Population Structure and Association Mapping Of Fruit Traits and Capsicum Content In Capsicum annuum

Ninety six pepper (Capsicum annuum L.) accessions were sequenced to generate a set of 11,500 SNPs using the technique “Genotyping by Sequencing”. This data set was used to resolve population structure using STRUCTURE program with 100,000 MCMC replications with a burnin period of 50,000 using high performance computer. Structure harvester is used to identify ideal K based on deltaK distribution. Based on this we concluded that the annuum cultivars exist in 7 sub-structured populations. Tomato Analyzer (TA) is an automatic software program that was originally developed for measuring 37 different attributes related to two-dimensional shape tomato fruits. We used this software to characterize all the cultivars in study. Many of the attributes, such as angles at the distal and proximal ends of the fruit and areas of indentation, which are otherwise difficult to quantify manually were measured. Some of the attributes were Fruit Shape Index, blockiness, homogeneity, proximal fruit end shape, distal fruit end shape, asymmetry, internal eccentricity, latitudinal section and morphometrics. The ancestry results (q matrix) were used as covariates in the association test (MLM procedure with GAPIT software and SVS software of Golden helix). Results will be discussed.  Further these 96 cultivars were tested for metabolome diversity of compounds using LC-MS Q-TOF (High performance Liquid Chromatography couples with Quadruple Time of Flight mass spectrometer with MS/MS capability). The high mass accuracy allows exact mass measurements of small molecules such as phenolic acids, and of larger molecules such as polymeric proanthocyanidins. This system accurately identified compounds based on retention time, absorbance values, and molecular weight. Many of these compounds could be identified by comparing results with existing metabolomic databases such as MetAlign®. We have generated a metabolite profile using LC-MS Q-TOF that identified several hundred novel compounds which comprise a quite diverse metabolome profile. Detailed results, including co-location of markers significant for various metabolites will be presented.