BonnMu: a novel sequence-indexed resource of transposon induced maize mutations for functional genomics studies

Authors: MARCONE, CAROLINE - University Of Bonn; ALTROGG, LENA; WIN, YAN NIANG; STOCKER, TYLL; GARDINER, JACK - University Of Missouri; Portwood Ii, John; OPITZ, NINA; ANNIKA, KORTZ; BALDAUF, JUTTA; Hunter Iii, Charles; MCCARTY, JOHN - University Of Florida; SCHOOF, HEIKO; KOCH, KAREN - University Of Florida; HOCHHOLDINGER, FRANK

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/27/2020
Publication Date: 8/1/2020
Citation: Marcon, C.; Altrogge, L.; Win Y.N.; Stöcker, T.; Gardiner, J.M.; Portwood, J.L. 2nd; Opitz, N.; Kortz, A.; Baldauf, J.A.; Hunter, C.T.; McCarty, D.R.; Koch, K.E.*; Schoof, H.; Hochholdinger, F. 2020 BonnMu: A sequence-indexed resource of transposon-Induced maize mutations for functional genomics studies. Plant Physiology 184(2):620-631. https://doi.org/10.1104/pp.20.00478
DOI: https://doi.org/10.1104/pp.20.00478

Interpretive Summary: Corn (Zea mays L., maize) is an agricultural crop of enormous importance to the U.S. and world economy which has undergone tremendous agronomic improvement in the last century. Most of this improvement is due to the careful work of corn researchers who have selected the “best of the best” gene combinations for corn’s 44,000 genes to develop superior corn varieties. Much of what has been learned is the result of detailed analysis of what happens to the corn plant when one of these genes acquires a mutation and no longer functions normally. To further understand the relationships between genes and traits, a Center for Medical, Agricultural, and Veterinary Entomology ARS scientists in Gainesville, FL, in collaboration with a Corn Insects and Crop Genetics Research Unit IT specialist and scientists from University of Bonn, University of Florida, and University of Missouri describe a method to create and retrieve mutations in ~16,000 corn genes. The authors then analyze the effects that these mutations have on the developing maize root, an understudied area of maize physiology that is critical for our understanding of the whole plant’s response to flooding, drought, and nutrient stress under field conditions. This study greatly expands resources for functional genetic studies in maize and provides important insights into the function and biology of Mutator transposons in maize.

Technical Abstract: Sequence-indexed insertional libraries in maize (Zea mays L.) are fundamental resources for forward and reverse genetic studies. Here, we constructed a novel Mutator (Mu) insertional library in B73 inbred background designated BonnMu. A total of 1,152 Mu tagged F2-families were sequenced using the Mu-seq approach detecting 225,936 genomic Mu insertion sites and 41,086 high quality germinal Mu insertions covering 16,392 of the annotated maize genes (37% of the v4 B73 genome). Together with the Asian ChinaMu and the North American UniformMu libraries the European BonnMu covers 25,140 of 44,117 maize genes, hence 57% of all genes. BonnMu contains 1,807 novel tagged genes not present in the other libraries. All BonnMu insertions and phenotypic seedling pictures of Mu tagged F2-families are deposited at MaizeGDB.org. Downstream examination of 137,410 somatic and germinal insertion sites revealed that 50% of the respective tagged genes have one single hotspot, targeted by Mu. By comparing our BonnMu data to a subset of the UniformMu library, we identified conserved insertion hotspots among affected genes of B73 (BonnMu) and W22 (UniformMu). Finally, the vast majority of BonnMu and UniformMu transposons was detected near the transcription start site of genes. Remarkably, 75% of all BonnMu insertions were in closer proximity to the transcription start site (distance: 542 bp) than to the start codon (distance: 704 bp) of the affected genes, which correlates to open chromatin especially in the 5’ regions of genes. Our novel European sequence-indexed library of Mu insertions provides an important resource for forward and reverse genetic studies for researchers around the globe.