ABSTRACT

PI: Esther van der Knaap (University of Georgia)

CoPIs: Ana Caicedo (University of Massachusetts); Denise Tieman (University of Florida); Lukas Mueller (Boyce Thompson Institute)

Collaborators: Joaquin Cañizares, Maria Jose Diez, Jose Blanca (Universitat Politecnica De Valencia); Sofia Visa, Dean Fraga, Simon Gray (College of Wooster)


A high quality tomato is expected to have good flavor, size, color and firmness. Years of selective breeding have produced the modern tomato, and yet the quality and production efficiency of the crop still needs improvement. Despite this need, desirable traits that will improve fruit quality are often hard to find, partly because the underlying factors that specify fruit traits are not fully known. Another impediment is that some beneficial traits were eliminated or hidden during breeding, thus reducing the available genetic diversity in modern tomato genomes. Project scientists have discovered an untapped resource to find new traits from wild tomato relatives and from ancestral populations growing in diverse geographic locations. These plants may appear undesirable by having small, seedy, soft or unpalatable fruits. However, these relatives are actually genetic gold mines: they hold within their DNA useful and untapped traits that were lost during tomato domestication. New technologies and genetic methods are now available to mine these wild tomato genomes for new suites of breeding traits. This project uses the selected wild populations to explore and capture quality traits associated with fruit weight, firmness, flavor and color. The project will identify the molecular basis of these fruit traits and will deliver new traits to improve the breeding potential of the modern tomato. The project provides interdisciplinary training in genomics, computational data analysis and breeding to all involved, including post-doctoral researchers and graduate students. Through summer workshops, high school and college students will be trained in tomato genomics and breeding, will interact directly with scientists, and will gain hands-on skills in research. These trained students will be critical additions to a workforce that advances agriculture through scientific discovery.

Wild relatives and semi-domesticated germplasm of cultivated plants provide a significant reservoir of genetic and epigenetic diversity for key regulators of agronomic traits. Future crop improvement relies on harnessing this diversity. However, mining semi-domesticated and wild germplasm for beneficial alleles of agriculturally important traits is not straightforward because fruit quality is quantitatively inherited. Consequently, visual inspection of unselected germplasm does not readily lead to the identification of accessions that have desirable characteristics to improve modern germplasm. The association of traits with genes controlling fruit quality and the identification of beneficial alleles that may have been lost during domestication should provide a model for studying how to efficiently mine germplasm of the closest wild relatives for quantitative trait loci leading to tangible crop improvement. To identify genes and pathways that control complex tomato fruit quality traits, this project will (1) assemble and phenotype a tomato population (Solanum spp.) constituting the continuum of wild, semi-domesticated and ancestral landraces; (2) identify loci underlying fruit quality traits through genome-wide association studies (GWAS) and differentially expressed small RNAs; (3) confirm genetically the traits associated with candidate regions to genes, and (4) analyze the developmental and biochemical pathways that control fruit quality. The project will result in genome sequence data for 150 tomato accessions, including 20 from the closest but fully wild relative of cultivated tomato, 110 from wild and semi-domesticated direct ancestors of domesticated tomatoes and 20 from the earliest landraces of cultivated tomatoes. In addition, the project will generate small RNA sequence data from different stages of tomato fruit development from a subset of this population, and will provide detailed fruit quality information about flavor, firmness, weight and palatability for each of the 150 accessions. The information will be available through a public resource, the Sol Genomic Network (SGN, http://www.sgn.cornell.edu/), and seeds of the accessions will be available from germplasm repository sites (TGRC, http://tgrc.ucdavis.edu/; and COMAV, http://www.comav.upv.es/).

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