Jayakodi, Murukarthick; Lu, Qiongxian; Pidon, Helene; Rabanus-Wallace, M. Timothy; Bayer, Micha; Lux, Thomas; Guo, Yu; Jaegle, Benjamin; Badea, Ana; Bekele, Wubishet; Brar, Gurcharn S.; Braune, Katarzyna; Bunk, Boyke; Chalmers, Kenneth J.; Chapman, Brett; Jorgensen, Morten Egevang; Feng, Jia-Wu; Feser, Manuel; Fiebig, Anne; Gundlach, Heidrun; Guo, Wenbin; Haberer, Georg; Hansson, Mats; Himmelbach, Axel; Hoffie, Iris; Hoffie, Robert E.; Hu, Haifei; Isobe, Sachiko; Koenig, Patrick; Kale, Sandip M.; Kamal, Nadia; Keeble-Gagnere, Gabriel; Keller, Beat; Knauft, Manuela; Koppolu, Ravi; Krattinger, Simon G.; Kumlehn, Jochen; Langridge, Peter; Li, Chengdao; Marone, Marina P.; Maurer, Andreas; Mayer, Klaus F. X.; Melzer, Michael; Muehlbauer, Gary J.; Murozuka, Emiko; Padmarasu, Sudharsan; Perovic, Dragan; Pillen, Klaus; Pin, Pierre A.; Pozniak, Curtis J.; Ramsay, Luke; Pedas, Pai Rosager; Rutten, Twan; Sakuma, Shun; Sato, Kazuhiro; Schueler, Danuta; Schmutzer, Thomas; Scholz, Uwe; Schreiber, Miriam; Shirasawa, Kenta; Simpson, Craig; Skadhauge, Birgitte; Spannagl, Manuel; Steffenson, Brian J.; Thomsen, Hanne C.; Tibbits, Josquin F.; Nielsen, Martin Toft Simmelsgaard; Trautewig, Corinna; Vequaud, Dominique; Voss, Cynthia; Wang, Penghao; Waugh, Robbie; Westcott, Sharon; Rasmussen, Magnus Wohlfahrt; Zhang, Runxuan; Zhang, Xiao-Qi; Wicker, Thomas; Dockter, Christoph; Mascher, Martin; Stein, Nils Structural variation in the pangenome of wild and domesticated barley Artikel In: NATURE, Bd. 636, Nr. 8043, 2024, ISSN: 0028-0836. @article{WOS:001353822800001,
title = {Structural variation in the pangenome of wild and domesticated barley},
author = {Murukarthick Jayakodi and Qiongxian Lu and Helene Pidon and M. Timothy Rabanus-Wallace and Micha Bayer and Thomas Lux and Yu Guo and Benjamin Jaegle and Ana Badea and Wubishet Bekele and Gurcharn S. Brar and Katarzyna Braune and Boyke Bunk and Kenneth J. Chalmers and Brett Chapman and Morten Egevang Jorgensen and Jia-Wu Feng and Manuel Feser and Anne Fiebig and Heidrun Gundlach and Wenbin Guo and Georg Haberer and Mats Hansson and Axel Himmelbach and Iris Hoffie and Robert E. Hoffie and Haifei Hu and Sachiko Isobe and Patrick Koenig and Sandip M. Kale and Nadia Kamal and Gabriel Keeble-Gagnere and Beat Keller and Manuela Knauft and Ravi Koppolu and Simon G. Krattinger and Jochen Kumlehn and Peter Langridge and Chengdao Li and Marina P. Marone and Andreas Maurer and Klaus F. X. Mayer and Michael Melzer and Gary J. Muehlbauer and Emiko Murozuka and Sudharsan Padmarasu and Dragan Perovic and Klaus Pillen and Pierre A. Pin and Curtis J. Pozniak and Luke Ramsay and Pai Rosager Pedas and Twan Rutten and Shun Sakuma and Kazuhiro Sato and Danuta Schueler and Thomas Schmutzer and Uwe Scholz and Miriam Schreiber and Kenta Shirasawa and Craig Simpson and Birgitte Skadhauge and Manuel Spannagl and Brian J. Steffenson and Hanne C. Thomsen and Josquin F. Tibbits and Martin Toft Simmelsgaard Nielsen and Corinna Trautewig and Dominique Vequaud and Cynthia Voss and Penghao Wang and Robbie Waugh and Sharon Westcott and Magnus Wohlfahrt Rasmussen and Runxuan Zhang and Xiao-Qi Zhang and Thomas Wicker and Christoph Dockter and Martin Mascher and Nils Stein},
doi = {10.1038/s41586-024-08187-1},
issn = {0028-0836},
year = {2024},
date = {2024-12-01},
urldate = {2024-12-01},
journal = {NATURE},
volume = {636},
number = {8043},
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.},
keywords = {Agricultural Genetics, Genomics, Plant Breeding, Plant genetics},
pubstate = {published},
tppubtype = {article}
}
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. |
