Structural variation in the pangenome of wild and domesticated barley

We thank S. Koenig, I. Walde, S. Sommerfeld, J. Fuller, N. McCallum and M. Macaulay for technical assistance and T. Muench, J. Bauernfeind and H. Miehe for IT administration. A. Boerner supported the development of the core1000 diversity panel. Sequencing of Chikurin Ibaraki 1 was performed at the Institute for Clinical Molecular Biology, Competence Centre for Genomic Analysis (CCGA), Kiel University, Kiel, Germany under the supervision of J. Fu ss. Sequencing of HOR 4224 was performed at Genomics & Transcriptomics Labor (BMFZ) Heinrich-Heine-Universitaet, Universitaetsklinikum Duesseldorf, Germany under the supervision of K. Koehrer. RGT Planet and Maximus were sequenced at Genomics WA under the supervision of A. Saxena and at Novogene, respectively. N.S., M. Mascher, K.F.X.M., M. Spannagl and U.S. were supported by grants from the German Ministry of Research and Education (grant nos. BMBF, 031B0190 and 031B0884). D.P. was supported by BMBF grant no. 031B0199B and the German Federal Ministry of Food and Agriculture (grant no. 2818BIJP01). U.S.'s research is supported by the German Research Foundation (DFG, grant no. 442032008). C.D., Q.L., P.R.P. and B.S. gratefully acknowledge support from the Carlsberg Foundation to B.S. (grant nos. CF15-0236, CF15-0476, CF15-0672) and thank F. Lok, S. Knudsen, G. B. Fincher and K. G. J & oslash;rgensen for providing valuable scientific thoughts and discussions on barley alpha-amylases and malt quality. R.W., M.B., M. Schreiber, W.G., R.Z. and C.S. received funding from the Rural and Environment Science and Analytical Services Division (RESAS, grant no. KJHI-B1-2). W.G. and R.Z. were supported by grant no. BB/S020160/1 from the Biotechnology and Biological Sciences Research Council (BBSRC). C.J.P. acknowledges support from Genome Canada and Genome Prairie. B.K. acknowledges a grant from the Swiss National Science Foundation (grant no. 310030_204165). C.L., K.J.C. and P.L. were supported by a grant from the Grain Research and Development Corporation (grant no. UMU1806-002RTX), by the Department of Primary Industry and Regional Development Western Australia and by Pawsey Australia (for computational resources). K.P. and T.S. received a grant from DFG (HAPPAN, grant no. 433162815). G.S.B. has received support from the Saskatchewan Ministry of Agriculture (grant no. ADF20200165) and from the Saskatchewan Barley Development Commission, Western Grains Research Foundation, Alberta Barley Commission and the Manitoba Crop Alliance (grant no. ADF20210677). A.B. and W.B. are recipients of the TUGBOAT grant from the Agriculture and Agri-Food Canada-Genomics Research and Development Initiative and the grant 'Unlocking barley endophyte microbiome to enhance plant health and grain quality' from Agriculture and Agri-Food Canada-A-Base-Foundational Science. M.H. is supported by the Swedish Research Council (grant no. VR 2022-03858), the Swedish Research Council for Environment, Agricultural Sciences, and Spatial Planning (grant no. FORMAS 2018-01026), the Erik Philip-Soerensen Foundation and the Royal Physiographic Society in Lund. K. Sato's research is funded by the Japan Science and Technology Agency (grant no. 18076896) and the Japan Society for the Promotion of Science (JSPS, grant no. 23H00333). K. Shirasawa is supported by the JSPS grants nos. 22H05172 and 22H05181. S.S. acknowledges the Research Support Project for the Next Generation at Tottori University. B.J.S. is supported by the Lieberman-Okinow Endowment at the University of Minnesota and S.G.K. by baseline funding at KAUST. The authors acknowledge the Research/Scientific Computing teams at The James Hutton Institute and NIAB for providing computational resources and technical support for the 'UK's Crop Diversity Bioinformatics HPC' (BBSRC grant no. BB/S019669/1), use of which has contributed to the results reported in this paper.