Location: National Clonal Germplasm RepositoryTitle: A Coordinated Approach to Peach SNP Discovery in RosBREED Author
|Gilmore, Barbara - Barb|
Submitted to: International Horticultural Congress
Publication Type: Abstract Only
Publication Acceptance Date: 3/31/2010
Publication Date: N/A
Citation: N/A Interpretive Summary: Recently, a USDA-funded multi-institutional and trans-disciplinary project was started to study plant members of the Rose family. This project called RosBREED has brought scientists together from twelve institutions including the USDA-ARS. The objective of this project is to create the infrastructure needed for discovering and implementing the use of DNA-based tests in breeding crops such as peach, apple, cherry and strawberry. Breeders can use these tests for faster release of desirable fruit crops. RosBREED focuses on fruit quality traits. In peach, we are using new DNA sequencing technology to obtain DNA sequence or code information from about 60 peach genotypes coordinated between the U.S. and the Italian Consortium for Peach Genome Sequencing (DRUPOMICS project). We are using cutting edge data analysis techniques to discover the locations of single sequence differences in these peaches and develop a fast method to assay thousands of these differences in peach. The resulting peach resource will be valuable and available to the worldwide peach research community.
Technical Abstract: In the USDA-funded multi-institutional and trans-disciplinary project, “RosBREED”, crop-specific SNP genome scan platforms are being developed for peach, apple, strawberry, and cherry at a resolution of at least one polymorphic SNP marker every 5 cM in any random cross, for use in Pedigree-Based Analysis. RosBREED focuses on fruit quality traits. The majority of genes targeted for SNP development will be those shared among crops, and specific cases of synteny will be exploited to leverage ancestral relatedness within the Rosaceae family. In peach, we are re-sequencing genomic DNA from about 60 peach accessions coordinated between the U.S. and the Italian Consortium for Peach Genome Sequencing (DRUPOMICS project). These accessions were chosen for worldwide use in peach breeding and for diversity of genetic background, geographical origin, and phenotype. The peach genomic libraries are being sequenced with the Illumina Genome Analyzer IIx (GAIIx) at 3X coverage using paired-end reads (2x80bp) and indexed adaptors. The resulting peach SNP platform will be a valuable resource available to the worldwide peach research community.