Hirokazu Handa¹, Fuminori Kobayashi¹, Jianzhong Wu^1,2, Takeshi Itoh³, Tsuyoshi Tanaka³, Hiroaki Sakai³, Takashi Matsumoto¹

¹Plant Genome Research Unit, ²Advanced Genomics Laboratory, ³Bioinformatics Research Unit

［Abstract］

In collaboration with the International Wheat Genome Sequencing Consortium (IWGSC), we have contributed in producing the first “draft sequence” of the wheat genome, which is 40 times bigger than the rice genome, and identified 124,201 sequences as genes or gene loci. The genome sequence data generated so far provide a unique resource for accelerating gene mapping and marker development in wheat breeding.

［Keywords］

Keywords: wheat, draft genome sequence, gene information, information of chromosomal location

［Background］

Wheat is one of major cereal crops with the second biggest production in the world, and together with rice and maize, is a major dietary component for many populations across the world. The development of novel varieties with desirable traits such as high yield and tolerance to biotic/abiotic stresses is therefore highly anticipated as a solution to food shortage due to an ever-increasing population. Deciphering the genome sequence and characterization of gene structure and function will accelerate our understanding of its biology with implications in agriculture. The IWGSC makes efforts to obtain the high quality reference sequence of the17GB bread wheat genome. As a member of IWGSC, we are working to sequence the wheat chromosome 6B and contributed to the release of the draft genome sequence of wheat.

［Results and Discussion］

1. The IWGSC is an international, collaborative consortium, established in 2005 by a group of wheat scientists in the world. The collaborators from Japan, which consist of research teams from the NIAS, Kyoto Univ., Yokohama City Univ. and Nisshin Flour Milling Co., are in-charge of wheat chromosome 6B, which corresponds to 2.5 times the size of the rice genome (Fig. 1).
   
2. Using the wheat variety “Chinese Spring”, each chromosome of wheat was picked up by flow cytometry technique and then DNAs were isolated from individual sorted chromosomes. Sequence information was produced using high throughput ‘Next Generation Sequencing’ technology (Fig. 2).
   
3. The sequences were assembled into contigs for each chromosome covering a total of 10.2 Gb, or approximately 61% of the wheat genome.
   
4. From the sequences represented in the assemblies, we have annotated 124,201 gene loci distributed nearly evenly across the homologous chromosomes (Fig. 3).
   
5. We have sequenced 508 Mb of chromosome 6B, corresponding to 56% of the estimated size (914 Mb), and identified 4,798 gene loci. Using this information, we carried the comparative analyses between wheat and other Gramineae plants, such as rice, sorghum and Brachypodium (Fig. 4).

1. The draft sequence and gene information are useful for isolation and functional analysis of wheat genes. Due to the complexity of the wheat genome, a hexaploid with AABBDD genome composition derived from three ancestral species (Fig. 5), it was difficult to distinguish the homoeologous gene copies which resemble each other. Although the draft sequence was able to identify and assign genes to individual chromosomes it does not provide information that will allow breeders to identify the differences between genes that lie on the chromosomes within the A, B and D subgenomes that will make it easier and more rapidly to localize specific genes for DNA marker assisted breeding.
   
2. The draft genome sequence will enable breeders to accelerate the improvement of wheat through genomics assisted breeding and biotechnology, which will result in new wheat varieties with higher yield, better resistance to diseases and pests, and tolerance to abiotic stresses. The sequence information of chromosome 6B is useful to improve wheat grain quality, resistance to Fusarium head blight, etc.
   
3. The ultimate goal of the IWGSC is to produce the complete wheat genome sequence, or the so-called reference sequence with 85% coverage of the 21 wheat chromosomes.

Fig. 1. Current status of genome sequencing in terms of physical map construction (top panel), draft genome sequencing (middle) and reference genome sequencing (bottom). The state of progress is shown in green

 

Fig. 2. Isolation of wheat chromosome 6B by flow cytometry.

 

Fig. 3. Distribution and total number of HC (high confidence) bread wheat genes identified on the A (green), B (purple), and D (orange) subgenomes.

 

Fig. 4. Distribution of chromosome 6B genes with significant similarity to O. sativa, B. distachyon and S. bicolor.

 

Fig. 5. Comparison of wheat and other cereal crop genomes.

 

[Reference]

1. International Wheat Genome Sequencing Consortium (2014) A chromosome-based draft sequence of the hexaploid bread wheat genome Science 345:1251788
   
2. Tanaka T, Kobayashi F, Joshi G.P, Onuki R, Sakai H, Kanamori H, Wu J, Šimková H, Nasuda S, Endo T.R, Hayakawa K, Dole?el J, Ogihara Y, Itoh T, Matsumoto T, Handa H (2014) Next-generation survey sequencing and the molecular organization of wheat chromosome 6B DNA Research 21 (2):103-114