Evolution 35: 2454-2462

Snodgrass, S.J., M.B. Hufford. 2018. Domestication Genomics - Untangling the complex history of African rice. Current Biology 28: R786-R788

Manchanda, N., S.J. Snodgrass, J. Ross-Ibarra, M.B. Hufford. 2018. Evolution and adaptation in the maize genome. In The Zea mays Genome, Bennetzen, Flint-Garcia, Hirsch, Tuberosa (Eds.), Springer Nature Publishing

Aburto-Oropeza, O., A. D. de la Vega, A. Ortinez…M.B. Hufford…V. H. P. Figueroa, S. Dominguez, W. Mautz. 2018. Harnessing cross-border resources to confront climate change. Environmental Science and Policy 87: 128-132

Wang, L., T.M. Beissinger, A. Lorant, C. Ross-Ibarra, J. Ross-Ibarra, M.B. Hufford. 2017. The interplay of demography and selection during maize domestication and expansion. Genome Biology 18: 215
Video Abstract highlighting Wang et al.’s main findings can be found here

Lorant, A., S. Pedersen, I. Holst, M.B. Hufford, K. Winter, D. Piperno, J. Ross-Ibarra. 2017. The potential role of genetic assimilation during maize domestication. PLoS ONE 12: e0184202

Bilinski, P., Y. Han, M.B. Hufford, A. Lorant, P. Zhang, M.C. Estep, J. Jiang, J. Ross-Ibarra. 2017. Genomic abundance is not predictive of tandem repeat localization in grass genomes. PLoS ONE 12: e0177896

Janzen, G.M. and M.B. Hufford. 2016. Crop Domestication: a sneak-peak into the midpoint of maize evolution. Current Biology 26: R1240-R1242

Hufford, M.B. 2016. Comparative genomics provides insight into maize adaptation in temperate regions. Genome Biology 17: 155

Beissinger, T. M., L. Wang, K. Crosby, A. Durvasula, M.B. Hufford, J. Ross-Ibarra. 2016. Recent demography drives changes in linked selection across the maize genome. Nature Plants 2: Article Number 16084

Sexton, J. P., M. B. Hufford, A. C. Bateman, D. B. Lowry, H. Meimberg, S. Y. Strauss, K. J. Rice. 2016. Climate structures genetic variation across a species’ elevation range-a test of range limits hypotheses. Molecular Ecology 25: 911-928

Takuno, S., P. Ralph, K. Swarts, R. J. Elshire, J. C. Glaubitz, E. S. Buckler, M. B. Hufford, J. Ross-Ibarra. 2015. Independent molecular basis of convergent highland adaptation in maize. Genetics 200: 1297-312

Vann L. E., T. Kono, T. Pyhäjärvi, M. B. Hufford, J. Ross-Ibarra. 2015. Natural variation in teosinte at the domestication locus teosinte branched1 (tb1). PeerJ 3: e900

Fonseca R. R., B. Smith, N. Wales, E. Cappellini, P. Skoglund, M. Fumagalli, J. A. Samaniego, C. Carøe, M. C. Avila-Arcos, D. E. Hufnagel, T.S. Korneliussen, F.G. Vieira, M. Jakobsson, B. Arriaza, E. Willerslev, R. Nielsen, M. B. Hufford, A. Albrechtsen, J. Ross-Ibarra, M. T. Gilbert. 2015. The origin and evolution of maize in the Southwestern United States. Nature Plants 1: Article Number 14003

Pyhäjärvi T., Hufford M.B., Mezmouk S., Ross-Ibarra J. 2013. Complex patterns of local adaptation in teosinte. Genome Biology and Evolution 5: 1594-1609

Hufford, M. B., P. Lubinsky, T. Pyhäjärvi, M. T. Devengenzo, N. C. Ellstrand, J. Ross-Ibarra. 2013. The genomic signature of crop-wild introgression in maize. PLoS Genetics 9: e1003477

Kanizay, L. B., T. Pyhäjärvi, E. G. Lowry, M. B. Hufford, D. G. Peterson, J. Ross-Ibarra, R. K. Dawe. 2013. Diversity and abundance of the Abnormal chromosome 10 meiotic drive complex in Zea mays. Heredity 110: 570-577

