Construction of Ready-to-Sequence Physical Map of Bread Wheat Chromosome 4A

Despite the progress in next generation sequencing technologies, whole genome shotgun sequencing is still not powerful enough to produce reference sequences of large plant genomes. This can only be achieved after sequencing large insert DNA clones from ready-to-sequence physical maps. However, even the production of physical maps may be difficult in allopolyploid species. One solution is to produce physical maps of individual chromosomes or individual chromosome arms. As part of the efforts to sequence the 17Gbp genome of hexaploid bread wheat, coordinated by the International Wheat Genome Sequencing Consortium, we have constructed physical maps of the short (S) and long (L) arms of wheat chromosome 4A. Physical maps of 4AS (317Mbp) and 4AL (539Mbp) were assembled into 415 and 1127 BAC contigs, respectively, using FPC and LTC. The map represents 94% and 87% of 4AS and 4AL, respectively. Three dimensional pools were produced from 4422 (4AS) and 8526 (4AL) MTP clones, sequenced by Illumina and used to anchor BAC contigs with 1780 DArT markers. To overcome limitations due to uneven distribution of recombination along the chromosome, a radiation hybrid (RH) panel was developed.  A total of 119 carefully selected RH lines were genotyped using 90k wheat SNP Infinium chip. Approximately 2390 SNPs were specific to chromosome 4A and will be used to build RH map. The mapped SNPs are used to anchor additional contigs of the physical maps. This work has been supported by the Czech Science Foundation (P501/10/1740) and Internal Grant Agency of Palacky University in Olomouc (PrF-2013-003).