A Newly Developed Software of GWAS for Mapping Quantitative Trait SNP (QTS) and Quantitative Trait Transcript (QTT) with 2D and 3D Epistasis and GE Interaction

With recent advances in molecular genotyping and high-throughput technology, great opportunity is provided for dissecting genetic architecture of complex traits. A new software QTLNetwork V3.0 has been developed by using mixed linear model approaches for GWAS. It can be used for mapping quantitative trait SNP (QTS), and quantitative trait transcript (QTT). Epistasis for two genes and three genes, as well as gene-environment interaction can also be estimated. GPU computation technology has been applied for dramatically increasing computing speed. This software can be use for Windows, Mac, and Linux systems. Demonstrations will be presented for mapping QTS and QTT of complex traits in crops, mice, and also human.