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De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

Hufford, Matthew B., Seetharam, Arun S., Woodhouse, Margaret R., Chougule, Kapeel M., Ou, Shujun, Liu, Jianing, Ricci, William A., Guo, Tingting, Olson, Andrew, Qiu, Yinjie, Della Coletta, Rafael, Tittes, Silas, Hudson, Asher I., Marand, Alexandre P., Wei, Sharon, Lu, Zhenyuan, Wang, Bo, Tello-Ruiz, Marcela K., Piri, Rebecca D., Wang, Na, Kim, Dong won, Zeng, Yibing, O’Connor, Christine H., Li, Xianran, Gilbert, Amanda M., Baggs, Erin, Krasileva, Ksenia V., Portwood, John L., Cannon, Ethalinda K. S., Andorf, Carson M., Manchanda, Nancy, Snodgrass, Samantha J., Hufnagel, David E., Jiang, Qiuhan, Pedersen, Sarah, Syring, Michael L., Kudrna, David A., Llaca, Victor, Fengler, Kevin, Schmitz, Robert J., Ross-Ibarra, Jeffrey, Yu, Jianming, Gent, Jonathan I., Hirsch, Candice N., Ware, Doreen, Dawe, R. Kelly·2021·Science
DOI 10.1126/science.abg5289PMC PMC8733867

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Abstract

An a-maize-ing set of genomes: Maize is an important crop cultivated worldwide. As maize spread across the world, selection for local environments resulted in variation, but the impact on differences between the genome has not been quantified. By producing high-quality genomic sequences of the 26 lines used in the maize nested association mapping panel, Hufford et al . map important traits and demonstrate the diversity of maize. Examining RNA and methylation of genes across accessions, the authors identified a core set of maize genes. Beyond this core set, comparative analysis across lines identified high levels of variation in the total set of genes, the maize pan-genome. The value of this resource was further exemplified by mapping quantitative traits of interest, including those related to pathogen resistance. —LMZ

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  • With GENESPACE and the recently released NAM parent genomes, it is now possible to evaluate candidate genes present in the genomes of other NAM founder lines but either absent or unannotated in the B73 reference genome.

    “however, with GENESPACE and the recently released NAM parent genomes (Hufford et al., 2021), it is now possible to evaluate candidate genes present in the genomes of other NAM founder lines but either absent or unannotated in the B73 reference genome.”

    From GENESPACE tracks regions of interest and gene copy number variation across multiple genomes (2022) · cites this paper as Hufford et al., 2021

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Metadata

Authors
Hufford, M. B., Seetharam, A. S., Woodhouse, M. R., Chougule, K. M., Ou, S., Liu, J., Ricci, W. A., Guo, T., Olson, A., Qiu, Y., Della Coletta, R., Tittes, S., Hudson, A. I., Marand, A. P., Wei, S., Lu, Z., Wang, B., Tello-Ruiz, M. K., Piri, R. D., Wang, N., Kim, D. W., Zeng, Y., O’Connor, C. H., Li, X., Gilbert, A. M., Baggs, E., Krasileva, K. V., Portwood, J. L., Cannon, E. K. S., Andorf, C. M., Manchanda, N., Snodgrass, S. J., Hufnagel, D. E., Jiang, Q., Pedersen, S., Syring, M. L., Kudrna, D. A., Llaca, V., Fengler, K., Schmitz, R. J., Ross-Ibarra, J., Yu, J., Gent, J. I., Hirsch, C. N., Ware, D., & Dawe, R. K.
Affiliations
  • Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
  • USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA.
  • Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
  • Department of Genetics, University of Georgia, Athens, GA 30602, USA.
  • Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
  • Department of Agronomy, Iowa State University, Ames, IA 50011, USA.
  • Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA.
  • Center for Population Biology, University of California, Davis, CA 95616, USA.
  • Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
  • Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
  • Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
  • Corteva Agriscience, Johnston, IA 50131, USA.
ORCID
Venue
Science
Publisher
American Association for the Advancement of Science (AAAS)
Published
2021-08-06
Volume
373
Issue
6555
Pages
655-662
ISSN
  • 0036-8075
  • 1095-9203
DOI
10.1126/science.abg5289
PMC
PMC8733867
Cited by
747
References
13
Language
en
Funders
  • National Science Foundation (1744001, 1546727, 1127112, 1546719, 1822330, IOS-1856627, 1905869, IOS-1744001, IOS-1546727, IOS-1127112, IOS-1546719, IOS-1822330, 1744592, 58-5030-8-064, 1546657, 1650042, DBI-1905869, DGE-1545463)
  • U.S. Department of Agriculture (58-5030-8-064, 8062-21000-041-00D, 2018-67013-27571, 5030-21000-068-00D, CA-D-PLS-2066-H, USDA-ARS 8062-21000-041-00D, NSF IOS-1856627)
  • Additional (NIH-OD S10 OD028632)
  • Iowa State University Trainee SJS (USDA-ARS 58-5030-8-064)

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