Publications and Media

@article{WOS:001411678300001,

title = {A barley pan-transcriptome reveals layers of genotype-dependent  transcriptional complexity},

author = {Wenbin Guo and Miriam Schreiber and Vanda B. Marosi and Paolo Bagnaresi and Morten Egevang Jorgensen and Katarzyna B. Braune and Ken Chalmers and Brett Chapman and Viet Dang and Christoph Dockter and Anne Fiebig and Geoffrey B. Fincher and Agostino Fricano and John Fuller and Allison Haaning and Georg Haberer and Axel Himmelbach and Murukarthick Jayakodi and Yong Jia and Nadia Kamal and Peter Langridge and Chengdao Li and Qiongxian Lu and Thomas Lux and Martin Mascher and Klaus F. X. Mayer and Nicola Mccallum and Linda Milne and Gary J. Muehlbauer and Martin T. S. Nielsen and Sudharsan Padmarasu and Pai Rosager Pedas and Klaus Pillen and Curtis Pozniak and Magnus W. Rasmussen and Kazuhiro Sato and Thomas Schmutzer and Uwe Scholz and Danuta Schueler and Hana Simkova and Birgitte Skadhauge and Nils Stein and Nina W. Thomsen and Cynthia Voss and Penghao Wang and Ronja Wonneberger and Xiao-Qi Zhang and Guoping Zhang and Luigi Cattivelli and Manuel Spannagl and Micha Bayer and Craig Simpson and Runxuan Zhang and Robbie Waugh},

doi = {10.1038/s41588-024-02069-y},

issn = {1061-4036},

year  = {2025},

date = {2025-02-01},

urldate = {2025-02-01},

journal = {NATURE GENETICS},

volume = {57},

number = {2},

abstract = {A pan-transcriptome describes the transcriptional and 

 post-transcriptional consequences of genome diversity from multiple 

 individuals within a species. We developed a barley pan-transcriptome 

 using 20 inbred genotypes representing domesticated barley diversity by 

 generating and analyzing short- and long-read RNA-sequencing datasets 

 from multiple tissues. To overcome single reference bias in transcript 

 quantification, we constructed genotype-specific reference transcript 

 datasets (RTDs) and integrated these into a linear pan-genome framework 

 to create a pan-RTD, allowing transcript categorization as core, shell 

 or cloud. Focusing on the core (expressed in all genotypes), we observed 

 significant transcript abundance variation among tissues and between 

 genotypes driven partly by RNA processing, gene copy number, structural 

 rearrangements and conservation of promotor motifs. Network analyses 

 revealed conserved co-expression module::tissue correlations and 

 frequent functional diversification. To complement the 

 pan-transcriptome, we constructed a comprehensive cultivar (cv.) Morex 

 gene-expression atlas and illustrate how these combined datasets can be 

 used to guide biological inquiry.},

keywords = {Gene expression, Pan-genome, Pan-transcriptome, Plant genetics, RNA sequencing},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@article{WOS:001220771900001,

title = {Investigating the genetic control of plant development in spring barley  under speed breeding conditions},

author = {Nicola Rossi and Wayne Powell and Ian J. Mackay and Lee Hickey and Andreas Maurer and Klaus Pillen and Karen Halliday and Rajiv Sharma},

doi = {10.1007/s00122-024-04618-9},

issn = {0040-5752},

year  = {2024},

date = {2024-05-01},

urldate = {2024-05-01},

journal = {THEORETICAL AND APPLIED GENETICS},

volume = {137},

number = {5},

abstract = {Key message This study found that the genes, PPD-H1 and ELF3, control 

 the acceleration of plant development under speed breeding, with 

 important implications for optimizing the delivery of climate-resilient 

 crops.Abstract Speed breeding is a tool to accelerate breeding and 

 research programmes. Despite its success and growing popularity with 

 breeders, the genetic basis of plant development under speed breeding 

 remains unknown. This study explored the developmental advancements of 

 barley genotypes under different photoperiod regimes. A subset of the 

 HEB-25 Nested Association Mapping population was evaluated for days to 

 heading and maturity under two contrasting photoperiod conditions: (1) 

 Speed breeding (SB) consisting of 22 h of light and 2 h of darkness, and 

 (2) normal breeding (NB) consisting of 16 h of light and 8 h of 

 darkness. GWAS revealed that developmental responses under both 

 conditions were largely controlled by two loci: PPDH-1 and ELF3. Allelic 

 variants at these genes determine whether plants display early flowering 

 and maturity under both conditions. At key QTL regions, domesticated 

 alleles were associated with late flowering and maturity in NB and early 

 flowering and maturity in SB, whereas wild alleles were associated with 

 early flowering under both conditions. We hypothesize that this is 

 related to the dark-dependent repression of PPD-H1 by ELF3 which might 

 be more prominent in NB conditions. Furthermore, by comparing 

 development under two photoperiod regimes, we derived an estimate of 

 plasticity for the two traits. Interestingly, plasticity in development 

 was largely attributed to allelic variation at ELF3. Our results have 

 important implications for our understanding and optimization of speed 

 breeding protocols particularly for introgression breeding and the 

 design of breeding programmes to support the delivery of 

 climate-resilient crops.},

keywords = {Cereal Crops, Developmental Genetics, Plant Breeding, Plant genetics, Quantitative trait},

pubstate = {published},

tppubtype = {article}

}