In Review:

Stitzer, M.C., A.S. Seetharam, A. Scheben, S.K. Hsu, A.J. Schulz, T.M. AuBuchon-Elder, M. El-Walid, T.H. Ferebee, C.O. Hale, T. La, Z.Y. Liu, S.J. McMorrow, P. Minx, A.R. Phillips, M.L. Syring, T. Wrightsman, J. Zhai, R. Pasquet, C.A. McAllister, S.T. Malcomber, P. Traiperm, D.J. Layton, J. Zhong, D.E. Costich, R.K. Dawe, K. Fengler, C. Harris, Z. Irelan, V. Llaca, P. Parakkal, G. Zastrow-Hayes, M.R. Woodhouse, E.K.S. Cannon, J.L. Portwood II, C.M. Andorf, P.S. Albert, J.A. Birchler, A. Siepel, J. Ross-Ibarra, M.C. Romay, E.A. Kellogg, E.S. Buckler, M.B. Hufford. Extensive genome evolution distinguishes maize within a stable tribe of grasses. [preprint]

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]

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:

Andorf, C.M., J. Ross-Ibarra, A.S. Seetharam, M.B. Hufford, M.R. Woodhouse. 2025. A unified VCF dataset from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize. G3 (Bethesda) 15(2): jkae281.

Cahn, J., M. Regulski, J. Lynn, E. Ernst, C. de Santis Alves, S. Ramakrishnan, K. Chougule, S. Wei, Z. Lu, X. Xu, U. Ramu, J. Drenkow, M. Kramer, A.S. Seetharam, M.B. Hufford, W.R. McCombie, D. Ware, D. Jackson, M.C. Schatz, T.R. Gingeras, R.A. Martienssen. 2024. MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication. Nature Communications 15(1): 10854.

S. Ou, A. Scheben, T. Collins, Y. Qiu, A.S. Seetharam, C.C. Menard, N. Manchanda, J.I. Gent, M.C. Schatz, S.N. Anderson, M.B. Hufford, C.N. Hirsch. 2024. Differences in activity and stability drive transposable element variation in tropical and temperate maize. Genome Research 34(8): 1140-1153.

Foster, T.L., M. Kloiber-Maitz, L. Gilles, U.K. Frei, S. Pfeffer, Y.R. Chen, S. Dutta, A.S. Seetharam, M.B. Hufford, T. Lübberstedt. 2024. Fine mapping of major QTL qshgd1 for spontaneous haploid genome doubling in maize (Zea mays L.). Theoretical and Applied Genetics 137(5): 117.

S. Ou, N. Jiang, C.N. Hirsch, M.B. Hufford. 2024. Response to Commentary: Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies. Genome Biology 25(1): 6.

Bapat, A.R., A.N. Moran Lauter, M.B. Hufford, N.A. Boerman, M.P. Scott. 2023. The Ga1 locus of the genus Zea is associated with novel genome structures derived from multiple, independent nonhomologous recombination events. G3 (Bethesda) 13(11): jkad196.

Sun, S., B. Wang, C. Li, G. Xu, J. Yang, M.B. Hufford, J. Ross-Ibarra, H. Wang, L. Wang. 2023. Unraveling Prevalence and Effects of Deleterious Mutations in Maize Elite Lines across Decades of Modern Breeding. Molecular Biology and Evolution 40(8): msad170.

Chen, J., Z. Wang, K. Tan, W. Huang, J. Shi, T. Li, J. Hu, K. Wang, C. Wang, B. Xin, H. Zhao, W. Song, M.B. Hufford, J.C. Schnable, W. Jin, J. Lai. 2023. A complete telomere-to-telomere assembly of the maize genome. Nature Genetics 55(7): 1221-1231.

Phillips, A.R., A.S. Seetharam, P.S. Albert, T. AuBuchon-Elder, J.A. Birchler, E.S. Buckler, L.J. Gillespie, M.B. Hufford, V. Llaca, M.C. Romay, R.J. Soreng, E.A. Kellogg, J. Ross-Ibarra. 2023. A happy accident: a novel turfgrass reference genome. G3 (Bethesda) 13(6): jkad073.

Hu, H., T. Crow, S. Nojoomi, A.J. Schulz, J.M. Estévez-Palmas, M.B. Hufford, S. Flint-Garcia, R. Sawers, R. Rellán-Álvarez, J. Ross-Ibarra, D.E. Runcie. 2022. Allele-specific Expression Reveals Multiple Paths to Highland Adaptation in Maize. Molecular Biology and Evolution 39(11): msac239.

