Structural variation in the pangenome of wild and domesticated barley
Murukarthick Jayakodi, Qiongxian Lu, Hélène Pidon, M. Timothy Rabanus‐Wallace, Micha Bayer, Thomas Lux, Yu Guo, Benjamin Jaegle, Ana Badea, Wubishet A. Bekele, Gurcharn S. Brar, Katarzyna Braune, Boyke Bunk, K. J. Chalmers, Brett Chapman, Morten Egevang Jørgensen, Jia‐Wu Feng, Manuel Feser, Anne Fiebig, Heidrun Gundlach, Wenbin Guo, Georg Haberer, Mats Hansson, Axel Himmelbach, Iris Hoffie, Robert E. Hoffie, Haifei Hu, Sachiko Isobe, Patrick König, Sandip M. Kale, Nadia Kamal, Gabriel Keeble‐Gagnère, Beat Keller, Manuela Knauft, Ravi Koppolu, Simon G. Krattinger, Jochen Kumlehn, Peter Langridge, Chengdao Li, Marina Püpke Marone, Andreas Maurer, Klaus Mayer, Michael Melzer, Gary J. Muehlbauer, Emiko Murozuka, Sudharsan Padmarasu, Dragan Perović, Klaus Pillen, Pierre A. Pin, Curtis Pozniak, Luke Ramsay, Pai Pedas, Twan Rutten, Shun Sakuma, Kazuhiro Sato, Danuta Schüler, Thomas Schmutzer, Uwe Scholz, Miriam Schreiber, Kenta Shirasawa, Craig G. Simpson, Birgitte Skadhauge, M. Spannagl, Brian J. Steffenson, Hanne Cecilie Thomsen, Josquin Tibbits, Martin Toft Simmelsgaard Nielsen, Corinna Trautewig, Dominique Vequaud, Cynthia Voss, Penghao Wang, Robbie Waugh, Sharon Westcott, Magnus Wohlfahrt Rasmussen, Runxuan Zhang, Xiao‐Qi Zhang, Thomas Wicker, Christoph Dockter, Martin Mascher, Nils Stein
Abstract
Pangenomes are collections of annotated genome sequences of multiple individuals of a species1. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants2. Here we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. An expanded catalogue of sequence variation in the crop includes structurally complex loci that are rich in gene copy number variation. To demonstrate the utility of the pangenome, we focus on four loci involved in disease resistance, plant architecture, nutrient release and trichome development. Novel allelic variation at a powdery mildew resistance locus and population-specific copy number gains in a regulator of vegetative branching were found. Expansion of a family of starch-cleaving enzymes in elite malting barleys was linked to shifts in enzymatic activity in micro-malting trials. Deletion of an enhancer motif is likely to change the developmental trajectory of the hairy appendages on barley grains. Our findings indicate that allelic diversity at structurally complex loci may have helped crop plants to adapt to new selective regimes in agricultural ecosystems. A pangenome analysis of 76 wild and domesticated barley accessions in combination with short-read sequence data of 1,315 barley genotypes indicates that allelic diversity at structurally complex loci may have helped crop plants to adapt to agricultural ecosystems.