Project Number: 3625-21220-004-42
Project Type: Specific Cooperative Agreement

Start Date: Aug 15, 2012
End Date: Sep 01, 2013

Objective:
Objectives are to develop and test statistically based graphics to visualize variation in genomic sequence relative to pedigrees, and identify haplotype blocks for the tracking of breeder 'signatures' in soybean pedigrees.

Approach:
The ability to analyze the genome using next-generation sequencing (NGS) data, provides the exciting opportunity to examine what gene sequences the breeders did actually select as the major yield advances occurred, and to identify the SNPs that are shared between these landmark lines. As a first step this new type of data will be checked for quality of the data using extensive data visualization tools. In the proposed work statisticians will collaborate with USDA to assess the data quality, and make initial suggestions about SNPS and haplotype blocks in a selection of major soybean lines. Statistical techniques using resampling and bootstrapping will be employed to evaluate reliability of the data, along with new developments in visualization methods. Most of the methods are available in the Bioconductor and R software, but as needs arise new tools will be developed that interface with existing technology.