Providing Functional Phenotypic Classifications for Comparison with Genotypic data: The Example of Anthocyanins in Potato Tubers

HUGO MARCELO ATENCIO; FERNANDO VILLARREAL; DIGILIO A; ARJEN TEN HAVE

Mar del Plata

Congreso; Noveno Congreso Argentino de Bioinformática y Biología Computacional; 2018

A2B2C

Background: Genotypification is a powerful method to determine the genetic profile of an organism and itsgenotypes in order to detect variations at the level of the DNA sequence. An important aspect usinggenotypification is to what it is compared. Comparison is often done by computational analysis of genotypesand phenotypes, preferably using binary data structures or quantitative data. Unfortunately, in manyagricultural or taxonomical studies, phenotypic characterizations are complex, based on historical aspects andthe result of subjective observations. To make more efficient use of phenotypic data, we need to adjusthistoric classification schemes to binary classifications. Here we present an example in which we want tostudy the presence of nutraceutical anthocyanins in potato tubers. The traditional characterization of potatotuber color includes four characters (primary and secondary color, intensity and distribution) with nineobservational states each. The color results from the sum of all colored metabolites of which the anthocyaninslikely form a major contribution.Objectives: To objectively evaluate the color of potato tubers and associated type of anthocyanin using imageanalysis in order to functionally classify potato landraces for phenotype/genotype comparison.Methods and Results: We set out to design a method for functional color classification using different Andeanpotato landraces (Solanum tuberosum subsp. andigena) present in the Active Germplasm Bank of the EEABalcarce ? INTA. The methodology for image analysis included correct setting of the photo camera andcalibration of colors of interest, here derived from a standard set of known anthocyanins and its parameters ofemission spectra in CIELAB color space. Since anthocyanin production is often, but not always, higher in skin,we compared measurements of skin and flesh, taking into account the likely presence of noise derived fromother compounds present in skin but not flesh. We first performed an analysis with eight landraces withdifferent anthocyanin content in order to tune the method. Finally, tuber?s phenotypic coloration will beassociated with the genotypic data using single nucleotide variations and microsatellites to study structuralgenes of the anthocyanin biosynthesis pathway.