About BonnMu

What is BonnMu?

BonnMu is a population of Mutator (Mu) induced mutants in several inbred lines of maize. To this end, the Mu-tagged maize F1-population was generated by crossing an active Mu line (Mu4 per se) into following inbred lines: B73, Co125, F7, EP1, DK105. The F1-generation, being heterozygous for new Mu insertions, was self-pollinated to produce segregating F2-families. The segregating F2-families, which are 50% inbred and 50% active Mu line genetic background, were then sequenced using the Mu-seq approach (McCarty et al., 2013). 

The initial analysis of 1,152 segregating F2-stocks in B73 background identified 41,086 germinal Mu insertions already covering 16,392 of 44,117 annotated maize genes (Marcon et al., 2020). The BonnMu resource is still expanding to archive additional genes tagged by germinal Mu insertions. For our new publication, we have sequenced an additional 6,912 Mu-tagged families, revealing 425,924 heritable Mu insertions affecting 36,612 (83%) of the 44,303 high-confidence gene models of maize (B73v5; Win et al., 2024). Mu insertions, corresponding F2-stocks and seedling photographs will be regularly updated on the MaizeGDB browser (https://www.maizegdb.org) for open access.

Mu-flanking sequences were sequenced using the Mu-seq approach (McCarty et al., 2013), coupling enrichment of Mu-flanking sequences with next generation sequencing. Mu insertions were aligned against B73 RefGen_v4.36 (BonnMu_3rd_Release_10-30-2020) and against B73 Ref-NAM-5.0 (BonnMu_4th_Release_02-10-2021; BonnMu_5th_Release_02-29-2024) using our Mu-seq workflow utility (MuWU) which is publicly available at https://github.com/Crop-Bioinformatics-Bonn/MuWU.

How many Mu-tagged genes were identified so far?

Sequencing of segregating F2-stocks is still ongoing. Currently, 8,640 segregating F2-stocks in different inbred background are analyzed.

Aligning Mu insertions to B73 Ref-NAM-5.0 identified more than 425,924 unique germinal Mu insertions covering 36,912 of all maize genes. Find the updated list of all Mu insertion sites here: BonnMu_5th_Release_02-29-2024.

How to look for a Mu insertion in your gene of interest?

BonnMu insertions of the 3rd and 4th release can be browsed at the MaizeGDB website (B73v4: https://www.maizegdb.org; B73v5: https://jbrowse.maizegdb.org ) as previously described for the UniformMu database (Liu et al., 2016). To access and visualize B73 insertions in maizegdb.org, a gene model identifier is needed for the genome browser view. Then, by clicking “select track” and “BonnMu”, insertion sites become visible in the locus. Clicking on the insertion site links to the Mu insertion identifiers and the respective F2-stock, i.e., F2-Mu-seq family and its respective phenotype 10 days after germination. To access and visualize B73 insertions in jbrowse.maizegdb.org select the gene of interest and activate the BonnMu insertion view by scrolling down the available tracks.

Table 1
A subset of Mu insertion sites of the updated BonnMu_Release_08-17-2020 is illustrated. One row and one column (col) pool (Sample-Pool) represent one germinal insertion, supported by at least 2 raw reads on either side of the insertion, which is represented by the 9 bp target site duplication (TSD). © Caroline Marcon

How to order Mu-induced stocks for your research?

Seeds can be requested by E-Mail to: BonnMu@uni-bonn.de.
We ship ten seeds per F2- or F3-stock which means you have to propagate them before using them. There is no fee for the seeds. We share the seeds on a collaborative basis. We will send you an MTA (material transfer agreement) according to our University‘s policy. Shipping to the US requires an import permit to be applied by the USDA. The import permit comes along with green/yellow labels that certify the small lots of seeds as quarantine material. We are not shipping via phytosanitary certificate! And we are only shipping via FedEx international transport. Detailed information for US requesters can be downloaded here: BonnMu_Infos for requesters_April 2022

How to validate Mu insertions in the stocks?

We recommend PCR confirmation of Mu insertions by using gene-specific primers (at least one upstream and one downstream of the insertion site) in combination with a MuTIR primer (Figure 1).

More details on the PCR-based confimation of Mu insertions are described by the UniformMu group: https://www.maizegdb.org/uniformmu.

Figure 1
A) One BonnMu stocks harbors a Mu insertion in the roothair defective 3 (rth3) gene (Hochholdinger et al., 2008). The rth3 mutants lack roothairs. B) Cartoon of the rth3 gene, disrupted by a Mu insertion in the single exon. The internal Mu-sequence is shown in yellow, the terminal inverted repeat (TIR) at either end of the transposon is shown in red. Positions of a rth3-specific forward (For) and reverse primer (Rev) are illustrated as green and purple arrows. These primers flank the insertion site. The red arrows display the outward reading TIR-specific primer of the Mu transposon. C) PCR analysis using WT DNA and rth3 mutant DNA as template. Gene-specific For and Rev primers amplified a specific PCR-product of expected size from WT DNA, wheras no PCR product was amplified with rth3 DNA samples as template. In contrast, only dominant products of expected size were amplified from the mutant DNA, when gene-specific primers were combined with the MuTIR primer. © Caroline Marcon


  •  Win YN, Stöcker T, Du X, Brox A, Pitz M, Klaus A, Schoof H, Hochholdinger F, Marcon C (2024) Expanding the BonnMu sequence-indexed repository of transposon induced maize (Zea mays L.) mutations in dent and flint germplasm. bioRxiv. https://doi.org/10.1101/2024.02.24.581857
  • Marcon C, Altrogge L, Win Y, Stöcker T, Gardiner JM, Portwood JL, Opitz N, Kortz A, Baldauf J, Hunter CT, McCarty DR, Koch KE, Schoof H, Hochholdinger F (2020) BonnMu: a sequence-indexed resource of transposon induced maize mutations for functional genomics studies. Plant Physiol. https://doi.org/10.1104/pp.20.00478
  • McCarty DR, Latshaw S, Wu S, Suzuki M, Hunter CT, Avigne WT, Koch KE (2013) Mu-seq: sequence-based mapping and identification of transposon induced mutations. PLOS ONE. https://doi.org/10.1371/journal.pone.0077172
  • Liu P, McCarty DR, Koch KE (2016) Transposon mutagenesis and analysis of mutants in UniformMu maize (Zea mays). Curr Protoc Plant Biol. https://doi.org/10.1002/cppb.20029
  • Hochholdinger F, Wen T-J, Zimmermann R, Chimont-Marolle P, da Costa e Silva O, Bruce W, Lamkey KR, Wienand U, Schnable PS (2008) The maize (Zea mays L.) roothairless3 gene encodes a putative GPI-anchored, monocot-specific, COBRA-like protein that significantly affects grain yield. Plant J. https://doi.org/10.1111/j.1365-313X.2008.03459.x
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