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The Maize Genome pp 131–142Cite as

The UniformMu Resource: Construction, Applications, and Opportunities

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Part of the book series: Compendium of Plant Genomes ((CPG))

Abstract

Invaluable insights into functional genomics have arisen from knockout and knockdown mutants generated by transposon mutagenesis. Thousands of insertional mutants are available free of charge from the UniformMu national public resource for maize. This resource was created using the native Robertson’s Mutator system and resulting features include (1) an inbred genetic background ideal for phenotype analysis; (2) effective genetic control of Mu transposon activity that facilitates genetic and molecular analyses; (3) precise mapping of transposon insertions enabled by targeted sequencing (Mu flanks identified by a Mu-seq protocol for high-throughput genotyping); (4) cost-free, worldwide distribution of high-quality, sustainable seed stocks through MaizeGDB.org and the Maize Genetics Cooperation Stock Center. Available materials have been especially useful for genetic analysis of complex, multi-genetic traits such as domestication, seed development, and disease resistance. Additional applications for UniformMu resources include new strategies for both forward- and reverse-genetics (phenotype-to-genotype or the reverse) as well as synergies with emerging gene-editing technologies (e.g., MuCRISPR).

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References

  • Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P, Stevenson DK, Zimmerman J, Barajas P, Cheuk R, Gadrinab C (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301(5633):653–657

    Article  Google Scholar 

  • Barquist L, Boinett CJ, Cain AK (2013) Approaches to querying bacterial genomes with transposon-insertion sequencing. RNA Biol 10(7):1161–1169

    Article  CAS  Google Scholar 

  • Belhaj K, Chaparro-Garcia A, Kamoun S, Patron NJ, Nekrasov V (2015) Editing plant genomes with CRISPR/Cas9. Curr Opin Biotechnol 32:76–84

    Article  CAS  Google Scholar 

  • Bensen RJ, Johal GS, Crane VC, Tossberg JT, Schnable PS, Meeley RB, Briggs SP (1995) Cloning and characterization of the maize An1 gene. Plant Cell 7(1):75–84

    Article  CAS  Google Scholar 

  • Bray RA, Brink RA (1966) Mutation and paramutation at the R locus in maize. Genetics 54(1):137–149

    CAS  PubMed  PubMed Central  Google Scholar 

  • Brutnell, TP Conrad, LJ (2003). Transposon tagging using Activator (Ac) in maize. Plant Functional Genomics, Humana Press, pp 157–175

    Google Scholar 

  • Cai M, Li S, Sun F, Sun Q, Zhao H, Ren X, Zhao Y, Tan BC, Zhang Z, Qiu F (2017) Emp10 encodes a mitochondrial PPR protein that affects the cis-splicing of nad2 intron 1 and seed development in maize. Plant J 91(1):132–144

    Article  CAS  Google Scholar 

  • Chen Y, Hou M, Liu L, Wu S, Shen Y, Ishiyama K, Kobayashi M, McCarty DR, Tan BC (2014) The maize DWARF1 encodes a gibberellin 3-oxidase and is dual localized to the nucleus and cytosol. Plant Physiol 166(4):2028–2039

    Article  Google Scholar 

  • Cresse AD, Hulbert SH, Brown WE, Lucas JR, Bennetzen JL (1995) Mu1-related transposable elements of maize preferentially insert into low copy number DNA. Genetics 140(1):315–324

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fahlgren N, Gehan MA, Baxter I (2015) Lights, camera, action: high-throughput plant phenotyping is ready for a close-up. Curr Opin Plant Biol 24:93–99

    Article  Google Scholar 

  • Hayes F (2003) Transposon-based strategies for microbial functional genomics and proteomics. Annu Rev Genet 37(1):3–29

    Article  CAS  Google Scholar 

  • Hirochika H, Guiderdoni E, An G, Hsing YI, Eun MY, Han CD, Upadhyaya N, Ramachandran S, Zhang Q, Pereira A, Sundaresan V (2004) Rice mutant resources for gene discovery. Plant Mol Biol 54(3):325–334

    Article  CAS  Google Scholar 

  • Hufford MB, Xu X, Van Heerwaarden J, Pyhäjärvi T, Chia JM, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, Lai J (2012) Comparative population genomics of maize domestication and improvement. Nat Genet 44(7):808

    Article  CAS  Google Scholar 

  • Hunter CT, Suzuki M, Saunders J, Wu S, Tasi A, McCarty DR, Koch KE (2014) Phenotype to genotype using forward-genetic Mu-seq for identification and functional classification of maize mutants. Fron Plant Sci 4:545

    Google Scholar 

  • Jeon JS, Lee S, Jung KH, Jun SH, Jeong DH, Lee J, Kim C, Jang S, Lee S, Yang K, Nam J (2000) T-DNA insertional mutagenesis for functional genomics in rice. Plant J 22(6):561–570

