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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Publications at this Location » Publication #345881

Research Project: MaizeGDB: Enabling Access to Basic, Translational, and Applied Research Information

Location: Corn Insects and Crop Genetics Research

Title: The maize W22 genome provides a foundation for functional genomics and transposon biology

Author
item Springer, Nathan - University Of Minnesota
item Anderson, Sarah - University Of Minnesota
item Andorf, Carson
item Ahern, Kevin - Cornell University - New York
item Bai, Fang - University Of Florida
item Barad, Omer - Nrgene
item Barbazuk, W. Brad - University Of Florida
item Bass, Hank - Florida State University
item Baruch, Kobi - Nrgene
item Gen-zvi, Gil - Nrgene
item Buckler, Edward - Ed
item Bukowski, Robert - Cornell University - New York
item Campbell, Michael - Cold Spring Harbor Laboratory
item Cannon, Ethalinda
item Chomet, Paul - Nrgene
item Dawe, R.kelly - University Of Georgia
item Davenport, Ruth - University Of Florida
item Dooner, Hugo - Rutgers University
item He Du, Limei - Rutgers University
item Du, Chunguang - Montclair State University
item Easterling, Katherine - Florida State University
item Gault, Christine - Cornell University - New York
item Guan, Jiahn-chou - University Of Florida
item Jander, Georg - Cornell University - New York
item Hunter, Charles
item Jiao, Yinping - Cold Spring Harbor Laboratory
item Koch, Karen - University Of Florida
item Kol, Guy - Nrgene
item Kudo, Toru - University Of Florida
item Li, Qing - University Of Minnesota
item Lu, Fei - Chinese Academy Of Agricultural Sciences
item Mayfield-jones, Dustin - Danforth Plant Science Center
item Mei, Wenbin - University Of Florida
item Mccarty, Donald - University Of Florida
item Noshay, Jaclyn - University Of Minnesota
item Portwood, John
item Ronen, Gil - Nrgene
item Settles, Mark - University Of Florida
item Shem-tov, Doron - Nrgene
item Shi, Jinghua - Bionano Genomics, Inc
item Soifer, Ilya - Nrgene
item Stein, Joshua - Cold Spring Harbor Laboratory
item Suzuki, Masaharu - University Of Florida
item Vera, Daniel - Florida State University
item Vollbrecht, Erik - Iowa State University
item Vrebalov, Julia - Cornell University - New York
item Ware, Doreen
item Wei, Xuehong - Cold Spring Harbor Laboratory
item Wimalanathan, Kokulapalan - Iowa State University
item Woodhouse, Margaret - University Of California, Davis
item Xiong, Wenwei - Montclair State University
item Brutnell, Thomas - Danforth Plant Science Center

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/9/2018
Publication Date: 7/30/2018
Citation: Springer, N., Anderson, S., Andorf, C.M., Ahern, K., Bai, F., Barad, O., Barbazuk, W., Bass, H.W., Baruch, K., Gen-Zvi, G., Buckler Iv, E.S., Bukowski, R., Campbell, M.S., Cannon, E.K., Chomet, P., Dawe, R., Davenport, R., Dooner, H.K., He Du, L., Du, C., Easterling, K., Gault, C., Guan, J., Jander, G., Hunter Iii, C.T., Jiao, Y., Koch, K.E., Kol, G., Kudo, T., Li, Q., Lu, F., Mayfield-Jones, D., Mei, W., Mccarty, D.R., Noshay, J., Portwood Ii, J.L., Ronen, G., Settles, M.A., Shem-Tov, D., Shi, J., Soifer, I., Stein, J.C., Suzuki, M., Vera, D.L., Vollbrecht, E., Vrebalov, J.T., Ware, D., Wei, X., Wimalanathan, K., Woodhouse, M.R., Xiong, W., Brutnell, T.P. 2018. The maize W22 genome provides a foundation for functional genomics and transposon biology. Nature Genetics. https://doi.org/10.1038/s41588-018-0158-0.
DOI: https://doi.org/10.1038/s41588-018-0158-0

Interpretive Summary: Maize has a complex genome with a lot of genetic diversity. To better understand this diversity, we sequenced, assembled, and annotated the W22 inbred. W22 has been utilized extensively to understand fundamental genetic and epigenetic processes such recombination, transposition and paramutation. The generation of this reference genome enables accurate placement of thousands of Mutator (Mu) and Dissociation (Ds) transposable element insertions for reverse and forward genetics studies.

Technical Abstract: The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have sequenced and de novo assembled a W22 reference genome using small-read sequencing technologies. We show that significant structural heterogeneity exists in comparisons to the B73 reference genome at multiple scales, from transposon composition and copy number variation to single nucleotide polymorphisms. The generation of this reference genome enables accurate placement of thousands of Mutator (Mu) and Dissociation (Ds) transposable element insertions for reverse and forward genetics studies. Annotation of the genome has been achieved using RNAseq analysis, differential nuclease sensitivity profiling, and bisulfite sequencing to fine map open reading frames, open chromatin sites, and DNA methylation profiles, respectively. Collectively, the resources developed here integrates W22 as a community reference genome.