A new computer app, known as the Pathway Association Studies Tool, allows users to build on the results of genome-wide association studies (GWAS) of crops. These GWAS take a bird's-eye look at a crop plant's genome for marker regions called single nucleotide polymorphisms (SNPs). Finding SNP markers near the gene or genes encoding a desired trait can flag the genomic whereabouts of those genes, and also help plant breeders follow the trait's inheritance and expression. This makes it easier to select plants that have the desired trait and develop new, elite varieties from them for producers.
However, GWAS's use of a statistical threshold means that only markers with the strongest gene associations are identified, noted Marilyn Warburton, a geneticist with Agriculture Research Service's Corn Host Plant Resistance Research Unit (CHPRRU) in Mississippi State. This can blind researchers to the presence of other gene markers that fall below the threshold, but are no less meaningful to their studies, she added.
PAST picks up the slack by taking an additional step known as metabolic pathway analysis. This added step doesn't just find interesting markers that GWAS misses; it also reveals important biological information about their associated genes and how each contributes to the biochemical assembly of a plant trait, function or response—regardless of the crop species.
Warburton's team published a paper describing PAST in the January 2020 issue of the journal Plants. About 900 users from around the world have downloaded the app so far, and Warburton hopes for even greater awareness of it following the March 12 release on the MaizeGDB website, a database with extensive genomics and genetics information about corn.
Warburton expects the app's ease of use and versatility could also buttress GWAS studies of animals and even humans, in which the identification of genes linked to inherited diseases can lead to personalized medicines to treat these diseases.