TY - JOUR
T1 - A physical map of the short arm of wheat chromosome 1A
AU - Breen, James
AU - Wicker, Thomas
AU - Shatalina, Margarita
AU - Frenkel, Zeev
AU - Bertin, Isabelle
AU - Philippe, Romain
AU - Spielmeyer, Wolfgang
AU - Šimková, Hana
AU - Šafář, Jan
AU - Cattonaro, Federica
AU - Scalabrin, Simone
AU - Magni, Federica
AU - Vautrin, Sonia
AU - Bergès, Hélène
AU - Paux, Etienne
AU - Fahima, Tzion
AU - Doležel, Jaroslav
AU - Korol, Abraham
AU - Feuillet, Catherine
AU - Keller, Beat
PY - 2013/11/21
Y1 - 2013/11/21
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84894379312&partnerID=8YFLogxK
U2 - https://doi.org/10.1371/journal.pone.0080272
DO - https://doi.org/10.1371/journal.pone.0080272
M3 - Article
C2 - 24278269
SN - 1932-6203
VL - 8
JO - PLoS ONE
JF - PLoS ONE
IS - 11
M1 - e80272
ER -