Quantifying and genetically mapping complex phenotypes in Mimulus hybrids

Hybrid novelty can arise from an interaction of two distinct genomes and plays a role in evolution and development of new phenotypes. Flowering plants such as the Mimulus genus act as good model systems for studying these genomic interactions, often producing unique, observable, and measurable phenotypic traits in hybrid populations. To understand some of the more spatially complex traits that are a result of hybridization, new tools are needed for quantifying petal pigmentation. In this study, we develop and test a streamlined method for analyzing complex phenotypes that can then be compared to genotypes for determining underlying genetic controls of observable traits. An F2 hybrid population of Mimulus luteus var. variegatus x Mimulus cupreus was used as an experimental platform. Multiple floral pigmentation traits, including anthocyanin proportion, carotenoid intensity, and spatial distribution of anthocyanin spots were analyzed using the method. Readily available imaging software, MATLAB scripts, Python, and high-throughput genomic sequencing were used to quantify the phenotypes and genotypes within the population. The genome wide association survey program called TASSEL was used to combine the phenotypic and genotypic data to genetically map the observable traits to regions of the genome. Our findings identify multiple regions of the genome that are strongly correlated to variation in specific quantified color patterning traits.