Abstract
We used a novel approach that incorporated chromosome sorting, next-generation sequencing, array hybridization, and systematic exploitation of conserved synteny with model grasses to assign ~86% of the estimated ~32,000 barley (Hordeum vulgare) genes to individual chromosome arms. Using a series of bioinformatically constructed genome zippers that integrate gene indices of rice (Oryza sativa), sorghum (Sorghum bicolor), and Brachypodium distachyon in a conserved synteny model, we were able to assemble 21,766 barley genes in a putative linear order. We show that the barley (H) genome displays a mosaic of structural similarity to hexaploid bread wheat (Triticum aestivum) A, B, and D subgenomes and that orthologous genes in different grasses exhibit signatures of positive selection in different lineages. We present an ordered, information-rich scaffold of the barley genome that provides a valuable and robust framework for the development of novel strategies in cereal breeding.
Highlights
Access to a genome sequence is considered pivotal for unraveling key questions in crop plant biology and interrogating the molecular mechanisms that underpin trait formation
A complete reference genome sequence remains an aspiration for the barley research community, primarily due to technical and economic constraints resulting from the size and inherent complexity of its 5.1-Gbp genome
As a step toward that goal, we report here a high resolution sequence-based gene map containing an estimated 86% of the genes in the barley genome
Summary
Access to a genome sequence is considered pivotal for unraveling key questions in crop plant biology and interrogating the molecular mechanisms that underpin trait formation. Despite their importance in global agriculture, the Triticeae species wheat (Triticum aestivum; 2n=6x=42) and barley (Hordeum vulgare; 2n=2x=14), ranked 1 and 5 in world food production (FAOSTAT, 2007; http://faostat.fao.org/), are two such crops where genome size and complexity (17 Gbp for wheat [Bennett and Smith, 1976] and 5.1 Gbp for barley [Dolezel et al, 1998]) so far preclude the development of such a gold standard reference genome sequence. Genomic data both from sequenced BAC clones and the application of next-generation sequencing (NGS) methodologies are available at a limited scale An increasing body of information supports the notion of treating the Triticeae as a single genetic system
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