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http://barleygenome.org/
progress towards efficient gene isolation and genomic
sequencing in barley
Mission statement
Barley (Hordeum vulgare L.) was one of the first domesticated cereal grains, originating in the Fertile Crescent over 10,000 years ago. Barley
ranks fifth in worldwide crop production and is widely cultivated in all temperate regions from the Arctic Circle to the tropics. In addition to its
geographic adaptability, barley is particularly noted for its tolerance to cold, drought, alkali, and salinity.
The barley genome - with 5.3 billion letters of genetic code - is one of the largest in cereal crops measuring about twice the size of the human
genome. Barley is a true diploid, thus, it is a natural archetype for genetics and genomics for the Triticeae tribe, including polyploid wheat, and
rye. Highly collaborative international efforts have produced a substantial body of genetic and genomic resources in the past several years.
The objective of IBSC is to physically map and sequence the barley gene space including the 5’ and 3’ regulatory regions of genes. The central
goal is to develop an ordered physical map linked to the genetic map in order to accelerate gene isolation and crop improvement and to
provide the basis for the longer-term goal of sequencing the barley genome.
Members
Australian Center for Plant Functional Genomics (ACPFG)
Peter Langridge
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
Andreas Graner (chair), Nils Stein (vice-chair)
MTT Agrifood / University of Helsinki
Alan Schulman
Scottish Crop Research Institute (SCRI)
Robbie Waugh
Okayama University
Kazuhiro Sato
&
National Institute of Agrobiological Sciences (NIAS)
Takashi Matsumoto
University of California, Riverside
Timothy J Close
&
USDA-ARS / Iowa State University
Roger Wise
Developing a physical map by High Information Content Fingerprinting (HICF) –
target: 15x haploid genome coverage
Research Agenda
Anchoring the physical map to the high-density and high-resolution genetic map
of barley: mapping of up to 10 - 15,000 barley genes, BAC end sequencing and
mapping, colinearity to model genomes
Sample sequencing the barley genome: Gene-enriched library sequencing
(GSS), contig- and sample-BAC sequencing
Contig-based and shotgun whole genome sequencing
Physical map construction:
HICF of 83000 gene-containing genes, collaborative project between UCR (TJ Close) and UC Davis (MC Luo)
- expiry: end 2007, funding: NSF Plant Genome Research
Program
10x genome coverage HICF ongoing as collaborative project between IPK, ACPTG and TU Munich
- ongoing (2007-2009), funding: Leibniz Association, ACPFG
200,000 BAC clones HICF
- ongoing 2007 – 2010, funding: BMBF
anchoring physical map for chromosomes 1H and 3H - approval pending, expected starting date: 2008, funding:
EU-FP7
Ongoing Activities
Genetic mapping:
3000 ESTs mapped via SNP, Okayama University (K Sato)
- completed
1000 EST consensus map, IPK (A Graner)
- completed
~2500 EST mapped via SNP ILLUMINA Golden Gate Assay (TJ Close, R Waugh, N Stein) - Completed. Funded by
NSF Plant Genome Research Program and BarleyCAP (TJC), AGOUEB (RW), IPK core funding and BMBF/GABI
(NS).
~4000 unigenes via SFP and eQTL analysis (R Waugh, R Wise)
- completed
Sequencing:
25,000 full length cDNAs, NIAS (T Matsumoto, K Sato)
500 chromosome 3H BACs of cv. Haruna Nijo (K Sato)
250,000 BAC clones end sequencing (SCRI, IPK, Udine University)
3000 BACs low-pass shotgun sequencing
- funding available, ongoing
- funding available, ongoing
- funding available ERA-PG
- funding available, BMBF