Development Of The Genetic Analysis Softwares OGAStation2.0and GMDR-GPU

Plant and animal breeding and human health care are two important domains concerned by genetics in real world. The important genetic issues concerned in plant and animal breeding are:the analysis of genetic components of complex traits, germplasm core collection, and mapping the chromosome intervals affecting complex traits, etc. While for human genetic research, besides the analysis of genetic components of complex traits, geneticists are facing more difficult problems. Because humen have huge genome, it is difficult to detect those loci associated with phenotype variation in genome.Aiming at the issues mentioned above, this paper developed two genetic analysis softwares, namely QGAStation2.0and GMDR-GPU. QGAStation2.0is developed for animal or plant breeders and a small number of human geneticists, it consists of five major modules and can analyze the data coming from diallel crosses, regional trials, germplasm core collections. QTL mapping and gene expression microarrays. All the modules except the fourth are based on mixed linear models. GMDR-GPU is developed mainly for genome-wide association studies (GWAS) in human genetics. It makes some minor improvements on the original GMDR gene interaction analysis algorithm, and parallelizes the GMDR algorithm with the many-core massive parallel computation technique brought by GPU. to make GMDR available for GWAS. We applied GMDR-GPU to the association analysis of a type2diabetes data publicly released by Wellcome Trust Case Control Consortium (WTCCC), and detect24core SNPs and6genes which are likely to be associated with type2diabetes.