Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond.
Martin Mascher,Todd Richmond,Daniel J. Gerhardt,Axel Himmelbach,Leah Clissold,Dharanya Sampath,Sarah Ayling,Burkhard Steuernagel,Matthias Pfeifer,Mark D'Ascenzo,Eduard Akhunov,Pete E. Hedley,Ana M. Gonzales,Peter L. Morrell,Benjamin Kilian,Frank R. Blattner,Uwe Scholz,Klaus F. X. Mayer,Andrew J. Flavell,Gary J. Muehlbauer,Robbie Waugh,Jeffrey A. Jeddeloh,Nils Stein +22 more
TLDR
An in-solution hybridization-based sequence capture platform to selectively enrich for a 61.6 megabase coding sequence target that includes predicted genes from the genome assembly of the cultivar Morex as well as publicly available full-length cDNAs and de novo assembled RNA-Seq consensus sequence contigs is developed.Abstract:
Summary
Advanced resources for genome-assisted research in barley (Hordeum vulgare) including a whole-genome shotgun assembly and an integrated physical map have recently become available. These have made possible studies that aim to assess genetic diversity or to isolate single genes by whole-genome resequencing and in silico variant detection. However such an approach remains expensive given the 5 Gb size of the barley genome. Targeted sequencing of the mRNA-coding exome reduces barley genomic complexity more than 50-fold, thus dramatically reducing this heavy sequencing and analysis load. We have developed and employed an in-solution hybridization-based sequence capture platform to selectively enrich for a 61.6 megabase coding sequence target that includes predicted genes from the genome assembly of the cultivar Morex as well as publicly available full-length cDNAs and de novo assembled RNA-Seq consensus sequence contigs. The platform provides a highly specific capture with substantial and reproducible enrichment of targeted exons, both for cultivated barley and related species. We show that this exome capture platform provides a clear path towards a broader and deeper understanding of the natural variation residing in the mRNA-coding part of the barley genome and will thus constitute a valuable resource for applications such as mapping-by-sequencing and genetic diversity analyzes.read more
Citations
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Journal ArticleDOI
A chromosome conformation capture ordered sequence of the barley genome
Martin Mascher,Heidrun Gundlach,Axel Himmelbach,Sebastian Beier,Sven Twardziok,Thomas Wicker,Volodymyr Radchuk,Christoph Dockter,Pete E. Hedley,Joanne Russell,Micha Bayer,Luke Ramsay,Hui Liu,Georg Haberer,Xiao-Qi Zhang,Qisen Zhang,Roberto A. Barrero,Lin Li,Stefan Taudien,Marco Groth,Marius Felder,Alex Hastie,Hana Šimková,Helena Staňková,Jan Vrána,Saki Chan,María Muñoz-Amatriaín,Rachid Ounit,Steve Wanamaker,Dan Bolser,Christian Colmsee,Thomas Schmutzer,Lala Aliyeva-Schnorr,Stefano Grasso,Jaakko Tanskanen,Anna Chailyan,Dharanya Sampath,Darren Heavens,Leah Clissold,Sujie Cao,Brett Chapman,Fei Dai,Yong Han,Hua Li,Xuan Li,Chongyun Lin,John K. McCooke,Cong Tan,Penghao Wang,Songbo Wang,Shuya Yin,Gaofeng Zhou,Jesse Poland,Matthew I. Bellgard,Ljudmilla Borisjuk,Andreas Houben,Jaroslav Doležel,Sarah Ayling,Stefano Lonardi,Paul J. Kersey,Peter Langridge,Gary J. Muehlbauer,Matthew D. Clark,Matthew D. Clark,Mario Caccamo,Mario Caccamo,Alan H. Schulman,Klaus F. X. Mayer,Matthias Platzer,Timothy J. Close,Uwe Scholz,Mats Hansson,Guoping Zhang,Ilka Braumann,Manuel Spannagl,Chengdao Li,Chengdao Li,Chengdao Li,Robbie Waugh,Robbie Waugh,Nils Stein,Nils Stein +81 more
TL;DR: The importance of the barley reference sequence for breeding is demonstrated by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.
Journal ArticleDOI
Natural Variations and Genome-Wide Association Studies in Crop Plants
Xuehui Huang,Bin Han +1 more
TL;DR: The development of sequencing-based genotyping and genome-wide association studies in crops are described and the advent of high-throughput sequencing technology enables rapid and accurate resequencing of a large number of crop genomes to detect the genetic basis of phenotypic variations in crops.
Journal ArticleDOI
Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives
Awais Rasheed,Yuanfeng Hao,Xianchun Xia,Awais Khan,Yunbi Xu,Yunbi Xu,Rajeev K. Varshney,Zhonghu He,Zhonghu He +8 more
TL;DR: It is proposed that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops.
Journal ArticleDOI
Genebank genomics highlights the diversity of a global barley collection
Sara Giulia Milner,Matthias Jost,Matthias Jost,Shin Taketa,Elena Rey Mazón,Axel Himmelbach,Markus Oppermann,Stephan Weise,Helmut Knüpffer,Martin Basterrechea,Patrick König,Danuta Schüler,Rajiv Sharma,Rajiv Sharma,Raj K. Pasam,Twan Rutten,Ganggang Guo,Dongdong Xu,Jing Zhang,Gerhard Herren,Thomas Müller,Simon G. Krattinger,Simon G. Krattinger,Beat Keller,Yong Jiang,Maria Y. Gonzalez,Yusheng Zhao,Antje Habekuß,Sandra Färber,Frank Ordon,Matthias Lange,Andreas Börner,Andreas Graner,Jochen C. Reif,Uwe Scholz,Martin Mascher,Nils Stein,Nils Stein +37 more
TL;DR: The analysis of genome-wide genotyping-by-sequencing data for almost all barley accessions of the German ex situ genebank provides insights into the global population structure of domesticated barley and points out redundancies and coverage gaps in one of the world’s major genebanks.
Journal ArticleDOI
A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
Jarrod Chapman,Martin Mascher,Aydin Buluc,Kerrie Barry,Evangelos Georganas,Evangelos Georganas,Adam M. Session,Veronika Strnadova,Jerry Jenkins,Sunish K. Sehgal,Sunish K. Sehgal,Leonid Oliker,Jeremy Schmutz,Katherine Yelick,Katherine Yelick,Uwe Scholz,Robbie Waugh,Jesse Poland,Gary J. Muehlbauer,Nils Stein,Daniel S. Rokhsar,Daniel S. Rokhsar +21 more
TL;DR: In this paper, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and 7.1 gb of this assembly to chromosomal locations is presented.
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