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Plant Physiol. Jan 2009; 149(1): 142–147.
PMCID: PMC2613708
Focus Issue on the Grasses

The International Barley Sequencing Consortium—At the Threshold of Efficient Access to the Barley Genome1,[W]

IMPORTANCE AND UTILITY OF BARLEY

Archaeological evidence indicates that barley (Hordeum vulgare) and wheat (Triticum aestivum) were domesticated 10,000 years ago in the Fertile Crescent (Zohary and Hopf, 2001). Among the cereals, barley currently ranks fourth after maize (Zea mays), rice (Oryza sativa), and wheat in terms of total production (Fig. 1). An early maturation and a high level of adaptability to stressful conditions (including cold, drought, alkali, and saline soils) make it well suited for cultivation throughout the world from boreal to equatorial regions. About two-thirds of the global barley crop is used for animal feed, while the remaining third underpins the malting, brewing, and distilling industries. Although the human diet is not a primary use, barley offers a wealth of potential health benefits (Baik and Ullrich, 2008) and is still the major calorie source in several parts of the world (Grando and Macpherson, 2005).

Figure 1.
Statistics for global barley production. Top left section: global barley production parameters for the past 45 years. The top right, bottom left, and bottom right sections give worldwide area, production, and yield parameters for barley for 2006 relative ...

BARLEY-POACEAE RELATIONSHIPS

Barley is a diploid inbreeding species with a large genome of >5 Gbp (Bennett and Smith, 1976). Barley, bread wheat, rye (Secale cereale), and their respective wild relatives are closely related and form the Triticeae tribe, which evolved some 12 million years ago within the Pooideae subfamily of the Poaceae (Gaut, 2002). Due to its simpler diploid genome, barley can be considered a good genomic model for hexaploid bread wheat.

The large size and comparatively low gene density of Triticeae genomes provide a substantial challenge to gene isolation. Therefore, model grass species (e.g. rice, Brachypodium) having small genomes may serve as vehicles for synteny-based gene isolation in large genome cereals (for review, see Stein and Graner, 2004). However, barley and rice shared their last common ancestor about 70 million years ago; only 50% of barley genes highly homologous to rice are collinearly arranged in both genomes (Stein et al., 2007). This limitation may not be fully overcome with the more closely related grass model species, Brachypodium distachyon (Draper et al., 2001). Recent, accelerated development of genomic resources for agricultural grass species are poised to alleviate these limitations, concomitantly strengthening our understanding of pan-grass genomics. The revised model of an ancestral grass genome obtained by comparing whole genome sequences and high density transcript maps of model and nonmodel grass species, respectively (Salse et al., 2008), provides a glimpse of the possibilities.

BARLEY—AN EXPERIMENTAL MODEL FOR POACEAE BIOLOGY

Molecular studies on barley genes and traits has provided (1) a better understanding of Poaceae and plant biology, (2) confirmed and generalized results obtained in other grass species, and (3) revealed barley-specific trait expression controlled by genes highly conserved in related grasses. For example, Poaceae seeds, called caryopses, share a common architecture whereby the embryo is attached to the starchy endosperm via the scutellum—a tissue from which the embryo derives nutrients during seed germination. Due to its paramount importance for the malting and brewing industry (malting is controlled seed germination) and through recent advances in functional genomics, the barley grain is one of the best-studied systems in cereal crops (Gubatz et al., 2007; Sreenivasulu et al., 2008b) and can be regarded as a general model for both Poaceae seed development and germination.

Studies of disease caused by powdery mildew (Blumeria graminis f. sp. hordei) pathogens have been pioneered in barley (Schulze-Lefert and Panstruga, 2003). Factors involved in pathogen recognition, signal transduction, and resistance response have been isolated and characterized, thereby accelerating analyses of host-pathogen interactions across taxonomic boundaries (Jones and Dangl, 2006).