    Article  CAS  Google Scholar 

  • Li XJ, Zhang YF, Hou M, Sun F, Shen Y, Xiu ZH, Wang X, Chen ZL, Sun SS, Small I, Tan BC (2014) Small kernel 1 encodes a pentatricopeptide repeat protein required for mitochondrial nad7 transcript editing and seed development in maize (Zea mays) and rice (Oryza sativa). Plant J 79(5):797–809

    Article  CAS  Google Scholar 

  • Li Y, Segal G, Wang Q, Dooner HK (2013) Gene tagging with engineered Ds elements in maize. Methods Mol Biol 1057:83–99

    Article  CAS  Google Scholar 

  • Lisch D, Chomet P, Freeling M (1995) Genetic characterization of the Mutator system in maize: behavior and regulation of Mu transposons in a minimal line. Genetics 139:1777–1796

    CAS  PubMed  PubMed Central  Google Scholar 

  • Liu P, McCarty DR, Koch KE (2016) Transposon mutagenesis and analysis of mutants in UniformMu maize (Zea mays). Curr Protoc Plant Biol 451–465

    Google Scholar 

  • Liu YJ, Xiu ZH, Meeley R, Tan BC (2013) Empty pericarp5 encodes a pentatricopeptide repeat protein that is required for mitochondrial RNA editing and seed development in maize. Plant Cell 25(3):868–883

    Article  CAS  Google Scholar 

  • May BP, Liu H, Vollbrecht E, Senior L, Rabinowicz PD, Roh D, Pan XK, Stein L, Freeling M, Alexander D, Martienssen R (2003) Maize-targeted mutagenesis: a knockout resource for maize. Proc Natl Acad Sci USA 100(20):11541–11546

    Article  CAS  Google Scholar 

  • McCallum CM, Comai L, Greene EA, Henikoff S (2000) Targeting induced locallesions in genomes (TILLING) for plant functional genomics. Plant Physiol 123(2):439–442

    Article  CAS  Google Scholar 

  • McCarty DR, Mark Settles A, Suzuki M, Tan BC, Latshaw S, Porch T, Robin K, Baier J, Avigne W, Lai J, Messing J (2005) Steady-state transposon mutagenesis in inbred maize. Plant J 44(1):52–61

    Article  CAS  Google Scholar 

  • McCarty DR, Latshaw S, Wu S, Suzuki M, Hunter CT, Avigne WT, Koch KE (2013a) Mu-seq: sequence-based mapping and identification of transposon induced mutations. PLoS ONE 8(10):e77172

    Article  CAS  Google Scholar 

  • McCarty DR, Suzuki M, Hunter C, Collins J, Avigne WT, Koch KE (2013b). Genetic and molecular analyses of UniformMu transposon insertion lines. Plant Transposable Elements, Humana Press, Totowa, pp 157–166

    Google Scholar 

  • McCarty DR (2017) 4 What Can We Learn from Maize Kernel Mutants? Maize Kernel Development, p 44

    Google Scholar 

  • Niehaus TD, Folz J, McCarty DR, Cooper AJ, Amador DM, Fiehn O, Hanson AD (2018) Identification of a metabolic disposal route for the oncometabolite S-(2-succino) cysteine in Bacillus subtilis. J Biol Chem pp jbc–RA118

    Google Scholar 

  • O’Malley RC, Ecker JR (2010) Linking genotype to phenotype using the Arabidopsis unimutant collection. Plant J 61(6):928–940

    Article  Google Scholar 

  • Piatek A, Ali Z, Baazim H, Li L, Abulfaraj A, Al-Shareef S, Aouida M, Mahfouz MM (2015) RNA-guided transcriptional regulation in planta via synthetic dCas9-based transcription factors. Plant Biotechnol J 13(4):578–589

    Article  CAS  Google Scholar 

  • Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152(5):1173–1183

    Article  CAS  Google Scholar 

  • Raizada MN, Nan GL, Walbot V (2001) Somatic and germinal mobility of the RescueMu transposon in transgenic maize. Plant Cell 13(7):1587–1608

    Article  CAS  Google Scholar 

  • Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z, Zhang K, Liu J, Xi JJ, Qiu JL, Gao C (2013) Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 31(8):686

    Article  CAS  Google Scholar 

  • Shen Y, Li C, McCarty DR, Meeley R, Tan BC (2013) Embryo defective12 encodes the plastid initiation factor 3 and is essential for embryogenesis in maize. Plant J 74(5):792–804

    Article  CAS  Google Scholar 

  • Shirley BW, Hanley S, Goodman HM (1992) Effects of ionizing radiation on a plant genome: analysis of two Arabidopsis transparent testa mutations. Plant Cell 4(3):333–347

    Article  CAS  Google Scholar 

  • Sosso D, Luo D, Li QB, Sasse J, Yang J, Gendrot G, Suzuki M, Koch KE, McCarty DR, Chourey PS, Rogowsky PM (2015) Seed filling in domesticated maize and rice depends on SWEET-mediated hexose transport. Nat Genet 47(12):1489

