Plant & Animal Genomes XIX Conference

January 15-19, 2011
Town & Country Convention Center
San Diego, CA

Applying Second Generation Sequencing Technology For The Analysis Of Isolated Wheat Chromosomes

Paul J Berkman¹ , Adam Skarshewski¹ , Michal T Lorenc¹ , Kaitao Lai¹ , Chris Duran¹ , Edmund YS Ling¹ , Jiri Stiller¹ , Lars Smits¹ , Michael Imelfort¹ , Sahana Manoli¹ , Megan McKenzie² , Song Weining³ , Marie Kubaláková⁴ , Hana Simkova⁴ , Jacqueline Batley² , Delphine Fleury⁵ , Jaroslav Doležel⁴ , David Edwards¹

¹  Australian Centre for Plant Functional Genomics, School of Land, Crop and Food Sciences, University of Queensland, Brisbane, QLD 4072, Australia

²  School of Land, Crop and Food Sciences and ARC Centre of Excellence for Integrative Legume Research, University of Queensland, Brisbane, QLD 4072, Australia

³  College of Agronomy, Northwest A&F University, 3 Taicheng Rd, Yangling, Shaanxi 712100, China

⁴  Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, CZ-77200 Olomouc, Czech Republic

⁵  Australian Centre for Plant Functional Genomics, Private Mail Bag 1, Glen Osmond, SA 5064, Australia

The genome of bread wheat (Triticum aestivum) is predicted to be greater than 16 Gbp in size and consist predominantly of repetitive elements, making the sequencing and assembly of this genome a major challenge. We have reduced genome sequence complexity by isolating wheat group 7 chromosome arms, and applied Illumina paired read sequencing technology and appropriate algorithmic analysis to sequence and assemble low copy and genic regions. Our approach enabled the assembly of all or nearly all genes and low copy regions. The syntenic relationship between wheat, B. distachyon and O. sativa, along with available genetic mapping data, has been used to produce annotated draft syntenic builds whereby the majority of genes have been placed in an approximate order and orientation. These annotated assemblies are maintained on a dedicated public GBrowse database. Our results suggest that the sequencing of isolated chromosome arms can provide valuable information of the gene content of wheat, and that these assemblies can be applied for the identification of candidate genes associated with genetically mapped traits as well as genome wide SNP discovery in this important crop.