Genome Wide Association (GWAS) Mapping of Trichome Density and Length in Watermelon

We have developed an association mapping population consisting 170 red-flesh watermelon cultivars representing wide spread geographical area across the world.  Genotyping by sequencing technique facilitated to identify 11,000 SNPs with 0.05 minor allele frequency with the call rate of >85%.  We have grown the entire set of these cultivars in three biological replications in greenhouse condition. Pedicels of second leaf from 30-day old seedlings were removed and pictures of them were taken under Leica Z16APO motorized microscope. Finally, trichome length was measured for 15 longest trichomes using imageJ software and trichome density was counted using Trichomenet software in 5mm length. The data of both the traits segregated in normal distribution indicating presence of poly genes controlling these traits. The range of trichome length and density was 0.490-1.505mm and 20-120/cm length, respectively. We performed GWAS using a single-locus mixed linear model developed with the EMMAX method and implemented in SVS v8.1.5. We used a PCA matrix (first 2 vectors) and the IBD matrix to correct for population stratification. Manhattan plots for associated SNPs were visualized by use of GenomeBrowse v1.0 (Golden Helix, Inc). The SNP P-values from GWAS underwent sequential Bonferroni correction as well as false discovery rate (FDR) analysis. Using this method, we identified few genes such as SCL1 (SCARECROW-LIKE 1), C3HC4-type RING finger, AGO1 (ARGONAUTE 1), etc. for trichome density, and group II intron splicing factor CRS1, PHD finger protein, Zinc finger (GATA type), etc. for trichome length.  All these genes have SNPs in the exons. Details will be presented.