Molecular Breeding

, Volume 30, Issue 1, pp 549–567 | Cite as

Identification of novel quantitative trait loci for increased lycopene content and other fruit quality traits in a tomato recombinant inbred line population

  • Hamid Ashrafi
  • Matthew P. Kinkade
  • Heather L. Merk
  • Majid R. Foolad


Epidemiological and clinical studies indicate that a steady dietary intake of bioavailable lycopene, a C40 carotenoid and potent natural antioxidant, may be associated with a decreased incidence of prostate cancer in humans. Since fresh tomatoes and processed tomato products represent approximately 85% of the average human’s dietary lycopene intake, the identification of novel genetic factors which regulate high fruit lycopene content in tomato is imperative for the improvement of nutritional quality in this commercially valuable specialty crop. To understand the genetic control of the extraordinarily high fruit lycopene content in an accession (LA2093) of the tomato wild species Solanum pimpinellifolium, a quantitative trait locus (QTL) mapping study was conducted using a recombinant inbred line (RIL) population of a cross between LA2093 and a cultivated tomato (S. lycopersicum) breeding line, NCEBR-1. The parental lines, F1 progeny, and F7-F10 RIL populations were grown in replicated field trials in four successive years and evaluated for lycopene content as well as several other traits, including fruit fresh weight, soluble solids content, pH of puree, and plant maturity. The lycopene content of ripe fruit was estimated using three methods: high-performance liquid chromatography (HPLC), spectrophotometry, and colorimetric assays. Based on these measurements, QTL were identified and compared across generations. Among the QTL identified for lycopene, two QTL, located on chromosomes 7 and 12, had very large effects and were consistent across generations. The genomic intervals in which these two QTL reside do not correspond to known map positions of carotenoid biosynthetic genes, indicating that these QTL may represent novel alleles with potentially important implications for tomato breeding as well as increased understanding of carotenoid accumulation in tomato. Several QTL were also identified for fruit weight, soluble solids content and plant maturity. The potential implications of these results for tomato crop improvement are discussed.


Carotenoids Molecular markers QTL mapping Recombinant inbred lines Solanum lycopersicum Solanum pimpinellifolium 



This research was supported in part by Agricultural Research Funds administered by the Pennsylvania Department of Agriculture, the Pennsylvania Vegetable Marketing and Research Program, and the College of Agricultural Sciences at the Pennsylvania State University. The authors graciously thank Dr. Randolph Gardner for providing seed of breeding line NCEBR-1, and all Penn State staff and undergraduates who helped with field experiments and data collection.


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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Hamid Ashrafi
    • 1
    • 2
    • 4
  • Matthew P. Kinkade
    • 1
    • 3
    • 5
  • Heather L. Merk
    • 1
    • 2
    • 6
  • Majid R. Foolad
    • 1
    • 2
    • 3
  1. 1.Department of HorticultureThe Pennsylvania State UniversityUniversity ParkUSA
  2. 2.The Intercollege Graduate Degree Program in GeneticsThe Pennsylvania State UniversityUniversity ParkUSA
  3. 3.The Intercollege Graduate Degree Program in Plant BiologyThe Pennsylvania State UniversityUniversity ParkUSA
  4. 4.Department of Plant Sciences, Seed Biotechnology CenterUniversity of CaliforniaDavisUSA
  5. 5.Campbell Soup Company, Vegetable R&D—Campbell’s SeedsDavisUSA
  6. 6.Department of Horticulture and Crop Science, OARDCOhio State UniversityWoosterUSA

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