Open Access
Ashrafi Nasrabadi, Hamid
Graduate Program:
Doctor of Philosophy
Document Type:
Date of Defense:
June 25, 2007
Committee Members:
  • Mark Guiltinan, Committee Chair
  • David Robert Huff, Committee Member
  • Seogchan Kang, Committee Member
  • David M Braun, Committee Member
  • Majid R Foolad, Committee Member
  • Genetic map
  • DNA markers
  • ESTs
  • Candidate resistance genes
  • QTL mapping
  • Early Blight
Early blight (EB) resistance and high fruit quality are among the most important and challenging characteristics in tomato breeding. This is due to complexity of these traits, which are also influenced by pleiotrophic and confounding effects of other characteristics. These challenges have undermined breeding efforts to improve tomatoes with genetic resistance to EB and higher fruit quality at the same time. The confounding and pleiotrophic effects of these traits with other horticulturally important traits can be detected by application of molecular breeding tools, such as genetic linkage maps, graphical genotyping, statistics and biometrical procedures and QTL analysis. The objectives of the current thesis research were to find the relationships and to identify QTLs for EB resistance and fruit quality traits. A Lycopersicon pimpinellifolium accession (PSLP125) was determined to be resistant to EB with exceptionally high lycopene and soluble solid content. In order to exploit the genetic recourses of this accession in breeding cultivated tomato, an F2:7 derived RIL population (n=172) of L. esculentum  L. pimpinellifolium cross was developed. The population was evaluated for EB resistance under field conditions and for fruit quality characteristics in the field and laboratory for three years and generations (2004-F7, 2005-F8 and 2006-F9). A genetic linkage map was constructed based on 275 RFLP, ESTs (mainly candidate resistant genes), CAPS and SSR markers to perform QTL analysis. The map spanned 1061 cM of the tomato genome with an average of 3.8 cM between markers. Skewed segregation was observed for ~29.5% of the markers on all chromosomes except chromosomes 11 and 12. The average heterozygosity in the population was 6.8%, which was 4.7 times greater than what was expected (1.5%) for a RIL population at F7 generation. In order to identify QTLs for EB resistance, the population was evaluated for EB resistance for three years in the field. Simple, composite and multiple interval mapping procedures were employed and QTL analysis was carried out. In total 10 QTLs (LOD ≥ 2.4, P ≤ 0.001) for resistance to EB were identified with individual effects ranging from 3.0% to 16%. Two QTLs on chromosomes 5 and 6 were highly consistent across the years/generations. Co-localizations of QTLs with several candidate genes such as Mi-1, ethylene response factor-5, lipoxygenase B, wound-induced protein-1 were observed, suggesting potential involvement of these genes in EB resistance. Thus, it is speculated that the candidate-gene approach is an effective way of identifying and mapping new disease resistance genes in tomato. The RIL population was also evaluated for three years in the field and laboratory for four fruit quality characteristics, including Fruit Weight (FW), Soluble Solids Concentration (SSC), pH and colorimetric parameters of purée. QTL analysis was employed to identify the QTLs for these fruit quality related traits. Several QTLs for FW on chromosomes 1, 2, 3, 4, 7 and 11, pH on chromosomes 1, 2, 6, 8, 10 and 12, SSC on chromosomes 1, 3, 6, 8, 9 and 10 lycopene on chromosomes 2, 4, 7, 11 and 12 were identified. The QTL analysis of lycopene using HPLC, spectrophotometer, statistical model derived data in previous generationsand fruit color evolutions in the field, led to the identification of two major QTLs for lycopene on tomato chromosomes 7 and 12 and three minor QTLs on chromosomes 2, 4, and 11. Because of the consistency of the QTLs on chromosomes 7 and 12, they seem to be promising for developing QTL-NILs, as well as for improving tomato lycopene content by marker-assisted breeding. In addition to QTL analysis, in 2006 (F9), HPLC and spectrophotometric assays were employed to measure the amount of lycopene in a sample (n=127) of RILs. The results indicate that the spectrophotometric assay preserves the accuracy of the measurement using HPLC but eliminates the cost and degradation issues inherent with HPLC-based assays. Lycopene estimates obtained from this assay were highly correlated (r = 0.94) with estimates obtained from the HPLC method, suggesting the utility of this method as a substitute for HPLC assay. Furthermore, based on the HPLC assay a simple regression model was developed to estimate the amount of lycopene in previous generations/years using colorimetric values as independent variables.