Genes that control responses to important abiotic or environmental factors, such as vernalization requirements (Fu et al., 2005) and photoperiod responses (Turner et al., 2005), have been isolated from barley and either informed previous work on wheat (Vrn1; Cockram et al., 2007) or the barley gene was used as a vehicle to study wheat gene function (e.g. Ppd-D1; Beales et al., 2007).

Three major genes controlling barley flower or inflorescence morphology have been isolated and characterized. The Vrs1 locus controls lateral spikelet fertility, which determines the number of rows in barley ears (Komatsuda et al., 2007). The Nud gene controls lipid biosynthesis in the pericarp, which glues the husks to the kernels and results in either covered or naked barley (Taketa et al., 2008). Dominant mutations in the hooded gene result in an extra flower with inverse polarity on the lemma of the barley spikelet (Müller et al., 1995). Vrs1 and Nud encode, respectively, homeodomain-Leu zipper I and ethylene response family transcription factors. In both cases, highly conserved orthologs with undetermined function are present in rice and likely in other Poaceae. The hooded phenotype is caused by ectopic expression of the barley Knox3 homeobox transcription factor gene in the lemma. In maize, ectopic expression of the orthologous Knotted1 gene results in knotted leaf blade anatomy (Smith et al., 1992). Comparative studies of such genes in barley and other Poaceae will lead to a more comprehensive understanding of plant development and evolution.

STATUS OF BARLEY GENETIC AND GENOMIC RESOURCES

Natural and Induced Genetic Variation

Despite the uniformity of modern, high-yielding, elite, inbred varieties, barley morphology is very diverse (Fig. 2). Representative collections of existing natural genetic diversity are maintained worldwide in ex situ genebanks (Supplemental Table S1), which hold an estimated 370,796 accessions of 31 Hordeum species (van Hintum and Menting, 2003). Since the late 1920s, barley has also been widely used to study and utilize induced genetic variability (summarized in Barley Genetics Newsletter Volume 26: http://wheat.pw.usda.gov/ggpages/bgn/26/bgn26tc.html). Recently, the TILLING technique (targeting induced local lesions in genomes; Caldwell et al., 2004; Talame et al., 2008) has reinvigorated mutation research in barley.

Figure 2.
Barley diversity. A sample of barley inflorescences (spikes) is shown to illustrate the highly polymorphic nature of barley genetic resources, in profound contrast to the uniform morphology of modern elite cultivars.

From Early Molecular Genetic Linkage Analysis to High-Throughput Genotyping

Molecular markers couple barley genome diversity with crop plant biology and facilitate positional cloning and knowledge transfer into crop improvement. Since the early RFLP mapping in barley (Graner et al., 1991), numerous genetic maps utilizing the full spectrum of molecular markers have been published (Supplemental Table S2; http://wheat.pw.usda.gov/ggpages/map_summary.html). Altogether, a minimum of 5,000 nonredundant barley genes have been genetically mapped so far (L. Ramsay and A. Druka, personal communication).

Barley Functional and Structural Genomics

Resources for barley functional genomics have improved over the last decade (for review, see Sreenivasulu et al., 2008a), initiated by systematic EST sequencing (Zhang et al., 2004). Currently, 478,734 public ESTs (dbEST summary 08.08.08, http://www.ncbi.nlm.nih.gov/dbEST/dbEST_summary.html) provide partial sequence information for 50,000 tentative unigenes (Sreenivasulu et al., 2008a). Based on this community resource the first comprehensive oligonucleotide array for a crop plant (22 K Barley 1 GeneChip; Close et al., 2004) was designed. PLEXdb (http://plexdb.org/; Wise et al., 2007) provides public, online access to over 1,200 GeneChip hybridizations from barley and wheat of diverse developmental stages and tissues (Druka et al., 2006). The WebComparator (http://contigcomp.acpfg.com.au/) facilitates interspecies comparisons of expression profiles for Triticeae homoeologs.

