In the last two decades international collaboration among the scientific community has led to quantum changes in the biological knowledge and genetics resources for barley. These resources include large collections of:
- expressed sequence tags (ESTs)
- Full-Length cDNA sequences (Matsumoto et al., 2011)
- bacterial artificial chromosome (BAC) libraries (Schulte et al., 2011)
- SNP markers, lately available as an Illumina iSelect chip (Comadran et al., 2012)
- microarrays, both Affymetrix and Agilent (Liu et al., 2011)
- biparental populations and genetic maps (Close et al., 2009)
- TILLING populations (Caldwell et al., 2004)
- new efficient genetic transformation methods (Harwood, 2012).
In 2006 the International Barley Genome Sequencing Consortium (IBSC) was created. Representatives of the principal worldwide barley research groups (Europe, USA, Japan and Australia) produced a whitepaper suggesting strategies and milestones including:
- developing a physical map of the barley genome
- anchoring the physical map
- ultimately producing a high-quality reference sequence of the barley genome.
The original strategy of sequencing was based on a BAC-by-BAC approach, however due the opportunities offered by new sequencing technologies, whole genome shotgun sequencing allowed the development of incremental draft assemblies that incorporate community-driven datasets.
The first publicly released sequence assembly of the barley genome, achieved in 2012 (Nature 479, 711-716), will help better understand cereal genomes and enable exhaustive comparative genetic analysis with model plants.
Progress so far
Barley ( Hordeum vulgare L.) is a diploid plant with a large haploid genome of 5.3 gigabases (Gb) distributed amongst seven chromosomes (1H-7H).
A genome-wide physical map of barley (cultivar Morex) was built by high-information-content fingerprinting and contig assembly of 571,000 bacterial artificial chromosome (BAC) clones. After assembly, the physical map presented a cumulative length of 5.0 Gb representing more than 95% of the barley genome. The genome shows abundance of repetitive DNA, with 84% of the sequence present as mobile elements, most of them retrotransposons.
The transcribed portion of the barley genome annotated thus far, was identified using RNAseq data obtained in this project, arising from eight important tissues/stages of development, along with 28,592 full-length cDNAs. In total, 79,379 transcript isoforms were identified and comparison with the genomes of other cereals Sorghum, rice and Brachypodium revealed homology in 26,159 of the transcripts (so-called High Confidence genes).
Strong evidence of alternative splicing, premature termination codons and novel transcriptionally active regions indicate significant and high-levels of post-transcriptional regulation. Extensive single-nucleotide variation was also identified. All these elements provide excellent resources for exploitation in biology-driven applications.