My academic profile at OSU

PhD PROGRAM AT THE OHIO STATE UNIVERSITY
Tomato Breeding and Genetics; David Francis, P.I.

Research interests & endeavors
My research interests encompass plant breeding for quality traits and the implementation of molecular tools to improve the efficiency of trait-specific selection. My research project aims at understanding and elucidating the genetics of tomato color and color uniformity. It will be addressed by (i) verifying and applying single nucleotide polymorphism (SNP) discovered via microarray analysis, (ii) studying the genetic structure most efficient for color improvement, and (iii) understanding the effect of yellow shoulder disorder (a blotchy ripening disorder) on the nutritional quality of tomato, as defined by its carotenoid content.

Publications & Presentations
Darrigues, A., M.D. Robbins, W. Yang, and D.M. Francis. 200#. Dissecting variation in tomato fruit color quality through digital phenotyping. Plant Breeding. In preparation.

Darrigues, A., J. Hall, N. Dujmovic, S. Gray, E. van der Knaap, and D.M. Francis. 200#. Tomato Analyzer – Color Test: a new tool for efficient digital phenotyping. J. Am. Soc. Hort. Sci. Submitted.

Darrigues, A., S. Schwartz and D.M. Francis. 200#. Optimizing sampling of tomato fruit for carotenoid content with application to assessing the impact of ripening disorders. J. Agric. Food Sci. In revision.

Darrigues, A., A. Clivati-McIntyre, S. Schwartz and D.M. Francis. 2007. Increasing the carotenoid content of tomato by managing variety choice and soil fertility for color and color uniformity. Acta Horticulturae 744:323-328.

Darrigues, A, J Hall, N Dujmovic, S Gray, E van der Knaap, D M. Francis. 2007. Dissecting variation in tomato fruit color quality through digital phenotyping and SNP mapping. XV Plant and Animal Genome Conference, San Diego, California. Poster presentation.

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. YSD reduces lycopene and beta-carotene concentrations by 18% and 22%, respectively. We have implemented a color measurement module in the Tomato Analyzer software to accurately measure color uniformity from scanned images of fruit. This approach improves the efficiency of collecting data, provides high correlations with data collected by colorimeter, and improves estimates of genetic contributions to color uniformity. Variance partitioning suggests that YSD incidence and severity are affected by both genetics and environment. To elucidate the genetic basis of YSD, we are developing SNPs for application in inbred backcross breeding populations. We are using both analyses of large public EST databases and hybridization to oligonucleotide arrays for SNP discovery. We have found seven putative QTL associated with chroma (color intensity), five QTL for hue (color), and four QTL for color uniformity. The presence of QTLs with positive alleles from both S. lycopersicum and S. pimpinellifolium suggests the possibility of obtaining transgressive segregants with improved color. Directional selection strategies are being used to confirm these QTL and evaluate genetic correlations to other fruit quality traits, disease resistance, and yield.

Darrigues, A, W Yang, and D M Francis. 2006. DNA-microarray discovery of molecular markers for the improvement of tomato color and nutritional quality. Plant Molecular Biology & Biotechnology, OSU/OARDC, Wooster, Ohio. Invited speaker and poster presentation.

Darrigues, A, W. Yang, and D. Francis. 2005. DNA-microarray detection of molecular markers for improving color and nutritional quality in tomato. EUCARPIA Tomato Workshop, Bari, Italy. Invited speaker.

Color is among the most important attributes of tomato for processing into whole and diced products. Both color and color uniformity are greatly affected by Yellow Shoulder Disorder (YSD), a ripening disorder that results in discoloration of the proximal end tissues of the fruit. We show that lycopene and beta-carotene concentrations are reduced by 18% and 22%, respectively, in fruits affected by YSD. Variance partitioning suggests that YSD incidence and severity is affected by both genetics and environment. In order to elucidate the genetic basis of YSD, we are developing single nucleotide polymorphisms (SNPs) as molecular markers for application in three inbred backcross populations derived from either L. esculentum x L. esculentum or L. esculentum x L. pimpinellifolium crosses. SNP discovery for application in these populations is based on both analyses of large public EST databases and on hybridization to a custom oligonucleotide array. The array was hybridized with target cDNA from L. esculentum (Ohio 7814) and L. pimpinellifolium (LA1589). We developed algorithms to detect outliers and identified 1,296 potential SNPs. These putative SNPs are being verified by sequencing, screened for utility as markers on a collection of 92 L. esculentum lines and wild relatives, and applied to the genetic dissection of YSD. Implementing SNP-based marker technology has the potential to dramatically alter our approach to genetic characterization. Results and interpretation from this study will help bridge the gap between the goals of genetic and crop improvement research by facilitating the use of population structures that favor simultaneous genetic analysis and crop improvement.

Darrigues, A, A. Clivati-McIntyre, S. Schwartz, and D. Francis. 2005. Increasing the Carotenoid content of tomato by managing variety choice and soil fertility for color and color uniformity. FAV Health: International Symposium on Human Health Effects of Fruits and Vegetables, Quebec City, Quebec. Invited speaker.

The predominant carotenoids in tomato, beta-carotene and lycopene, provide health benefits. Beta-carotene is recognized as a nutrient due to pro-vitamin A activity and lycopene consumption has been correlated with a reduction in certain cancers. Despite the potential benefits, the processing industry does not place value on carotenoid content in contract fee structures or processor grades. Color, an indirect measurement of carotenoid content, and color uniformity are valued in the grading system. The quality of tomato, as defined by its grade, can be reduced by ripening disorders such as yellow should disorder (YSD) that affect the uniformity of fruit color. We show that lycopene and beta-carotene are reduced by 18% and 22%, respectively, in fruits affected by YSD. A survey of YSD incidence in the Midwest, USA, between 2001-2003 indicated that soils with lower Phosphorous (P) and lower available Potassium (K) are more prone to YSD. Currently 23% of the tomato processing fields in this region are at a higher risk of YSD due to soil fertility. Targeted application of K by drip irrigation and adequate soil nutrition have a positive impact on both yield, fruit color, and color uniformity. YSD also has a genetic cause. Best management practices to reduce the risk of YSD combine fertility management with varieties that are more resistant to the disorder. These approaches can be used to optimize the potential for health benefits due to higher carotenoid content and may be encouraged under current contract structures.