The current understanding of barley genome structure is based mainly on the sequence of a handful of bacterial artificial chromosome (BAC) clones (summarized in Stein, 2007) selected for map-based cloning. Map-based gene isolation is feasible in barley at the single-gene scale. However, the efficiency of the entire procedure remains limited by the lack of a complete physical map or a reference genome sequence.

INTERNATIONAL COLLABORATION TO ACHIEVE A HIGH-QUALITY REFERENCE GENOME SEQUENCE

The lack of a physical map and complete sequence of the barley genome is related to the scale of a barley genome project. As this far exceeds the capacity of individual laboratories, it triggered the formation of the International Barley Genome Sequencing Consortium (IBSC; http://barleygenome.org) in 2006. Barley researchers of the eight founding institutions from six different countries comprise a steering committee that elects from its members a chair and a cochair who represent the consortium to the scientific community, funding bodies, and governments. Semiannual steering committee meetings are held to review the progress made toward IBSC goals and to reassess the consortium's strategy for sequencing in view of technological developments and progress made. Similar to previous initiatives, particularly rice and maize (Sasaki and Burr, 2000; Coe et al., 2002), the barley roadmap toward a high-quality genome sequence includes the construction of a genetically anchored physical map. Such a map is not indispensible in some whole-genome sequencing strategies, but in itself it forms an invaluable resource to the scientific community for gene isolation. It represents a milestone that can be reached at a fraction of the cost required for sequencing the whole barley genome.

A PHYSICAL MAP OF BARLEY

To initiate physical map development, a set of 83,381 gene-bearing clones were identified by overgo hybridizations to the original public barley BAC library (Yu et al., 2000; Madishetty et al., 2007), then analyzed and assembled through high information content fingerprinting (Luo et al., 2003; preliminary contig information: http://phymap.plantsciences.ucdavis.edu:8080/barley/). Subsequently, a generic approach to building a genome-wide physical map of barley by high information content fingerprinting was initiated and scheduled to be accomplished by the end of 2009 (status September 2008: 308,764 high-quality fingerprints, approximately seven haploid genome equivalents; D. Schulte, N. Stein, P. Langridge, and A. Graner, unpublished data). This effort takes advantage of new BAC library resources (Supplemental Table S3) and aims at fingerprinting BAC clones representing up to 14 genome equivalents (based on an average insert size of 125 kb). Based on previous calculations (Lander and Waterman, 1988; Wendl and Waterston, 2002), this should resolve a total of approximately 7,000 to 10,000 contigs for the entire barley genome (approximately 1,000 contigs/chromosome), with 70% overlap between individual BACs.

INTEGRATION OF THE PHYSICAL AND GENETIC MAPS

A physical map becomes effective only after anchoring to a genetic map. Large numbers of mapped markers are available for the barley genome (Supplemental Table S2) and an IBSC goal is to obtain 10,000 mapped barley genes (theoretical coverage of two mapped genes/megabase). Mapped marker and BAC address relationships can be determined by hybridization to high-density colony filters (Madishetty et al., 2007) or by PCR screening of multidimensional BAC DNA pools (i.e. Yim et al., 2007). Higher anchoring throughput may be achieved if established multiplex marker platforms in barley, e.g. DArT (Wenzl et al., 2006) and the Golden Gate Assay (Rostoks et al., 2006), can be adopted to BAC DNA pool screening.

The integration of physical and genetic maps in barley is challenged by the limited genetic resolution of current mapping populations. High-density maps in barley mostly represent composite maps providing limited genetic resolution (approximately 1 cM). Large recombinant inbred populations of approximately 4,000 individuals are under development (P. Langridge and N. Stein, unpublished data) to increase genetic resolution. Larger populations or alternative population designs, e.g. intermated recombinant inbred populations (Liu et al., 1996), will be unlikely to resolve regions lacking recombination like the genetic centromeres of the barley chromosomes. Ordering of contigs for these will require the use of alternative methods such as HAPPY mapping (Thangavelu et al., 2003) to reveal physical marker order. Colinear gene order between barley and sequenced grass genomes, combined with chromosome evolution models (Salse et al., 2008), will serve to predict the placement of BAC clones and contigs to genomic regions lacking genetic mapping information.