Hufford, M. B., E. Martínez-Meyer, B. S. Gaut, L. E. Eguiarte, and M. I. Tenaillon. 2012. Inferences from the historical distribution of wild and domesticated maize provide ecological and evolutionary insight. PLoS ONE 7: e47659

Hufford, M. B., P. Bilinski, T. Pyhäjärvi, J. Ross-Ibarra. 2012. Teosinte as a model system for population and ecological genomics. Trends in Genetics 28: 606-615

van Heerwaarden, M. B. Hufford, and J. Ross-Ibarra. 2012. Historical genomics of North American maize. Proceedings of the National Academy of Sciences of the United States of America 109: 12420-12425

Hufford, M. B., X. Xu, J. van Heerwaarden, T. Pyhäjärvi, J.-M. Chia, R. A. Cartwright, R. J. Elshire,J. C. Glaubitz, K. E. Guill, S. Kaeppler, J. Lai, P. L. Morrell, L. M. Shannon, C. Song, N. M. Springer, R. A. Swanson-Wagner, P. Tiffin, J. Wang, G. Zhang, J. Doebley, M. D. McMullen, E. S. Buckler, D. Ware, S. Yang, and J. Ross-Ibarra. 2012. Comparative population genomics of maize domestication and improvement. Nature Genetics 44: 808-811

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

Swanson-Wagner, R., R. Briskine, R. Schaefer, M. B. Hufford, J. Ross-Ibarra, C. L. Myers, P. Tiffin, and N. M. Springer. 2012. Reshaping of the maize transcriptome by domestication. Proceedings of the National Academy of Sciences of the United States of America 109: 11878-11883

Hufford, M. B., P. Gepts, and J. Ross-Ibarra. 2011. Influence of cryptic population structure on observed mating patterns in the wild progenitor of maize (Zea mays ssp. parviglumis). Molecular Ecology 20: 46-55

Tenaillon, M. I., M. B. Hufford, B. S. Gaut, and J. Ross-Ibarra. 2011. Genome size and TE content as determined by high-throughput sequencing in maize and Zea luxurians. Genome Biology and Evolution 3: 219-229

Epanchin-Niell, R., M. B. Hufford, C. E. Aslan, J. P. Sexton, J. D. Port, and T. M. Waring. 2010. Controlling invasive species in complex social landscapes. Frontiers in Ecology and the Environment 8: 210-216

Gepts P., M. Hufford, and K. Kraft. 2010. Domestication of plants. In: Encyclopedia of Geography. (B. Warf, editor). SAGE Publications, Thousand Oaks, CA

Aslan, C. E., M. B. Hufford, R. S. Epanchin-Niell, J. D. Port, J. P. Sexton, and T. M. Waring. 2009. Practical challenges in private stewardship of rangeland ecosystems: yellow starthistle control in Sierra Nevadan foothills. Rangeland Ecology and Management 62: 28-37

Piñeyro-Nelson, A., J. van Heerwaarden, H. R. Perales, A. Serratos-Hernández, A. Rangel, M. B. Hufford, P. Gepts, A. Garay-Arroyo, R. Rivera-Bustamante, and E. R. Álvarez-Buylla. 2009. Transgenes in Mexican maize: molecular evidence and methodological considerations for GMO detection in landrace populations. Molecular Ecology 18: 750-761

Zizumbo D., R. Papa, M. Hufford, S. Repinski , and P. Gepts.2009. Identification of new wild populations of Phaseolus vulgaris in western Jalisco. Annual Report of the Bean Improvement Cooperative 52: 24-25

Pasquet, R. S., A. Peltier, M. B. Hufford, E. Oudin, J. Saulnier, L. Paul, J. T. Knudsen, H.R. Herren, and P. Gepts. 2008. Long-distance pollen flow assessment through evaluation of pollinator foraging range suggests transgene escape distance. Proceedings of the National Academy of Sciences of the United States of America 105(36): 13456-13461

Hromas, R., M. Hufford, J. Sutton, D. W. Xu, X. X. Li, and L. Lu.1997. Plab, a novel placental bone morphogenetic protein. Biochimica Et Biophysica Acta 1354: 40-44