DNA microarray-based discovery of molecular markers for the improvement of tomato color and nutritional quality

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Color is among the most important attributes of tomato for processing into whole and diced products.  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.  We show that lycopene and b-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.  The objectives of this project were to: (1) develop single nucleotide polymorphisms (SNPs) as molecular markers and (2) elucidate the genetic basis of YSD.  We hypothesized that a QTL mapping approach would identify loci that affect both color and color uniformity.  SNP discovery in breeding populations was 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 S. lycopersicum (Ohio 7814) and S. 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 99 S. lycopersicum 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.



Tomato color, Microarray, Molecular markers, Carotenoids, Yellow shoulder disorder