SEQUENCING THE BARLEY GENOME

IBSC aims at developing a high-quality gold standard reference sequence for barley as the basis for whole-genome single nucleotide polymorphism surveys and genome resequencing. To this end, next generation sequencing (NGS) technologies provide new options by reducing sequencing costs and increasing throughput (Shendure and Ji, 2008). Initial studies demonstrated that NGS technologies can be suitable for determining gene content of barley BAC clones (Wicker et al., 2006) and can support automated repeat annotation of barley genomic DNA (Wicker et al., 2008). New technologies impact sequencing strategies because whole-genome shotgun sequencing (WGS), a proven means of sequencing medium-sized plant genomes such as grapevine (The French-Italian Public Consortium for Grapevine Genome Characterization, 2007), promises to become a rapid, universal approach. However, so far there are no published examples demonstrating that WGS can be applied to large genomes like barley that feature >80% of repetitive DNA. Therefore, a combinatorial approach, combining the strengths of map-based sequencing (classical Sanger or NGS) of a minimal tiling path with paired-end WGS sequencing, can be envisaged currently as a strategy for sequencing the barley genome.

Future challenges lie in the area of barley genome annotation and database construction. The specific aspects of Triticeae genome organization will require new or advanced tools for gene and repeat structure annotation. Here, ongoing sequencing of 25,000 full-length cDNA sequences of barley will provide valuable information (5,000 sequences have been deposited at the DNA Data Bank of Japan; http://www.shigen.nig.ac.jp/barley/; K. Sato and T. Matsumoto, unpublished data). The development of repeat annotation strategies (Wicker et al., 2007) will be critical for structural, functional, and comparative barley genomics with the accumulated knowledge connected wherever possible to public genomics resources (e.g. graingenes: http://wheat.pw.usda.gov/GG2/index.shtml; gramene: http://www.gramene.org/). To achieve this, vigorous links to related grass genome initiatives (rice, maize, Brachypodium, wheat) have been established. Furthermore, IBSC members are committed to raising funding for an international effort to develop a data warehouse environment for Triticeae genomics.

SUMMARY AND OUTLOOK

Sequencing the genome of barley, an agriculturally and industrially important cereal crop and a useful diploid model for bread wheat, has become a realistic undertaking. Important steps have been initiated to improve genomics tools, build and anchor a physical map, develop a high-density genetic map, assess new sequencing technologies, and generate substantial datasets of genomic survey information. These are coordinated through an international consortium. A high-quality reference genome sequence will not only further promote our understanding of genome evolution but also blaze the trail toward genomics-based crop improvement. It will inform our understanding of previously sequenced grass and other plant genomes and will become a further milestone toward understanding grass (or even general plant) genomics and systems biology.

Supplemental Data

The following materials are available in the online version of this article.

  • Supplemental Table S1. Ex situ genebanks hosting large collections of barley accessions and genetic stocks.
  • Supplemental Table S2. Overview of recent high-density biparental and consensus genetic maps of barley.
  • Supplemental Table S3. BAC library resources for barley physical mapping.

Supplementary Material

[Supplemental Data]

Notes

1This work was supported by grants to K.S. (NBRP, BRAIN, and MAFF, Japan), T.J.C. (National Science Foundation grant no. DBI–0321756, U.S. Department of Agriculture CSREES), and N.S. (WGL-Pakt für Forschung und Innovation, Germany).

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Nils Stein (ed.nebelsretag-kpi@niets).

[W]The online version of this article contains Web-only data.

www.plantphysiol.org/cgi/doi/10.1104/pp.108.128967

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