Toward the Sequence-Ready Physical Map of Bread Wheat Chromosome 4A

Due to its size and complexity wheat genome represents a challenge for sequencing and marker assisted breeding. To facilitate wheat genomics we are developing sequence-ready chromosome arm specific physical maps for both arms of chromosome 4A. BAC libraries were constructed for both arms, fingerprinted and assembled to contigs using both, LTC and FPC software. Topology of the FPC contigs was verified by the LTC. The 4AS and 4AL libraries were assembled into 415 and 1127 contigs, respectively. The MTPs of the 4AS and 4AL maps consist of 4422 and 8369 clones and represent 94% and 87% of 4AS and 4AL, respectively. Contigs of the physical maps were further merged to super-contigs using combination of advanced tools of the LTC software and manual assembly. In the 4AS and 4AL physical maps, 67 and 74 super-contigs were obtained, respectively, with more than 100 clones. In both physical maps, the super-contigs contain about half of informative clones. The longest super-contigs in the 4AS and 4AL map comprised 582 and 1018 clones, respectively. 3D pools of MTP clones were prepared to facilitate screening of the library. Large-scale physical map anchoring will be performed in silico after sequencing the MTP BAC clones. The anchoring sequences will be genetically mapped using available recombination mapping populations and endosperm radiation hybrid panel consisting of 1100 lines. This work has been supported by the Czech Science Foundation (P501/10/1740), MSMT CR and EU (Operational Programme Research and Development for Innovations No. ED0007/01/01) and Internal Grant Agency PrF-2012-001.