Dissecting variation in tomato fruit color quality through digital phenotyping and genetic mapping

by Darrigues, Audrey.

Color is among the most important attributes of tomatoes for processing. Both color and color uniformity are affected by yellow shoulder disorder (YSD), a ripening disorder that results in discoloration of the proximal end tissues of the fruit. Cells from YSD tissue are smaller and more randomly organized, and the development of the chromoplast is altered. We show juice from YSD-affected tomato had 13-24% significantly less lycopene relative to juice from non-affected tomato. Beta-carotene content was reduced by 4-8% in juice from YSD-affected tomato, although this reduction was not statistically significant. Quantification of lycopene and betacarotene concentration in tomato juice samples was more precise by increasing biological replications rather than analytical replications. Variance partitioning suggests that YSD incidence and severity are affected by both genetics and environment. In order to assess genetic contributions to YSD, a color measurement module in the Tomato Analyzer software was tested to accurately quantify color and color uniformity from digital images. This approach improved the efficiency of collecting data, provided high correlations with data collected by colorimeter, and improved estimates of genetic contributions to color uniformity. We hypothesize that with increased precision and accuracy in measuring color, sampling strategies ii for higher carotenoid content can be optimized and the genetic control underlying color and color uniformity in tomato can be uncovered. To elucidate the genetic basis of YSD, molecular markers were exploited for application in breeding populations. An advanced backcross population (BC2) derived from Solanum lycopersicum (OH88119) x S. pimpinellifolium (PI128216) was evaluated for color (L*, a*, b*, hue and chroma) and color uniformity (%YSD and %RED). Indices were developed to circumvent the highly correlated traits and to simplify the trait complexity based on principal component analysis. These indices capture the essential features of color intensity and color uniformity. The BC2 population was genotyped with 70 polymorphic markers for marker-trait analysis. The population was selfed through four generations to generate an inbred backcross population (BC2S4), which was evaluated for the same traits and genotyped with the same markers as the BC2 population. An F2 population and elite processing varieties were evaluated for color as confirmation of the marker-trait associations. We found QTL for color intensity on chromosomes 2, 8, and 9, and a QTL for color uniformity on chromosome 6. Positive gain under selection was realized for selection by phenotype and by marker-assisted selection (MAS). Higher gains were realized from MAS. Directional selection strategies are being used to further characterize these QTL and evaluate genetic correlations to other fruit quality traits, disease resistance, and yield. iii À ma famille. À la mémoire de Papa… iv