A physical map of the short arm of wheat chromosome 1A
2013
Breen, James | Wicker, Thomas | Shatalina, Margarita | Frenkel, Zeev | Bertin, Isabelle | Philippe, Romain | Spielmeyer, Wolfgang | Šimková, Hana | Šafář, Jan | Cattonaro, Federica | Scalabrin, Simone | Magni, Federica | Vautrin, Sonia | Berges, Helene | Paux, Etienne | Fahima, Tzion | Doležel, Jaroslav | Korol, Abraham | Feuillet, Catherine | Keller, Beat
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 similar to 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 similar to 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.
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