Studies are underway to catalog genetic diversity in plants and animals and identify genetic variants predictive of economically important traits (e.g., yield, resistance to disease). The high-throughput DNA genotyping and sequencing technologies used in these studies produce large amounts of complex data. Agriculture geneticists are faced with numerous computational obstacles with storing, processing, and analyzing genetic and trait data. We introduce a web application for large-scale

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... re genetic diversity and association studies that aims to simplify and automate many of the data management and analysis tasks common across studies. We present a case study where our software is configured and populated with genome-wide data of over 750,000 genetic markers from the commercially available BovineHD array (Illumina Inc.). Our software is scalable to multiple species and applicable to a wide range of genotyping and sequencing technologies and study designs.