Project Number: 5442-21000-033-07
Project Type: Reimbursable

Start Date: Oct 01, 2006
End Date: Aug 31, 2009

Objective:
The specific objectives of ARS are to anchor physical BAC contigs to cytogenetic and genetic maps using molecular markers, assist in the annotation of BAC sequences, and to conduct comparative sequence analysis of 3A BACs with homoeologous regions of chromosome 3B. This work will contribute to the overall objectives of the project, which are to 1) generate an anchored physical map for the short arm of chromosome 3A of hexaploid wheat, 2) sequence portions of chromosome 3A to assess the efficiency of chromosome-specific libraries to sequence the wheat genome, 3) annotate these sequences to further our understanding of the wheat genome landscape/architecture, 4) perform comparative sequencing with homoeologous regions in 3B, and 5) develop bioinformatics tools for wheat genomics, genetics, and breeding.

Approach:
A BAC library specific for wheat chromosome arm 3AS will be fingerprinted and assembled into contigs. The contigs will be anchored to cytogenetic and genetic maps using a combination of available markers and markers developed from BAC end sequences (BES). A total of 18.4 Mb of sequence for chromosome 3AS will be obtained by sequencing 48 targeted BAC clones (5.8 Mb) to 8X sequence coverage and BAC end sequencing of 10,000 random clones (12.6 Mb). These sequences will be annotated for repeats and genes using a combination of automated and manual annotation and chromosome specific markers from the BES for physical and genetic mapping will be identified. Comparative sequence analysis of the 48 sequenced BAC clones from 3AS with corresponding homoeologous regions of 3BS sequenced by INRA, France, will be conducted to provide insights regarding microcolinearity and homoeologous genome evolution. The wheat genomic sequences will be annotating using a combination of automated and manual annotation.