A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms

Ruvini Ariyadasa,Marius Felder,Burkhard Steuernagel,Thomas Schmutzer,Pete E Hedley,Gary J Muehlbauer,Nils Stein,Uwe Scholz,Stefan Taudien,Matthias Platzer,Daniela Schulte,Zeev Frenkel,Robbie Waugh,Ruonan Zhou,Andreas Graner,Heidrun Gundlach,Peter Langridge,Naser Poursarebani,Martin Mascher,Axel Himmelbach,Abraham B Korol ,Thomas Nußbaumer ,Klaus Mayer

doi:10.1104/pp.113.228213

Abstract

Barley (Hordeum vulgare) is an important cereal crop and a model species for Triticeae genomics. To lay the foundation for hierarchical map-based sequencing, a genome-wide physical map of its large and complex 5.1 billion-bp genome was constructed by high-information content fingerprinting of almost 600,000 bacterial artificial chromosomes representing 14-fold haploid genome coverage. The resultant physical map comprises 9,265 contigs with a cumulative size of 4.9 Gb representing 96% of the physical length of the barley genome. The reliability of the map was verified through extensive genetic marker information and the analysis of topological networks of clone overlaps. A minimum tiling path of 66,772 minimally overlapping clones was defined that will serve as a template for hierarchical clone-by-clone map-based shotgun sequencing. We integrated whole-genome shotgun sequence data from the individuals of two mapping populations with published bacterial artificial chromosome survey sequence information to genetically anchor the physical map. This novel approach in combination with the comprehensive whole-genome shotgun sequence data sets allowed us to independently validate and improve a previously reported physical and genetic framework. The resources developed in this study will underpin fine-mapping and cloning of agronomically important genes and the assembly of a draft genome sequence.

Highlights

Barley (Hordeum vulgare) is an important cereal crop and a model species for Triticeae genomics
While we demonstrated that POPSEQ anchoring of a whole-genome shotgun assembly is independent of physical map construction, we argued that the data obtained should expedite the ongoing physical mapping project
Restricting attention to single bacterial artificial chromosomes (BACs) clones reduces the algorithmic complexity of sequence assembly, enabling the use of short next-generation sequencing (NGS) reads and established assembly programs that would result in highly fragmented assemblies when applied on a wholegenome scale

Summary

Introduction

Barley (Hordeum vulgare) is an important cereal crop and a model species for Triticeae genomics. We integrated whole-genome shotgun sequence data from the individuals of two mapping populations with published bacterial artificial chromosome survey sequence information to genetically anchor the physical map. As a result of these difficulties, socalled gene-space assemblies from whole-genome sequencing data have been widely adopted as an enabling alternative for many research applications, when the majority of the gene complement has been successfully embedded into a broader genomic context Such a milestone was recently completed for barley with the release of a gene-space assembly embedded in a sequence-enriched physical and genetic framework (The International Barley Genome Sequencing Consortium, 2012). The integration of transcriptome sequence into this framework defined and provided context and definition for 26,159 high-confidence gene models

Methods

Results

Conclusion