Chen, L., J. Luo, M. Jin, N. Yang, X. Liu, Y. Peng, W. Li, A. Phillips, B. Cameron, J.S. Bernal, R. Rellán-Álvarez, R.J.H. Sawers, Q. Liu, Y. Yin, X. Ye, J. Yan, Q. Zhang, X. Zhang, S. Wu, S. Gui, W. Wei, Y. Wang, Y. Luo, C. Jiang, M. Deng, M. Jin, L. Jian, Y. Yu, M. Zhang, X. Yang, M.B. Hufford, A.R. Fernie, M.L. Warburton, J. Ross-Ibarra, J. Yan. 2022. Genome sequencing reveals evidence of adaptive variation in the genus Zea. Nature Genetics 54(11): 1736-1745.

Barnes, A.C., F. Rodríguez-Zapata, K.A. Juárez-Núñez, D.J. Gates, G.M. Janzen, A. Kur, L. Wang, S.E. Jensen, J.M. Estévez-Palmas, T.M. Crow, H.S. Kavi, H.D. Pil, R.L. Stokes, K.T. Knizner, M.R. Aguilar-Rangel, E. Demesa-Arévalo, T. Skopelitis, S. Pérez-Limón, W.L. Stutts, P. Thompson, Y.C. Chiu, D. Jackson, D.C. Muddiman, O. Fiehn, D. Runcie, E.S. Buckler, J. Ross-Ibarra, M.B. Hufford, R.J.H. Sawers, R. Rellán-Álvarez. 2022. An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time. Proceedings of the National Academy of Sciences U S A 119(27): e2100036119.

Chamberlain-Irwin, H.N., M.B. Hufford. 2022. Convergent domestication: Finding the genes that make crops. Current Biology 32(12): R585-R588.

G.M. Janzen, M.R. Aguilar-Rangel, C. Cíntora-Martínez, K.A. Blöcher-Juárez, E. González-Segovia, A.J. Studer, D.E. Runcie, S.A. Flint-Garcia, R. Rellán-Álvarez, R.J.H. Sawers, M.B. Hufford. 2022. Demonstration of local adaptation in maize landraces by reciprocal transplantation. Evolutionary Applications 15(5): 817-837.

Perez-Limón, S., M. Li, G.C. Cintora-Martinez, M.R. Aguilar-Rangel, M.N. Salazar-Vidal, E. González-Segovia, K. Blöcher-Juárez, A. Guerrero-Zavala, B. Barrales-Gamez, J. Carcaño-Macias, D.E. Costich, J. Nieto-Sotelo, O. Martinez de la Vega, J. Simpson, M.B. Hufford, J. Ross-Ibarra, S. Flint-Garcia, L. Diaz-Garcia, R. Rellán-Álvarez, R.J.H. Sawers. 2022. A B73×Palomero Toluqueño mapping population reveals local adaptation in Mexican highland maize. G3 (Bethesda) 12(3): jkab447.

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. 2021. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science 373: 655-662

Song, B., E.S. Buckler, H. Wang, Y. Wu, E. Rees, E.A. Kellogg, D.J. Gates, M. Khaipho-Burch, P.J. Bradbury, J. Ross-Ibarra, M.B. Hufford, M.C. Romay. 2021. Conserved non-coding sequences provide insights into regulatory sequence and loss of gene expression in maize. Genome Research 31(7): 1245-1257.

Bornowski, N., K.J. Michel, J.P. Hamilton, S. Ou, A.S. Seetharam, J. Jenkins, J. Grimwood, C. Plott, S. Shu, J. Talag, M. Kennedy, H. Hundley, V.R. Singan, K. Barry, C. Daum, Y. Yoshinaga, J. Schmutz, C.N. Hirsch, M.B. Hufford, N. de Leon, S.M. Kaeppler, C.R Buell. 2021. Genomic variation within the maize Stiff Stalk heterotic germplasm pool. The Plant Genome (Published online ahead of print)

L. Wang, E.B. Josephs, K.M. Lee, L.M. Roberts, R. Rellán-Álvarez, J. Ross-Ibarra, M.B. Hufford. 2021. Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces. Molecular Biology and Evolution 38(9): 3567–3580.

Verzegnazzi, A.V., 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 134: 1355–1368.

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

A.S. Seetharam, Y. Yu, S. Bélanger, L.G. Clark, B.C. Meyers, E.A. Kellogg, M.B. Hufford. 2021. The Streptochaeta Genome and the Evolution of the Grasses. Frontiers in Plant Science 12: 710383.

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, D. 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.S. 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., M.B. Hufford, S. Mezmouk, J. Ross-Ibarra. 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, J., 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.