Plant & Animal Genomes XVIII Conference Plant & Animal Genomes XVIII ConferenceJanuary 9-13, 2010
Town & Country Convention Center
San Diego, CA
Zhi-Liang Hu , Rex Fernando , Dorian Garrick , James M. Reecy
High throughput SNP genotyping has empowered livestock researchers to perform genome wide association studies to discover genes responsible for complex traits or economically important quantitative traits. The analysis of large numbers of genotypes is not only a challenge for statistical data analysis but also presents a tedious job for users to interpret and comprehend the large number of statistics that are generated. A simple and fast approach is to plot the phenotypic association values of each SNP against their genome locations. The benefit of this is twofold: (1) certain genome locations may quickly draw attention if a lot of closely located SNPs are found to show higher degree of associations to traits. (2) It is feasible to locate candidate genes that might be causing the association when the genome plot is aligned with genomic features such as transcripts, genes, or mapped QTL. We have developed an interactive genome plotting tool for SNP association studies to achieve these goals. The software can plot any values associated with individual SNPs, such as estimates of their effects, with respect to their genome locations. The tool also enables dynamic link of each data point to GBrowse to visualize the SNP locations with respect to genome annotations such as known genes, curated QTL, etc. The program is being further developed to: (1) embed with Gensel software for Bayesian analyses of SNPs, accommodating flexible data columns and various manifest mappings within and across species; (2) build as a generic web application to serve any species and genetic markers.