Nie Xiaojun1, Wang Le1, Simkova Hana2, Safar Jan2,
Dolezel Jaroslav2, Mingcheng Luo2, Song Weining1
1 State key Lab of Crop Stress Biology for Arid Areas, College of Agronomy; Yangling Branch of China Wheat Improvement Center, Northwest A&F University
2  Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany
3 Department of Plant Sciences, University of California, Davis

Complex bread wheat (Triticeae aestivum) genome presents significant problems in elucidating its DNA sequence, due to its size, hexaploid genome composition and repetitive elements nature. Nevertheless construction of a physical map of individual chromosomes/arms is an alternative to reduce the complexity of the task and provide the foundation to sequence the chromosome genome. As part of the efforts of the International Wheat Genome Sequencing Consortium to sequence the wheat genome, we have reduced genome sequence complexity by isolating chromosome arm 7DL and constructed a physical map of chromosome arm 7DL. This chromosome arm carries genes underlying many important agronomic traits, such as yield, dwarfing and pathogen/pest resistance. At present, a total of 50,352 clones have been fingerprinted using the high information content fingerprinting technique (Luo et al. 2003.Genomics 82:378-389). There are 43,219 clone fingerprints which are suitable for assembly, representing ca. 15x equivalent of the chromosome arm. An automated assembly with the FPC software (Soderlund et al. 2000. Genome Research 10:1772-1787) resulted in 1,685 contigs and 7,307 clones remained as singletons. The Minimal Tilling Path (MTP) contained 4,335 clones which represents coverage of 91% of the 7DL arm. The survey sequence was assembled with the method of Zerbino and Birney (2008). Using bioinformatics tools, pre-miRNAs were predicted and analysed from sequences of the chromosome arm 7DL. At the same time, the repeat element was found from the sequences of the chromosome arm 7DL. A total of 23,272 simple sequence repeats have been found which distribute on the chromosome arm 7DL. Now, 80 chromosome specific SSR markers derived from the survey sequences and BAC-end sequences were designed and will be further investigated in the integration of the physical map and the genetic map as well as in our wheat breeding program.