Project Number: 6618-21000-013-07
Project Type: Nonfunded Cooperative Agreement

Start Date: Apr 11, 2006
End Date: Jan 01, 2011

Objective:
The objective of this cooperative research project is to probe the citrus sinensis BAC library to identify specific clones containing heterozygous SSR markers. Clones containing each SSR allele will be sequenced by JGI and assembled to determine the difficulty of assembling sequence in known heterozygous regions of the sweet orange genome.

Approach:
Libraries of BAC clones, which are arranged in a manner to allow high-density filter production and high-confidence recovery of targeted clones, will be provided by USDA. Filters will be hybridized with oligo probes designed to identify clones containing specific SSR markers that are heterozygous in sweet orange. Oligo probes were designed from known DNA sequence for several SSR markers developed from genomic DNA sequence data using software described essentially by Zheng et al. (2004, Bioinformatics 20:2101-2112). Labeled oligo probes will be hybridized to library filters and clones identified as containing the SSR-flanking sequence will be selected for further analysis. DNA of these clones will be genotyped for the targeted SSR marker and several clones containing each allele will then be selected for sequencing.