Abstract
Bread wheat (Triticum aestivum) has a large and highly repetitive genome which poses major technical challenges for its study. To aid map-based cloning and future genome sequencing projects, we constructed a BAC-based physical map of the short arm of wheat chromosome 1A (1AS). From the assembly of 25,918 high information content (HICF) fingerprints from a 1AS-specific BAC library, 715 physical contigs were produced that cover almost 99% of the estimated size of the chromosome arm. The 3,414 BAC clones constituting the minimum tiling path were end-sequenced. Using a gene microarray containing ∼40 K NCBI UniGene EST clusters, PCR marker screening and BAC end sequences, we arranged 160 physical contigs (97 Mb or 35.3% of the chromosome arm) in a virtual order based on synteny with Brachypodium, rice and sorghum. BAC end sequences and information from microarray hybridisation was used to anchor 3.8 Mbp of Illumina sequences from flow-sorted chromosome 1AS to BAC contigs. Comparison of genetic and synteny-based physical maps indicated that ∼50% of all genetic recombination is confined to 14% of the physical length of the chromosome arm in the distal region. The 1AS physical map provides a framework for future genetic mapping projects as well as the basis for complete sequencing of chromosome arm 1AS.
Highlights
The Poaceae family of grass species includes some of the most economically important agricultural crop species in the world
A partial genome sequence became recently available which covers gene space but is incomplete in repetitive intergenic regions [5]. Model genomes such as rice [2], sorghum [3] and Brachypodium [5] have been used to infer gene order in wheat and barley: positional information of genes from syntenic regions in these three model genomes was compiled for the production of ‘‘chromosome zippers’’ [6]
The largest contig has a size of approximately 2,114 kb and is comprised of 211 bacterial artificial chromosome (BAC)
Summary
The Poaceae family of grass species includes some of the most economically important agricultural crop species in the world. In order to increase crop productivity, genome sequencing projects have been initiated to provide genetic tools for plant improvement [1] Grass species such as rice [2], sorghum [3], Brachypodium distachyon [4] have had their genomes completely sequenced. A partial genome sequence became recently available which covers gene space but is incomplete in repetitive intergenic regions [5] Model genomes such as rice [2], sorghum [3] and Brachypodium [5] have been used to infer gene order in wheat and barley: positional information of genes from syntenic regions in these three model genomes was compiled for the production of ‘‘chromosome zippers’’ [6]. Genome sequencing efforts are hampered by a large 17,000 Mb genome size (over 43 times larger than the rice genome), .80% repetitive sequence [10,11] and hexaploid (AABBDD) genome structure
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