1. DArT Markers for Cucurbita Phylogenies and Association Mapping

We used 1200 genome wide DArT markers on 233 accessions belonging to all the representative Cucurbita species and resolved genetic and evolutionary relationships among various species. Based on Delta K across the clusters (estimated using the program STRUCTURE 2.3.2), we noted that the Cucurbita spp. collections in our study have 8 (K-8) sub-clusters. We performed association mapping using General Linear Model (GLM) and Mixed Linear Model (MLM) with shared ancestry (Q-matrix) for both GLM and MLM and Kinship for MLM alone) using both sets of data (mapped and unmapped) across the two growing seasons (2010 and 2011) using the program TASSEL 3.0. We used 75 FW (fruit weight) markers and 89 SS (soluble solids) markers separately to analyze LD (Linkage Disequilibrium) in whole Cucurbita genome and separately in various species. We undertook combined approaches of model based association mapping with population genetics to identify distribution of FW and SS markers and their pattern selection and role in evolution of various species. Our LD study showed that the blocks of markers (red) distribution is quite varied from species to species and some species have more blocks (red spots on top edge) when compared to the other species. For example, C. pepo was with fewer alleles for FW and SS than the other species. C. argyrosperma and C. moschata indicated a shared ancestry for both fruit weight and soluble solids. C. maxima contained alleles for FW and SS that are completely unshared indicating that this species belong to different lineage than the others. More detailed linkage of markers with various traits will be presented.