E-MTAB-1912 - Comparative genomic hybridization by array of Triticum aestivum to investigate gene mapping in the physical map of the Triticum aestivum chromosome arm 1BS
Released on 6 December 2013, last updated on 3 June 2014
To improve our understanding of the organization and evolution of the wheat gene space, we established the first map of genes of the wheat chromosome 1BS by hybridizing the newly developed INRA GDEC Triticum aestivum NimbleGen 12x40k unigenes microarray (A-MEXP-2314) with 3D-pools of MTP BACs of from the 1BS physical map. By hybridizing the BAC pools with the wheat NimbleGen 40K unigenes chip we managed to map almost 1063 unigenes on the wheat chromosome 1BS BACs. By comparison with 454 sequences and Illumina survey sequence contigs from the sorted chromosome 1BS, we confirmed the assignation of 849 unigenes in individual BACs from the chromosome 1BS. This data allowed us to study the organization of the wheat gene space along chromosome 1BS. The sequences of the unigenes helped to perform synteny and evolutionary analyses of these unigenes. DNA from MTP clones were pooled into 3D manner: library of MTP clones was stored in 17 plates of 384 wells (24 columns x 16 rows); plate1 pool consist of mixture of DNA from all MTP clones situated in plate 1, Row A pool consist of mixture of DNA from all MTP clones situated in Rows A (from all 17 plates, etc). The set of positive plate, column and row pools for the unigene (represented in microarray) allow to detect the list of putative positive clones (clones from the intersection of positive pools, cleaned using information on physical intersection clones based on clone fingerprints). Hence, all 57 experiments (17 for plate pools, 24 for column pools, and 16 for row pools) have the same experimental factor.
comparative genomic hybridization by array, all pairs , genotype design, normalization testing design
The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution. Dina Raats, Zeev Frenkel, Tamar Krugman, Itay Dodek, Hanan Sela, Hana Simkova, Federica Magni, Federica Cattonaro, Sonia Vautrin, Helene Berges, Thomas Wicker, Beat Keller, Philippe Leroy, Romaine Philippe, Etienne Paux, Jaroslav Doležel, Catherine Feuillet, Abraham Korol and Tzion Fahima.