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Development of the BAC Physical Maps of Wheat Chromosome 6B for Its Genomic Sequencing

Genome Sequencing Project for Chromosome 6B

The International Wheat Genome Sequencing Consortium (IWGSC) has been promoting the decoding of the wheat genome sequence to enhance our knowledge of the structure and function of the wheat genome. The vision of the consortium is to establish a high quality reference sequence with a strategy to sequence its whole genome using BAC (bacterial artificial chromosome) clones aligned on the physical map of each chromosome. Under the framework of IWGSC, we are in charge of the chromosome 6B with the financial support from the Japanese Ministry of Agriculture, Forestry and Fisheries (“Genomics for Agricultural Innovation” project and “Genomics-based Technology for Agricultural Improvement” project) and Nisshin Flour Milling Inc. The “KomugiGSP” (Genome Sequence Program) (komu- gigsp.dna.affrc.go.jp/index.html) currently consists of the following four main research subjects: (1) Construction of 6B-specific BAC library and development of DNA markers, (2) comprehensive analysis of transcripts for gene annotation, (3) construction of the BAC physical map and genome sequencing (BAC-by-BAC and whole chromosome survey sequencing), and (4) development of annotation pipeline. Here, we report our current progresses on the construction of a physical map for chromosome 6B using chromosome arms-specific BAC libraries with DNA markers and BAC-based genomic sequencing.

Chromosome 6B-Specific BAC Libraries

Common wheat (Triticum aestivum L.) has a large genome, of approximately 17 Gb, and is allohexaploid with three homoeologous genomes (2n = 6x = 42, genome formula AABBDD). Chromosome 6B is one of the largest chromosomes among its 21 chromosomes, with an estimated size of 914 Mb, in which the short-arm (6BS) and long-arm

(6BL) contain 415 Mb and 498 Mb, respectively (Šafář et al. 2010). Because of the large size, individual chromosomes or chromosome arms can be isolated using the flow

cytometry to reduce the complexity of its genome for the construction of physical maps and genomic sequencing as well. The sorting of single chromosomes or chromosome arms from common wheat cultivar 'Chinese Spring' (CS) and its aneuploid lines has enabled the construction of chromosome (arm)-specific BAC libraries (Šafář et al. 2010), that have served as the critical resources for the development of physical maps and map-based genome sequencing by IWGSC. A double ditelosomic 6B line of CS

was supplied for the flow sorting of mitotic chromosomes to construct chromosome arm-specific BAC libraries by collecting more than five millions of each chromosome arms. Using the chromosomal DNA extracted from each arm, two BAC libraries with the specificities to 6BS and 6BL, comprising 57,600 and 76,032 BACs with an average insert length of about 130 kb to represent 15.3 and 18 times equivalents of their estimated sizes of each arm, respectively, were successfully constructed.

BAC Contig Construction

For physical mappings of chromosome 3B, chromosome arm 1AL and whole genome of Aegilops tauschii Coss., BAC clones were fingerprinted through the method of SNaPshotTM (Paux et al. 2008; Lucas et al. 2013; Luo et al. 2013), which is an automated fingerprinting technique by sizing restriction fragments of each BAC (Luo et al. 2003). However, restriction fragment sizes shared randomly between two non-overlapping BACs often lead to chimerical contigs or misassembled BACs particularly in the large and repetitive genomic regions. Whole Genome Profiling (WGPTM) is an alternative method for the establishment of the chromosome physical maps developed based on a next-generation sequencingbased technology (van Oeveren et al. 2011). The efficiency of WGP on physical mappings of wheat chromosomes has been demonstrated by comparison with that of SNaPshot (Philippe et al. 2012).

In our project, chromosome 6B BAC clones were fingerprinted by WGP for a robust physical map. Pooled BAC DNAs were digested with the two restriction enzymes, EcoRI and MseI, and the restriction fragments with adaptors were sequenced using the Illumina HiSeq2000 sequencer to yield WGP tags. Deconvolution enables the assignment of the WGP tags to individual BACs. We excluded the low quality BACs during the contig building process in order to construct the physical map with high accuracy. After filtering BACs, assembly of the fingerprints representing nine and ten times equivalent of 6BS and 6BL, respectively, was performed with the FingerPrinted Contigs (FPC) software (Soderlund et al. 1997). A stepwise method was used for the assembly to further improve the quality of BAC contigs, which was defined by Paux et al. (2008) during the construction of chromosome 3B physical map and finally modified by Philippe et al. (2012). The physical maps of chromosome 6B have been successfully established to have an estimated chromosomal coverage of more than 90 %. Overlap analysis between the neighboring clones within BAC contigs enabled us to select minimal tiling path clones along each chromosome arm, which were subjected to the genomic sequencing.

 
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