Improvement of Pseudomolecule for Wheat Chromosome 6B

The International Wheat Genome Sequencing Consortium (IWGSC) continues their efforts to make a high quality reference genome sequence of the bread wheat genome from cv. Chinese Spring, which is anchored to the genetic maps. Our team in Japan have made the physical map using the chromosome 6B-specific BAC library and have sequenced individually with 96-Tag sequencing system.

To further improve a 6B pseudomolecule (ver1.0) which was reported in the PAG XXIV last year, the BAC clones covering gap regions were sequenced with GS FLX. And also two mate-pair libraries (3~4 kb, 8~11 kb) using pooled BAC clones were constructed and sequenced with MiSeq. After the integration of information of the newly sequenced BAC clones into the data for the previous pseudomolecule, all of the BAC clones were checked for their overlaps with neighbors and then were ordered manually using the outputs from SSPACE.

And also, to anchor unmapped scaffolds onto the 6B physical map, ISBP (Insertion Site Based Polymorphism) markers were further designed based on the unmapped BAC sequences. As a result, some of unmapped scaffolds were connected to the mapped scaffolds by their sequences and/or were anchored onto the 6B physical map.

Combined with all data, we constructed the new version of 6B pseudomolecule (ver. 2.0), which is 648.30 Mb in size. The number of scaffolds was 5,455 and the size of the largest scaffold was about 3.9Mb.

This work was supported by a grant from the Ministry of Agriculture, Forestry, and Fisheries of Japan. (Genomics-based Technology for Agricultural Improvement, NGB1003, 1007).