    Article  CAS  Google Scholar 

  • Springer N, W22 Genome Consortium et al (2018) The W22 genome: a foundation for maize functional genomics and transposon biology. Nat Genet https://doi.org/10.1038/s41588-018-0158-0

  • Sun F, Wang X, Bonnard G, Shen Y, Xiu Z, Li X, Gao D, Zhang Z, Tan BC (2015) Empty pericarp7 encodes a mitochondrial E–subgroup pentatricopeptide repeat protein that is required for ccmFN editing, mitochondrial function and seed development in maize. Plant J 84(2):283–295

    Article  CAS  Google Scholar 

  • Suzuki M, Mark Settles A, Tseung CW, Li QB, Latshaw S, Wu S, Porch TG, Schmelz EA, James MG, McCarty DR (2006) The maize viviparous15 locus encodes the molybdopterin synthase small subunit. Plant J 45(2):264–274

    Article  CAS  Google Scholar 

  • Suzuki M, Latshaw S, Sato Y, Settles AM, Koch KE, Hannah LC, Kojima M, Sakakibara H, McCarty DR (2008) The maize Viviparous8 locus, encoding a putative ALTERED MERISTEM PROGRAM1-like peptidase, regulates abscisic acid accumulation and coordinates embryo and endosperm development. Plant Physiol 146(3):1193–1206

    Article  CAS  Google Scholar 

  • Suzuki M, Sato Y, Wu S, Kang BH, McCarty DR (2015) Conserved functions of the MATE transporter BIG EMBRYO1 in regulation of lateral organ size and initiation rate. Plant Cell 27(8):2288–2300

    Article  CAS  Google Scholar 

  • Vollbrecht E, Duvick J, Schares JP, Ahern KR, Deewatthanawong P, Xu L, Conrad LJ, Kikuchi K, Kubinec TA, Hall BD, Weeks R, Unger-Wallace E, Muszynksi M, Brendel VP, Brutnell TP (2010) Genome-wide distribution of transposed dissociation elements in maize. Plant Cell 22(6):1667–1685

    Article  CAS  Google Scholar 

  • Walbot V, Qüesta J (2012) Using MuDR/Mu transposons in directed tagging strategies. Methods Mol Biol 1057:143–155

    Article  Google Scholar 

  • Williams-Carrier R, Stiffler N, Belcher S, Kroeger T, Stern DB, Monde RA, Coalter R, Barkan A (2010) Use of Illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy mutator lines of maize. Plant J 63(1):167–177

    CAS  PubMed  Google Scholar 

  • Xiu Z, Sun F, Shen Y, Zhang X, Jiang R, Bonnard G, Zhang J, Tan BC (2016) EMPTY PERICARP16 is required for mitochondrial nad2 Intron 4 cis-splicing, complex I assembly and seed development in maize. Plant J 85(4):507–519

    Article  CAS  Google Scholar 

  • Yang Q, He Y, Kabahuma M, Chaya T, Kelly A, Borrego E, Bian Y, El Kasmi F, Yang L, Teixeira P, Kolkman J (2017a) A gene encoding maize caffeoyl-CoA O-methyltransferase confers quantitative resistance to multiple pathogens. Nat Genet 49(9):1364

    Article  CAS  Google Scholar 

  • Yang YZ, Ding S, Wang HC, Sun F, Huang WL, Song S, Xu C, Tan BC (2017b) The pentatricopeptide repeat protein EMP9 is required for mitochondrial ccmB and rps4 transcript editing, mitochondrial complex biogenesis and seed development in maize. New Phytol 214(2):782–795

    Article  CAS  Google Scholar 

  • Yang YZ, Ding S, Wang Y, Li CL, Shen Y, Meeley R, McCarty DR, Tan BC (2017c) Small kernel2 encodes a glutaminase in vitamin B6 biosynthesis essential for maize seed development. Plant Physiol 174(2):1127–1138

    Article  CAS  Google Scholar 

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Acknowledgements

This work was supported by a grant to DRM and KEK from USA National Science Foundation (IOS-1116561).

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Authors and Affiliations

  1. Horticultural Sciences Department, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, USA

    Donald R. McCarty, Peng Liu & Karen E. Koch

  2. Genetics Institute, University of Florida, Gainesville, FL, USA

    Donald R. McCarty & Karen E. Koch

Authors
  1. Donald R. McCarty
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  2. Peng Liu
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  3. Karen E. Koch
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Corresponding author

Correspondence to Donald R. McCarty .

Editor information

Editors and Affiliations

  1. Department of Genetics, University of Georgia, Athens, GA, USA

    Jeffrey Bennetzen

  2. USDA-ARS, Columbia, MO, USA

    Sherry Flint-Garcia

  3. Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA

    Candice Hirsch

  4. Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy

    Roberto Tuberosa

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McCarty, D.R., Liu, P., Koch, K.E. (2018). The UniformMu Resource: Construction, Applications, and Opportunities. In: Bennetzen, J., Flint-Garcia, S., Hirsch, C., Tuberosa, R. (eds) The Maize Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-97427-9_9

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