Identification of gene expression markers associated with late blight resistance in tomato using gene expression profiling of a segregating F2 population

Open Access
Lin, Xin
Graduate Program:
Plant Biology
Master of Science
Document Type:
Master Thesis
Date of Defense:
Committee Members:
  • Timothy W Mcnellis, Thesis Advisor
  • Trait Associated Gene Expression Markers
  • Tomato Late Blight Resistance
Transcript profiling using DNA microarray was applied to 48 F2 tomato plants in which resistance to late blight disease caused by Phytophthora infestans segregates. The DNA microarray was designed using the publicly available cDNA library of Solanum lycopersicum and contains probes for 26,981 transcripts out of the total of 33,840 transcripts in the library. A group of 180 F2 tomato plants, derived from a cross between FL8059 (late blight susceptible fresh market tomato Solanum lycopersicum) and PSLP151 (late blight resistant accession of wild type tomato Solanum pimpinellifolium), were evaluated for resistance to late blight by inoculation with P. infestans (US-13) in the greenhouse. Prior to inoculation, healthy leaf tissues were collected from all of the F2 plants. The 24 most resistant and 24 most susceptible F2 plants were selected for RNA extraction and microarray hybridization. Genes that were differentially expressed between the two pools of resistant and susceptible F2 plants were defined as trait associated gene expression markers (TAGEMs) and identified by differential expression analysis of the microarray data. Of the 26,981 transcripts probed on the arrays, 269 were identified as TAGEMs associated with the inheritance of late blight resistance. The 269 transcripts were mapped on the tomato genome based on the published tomato genome sequence. Clusters of the transcripts on specific locations of the chromosomes were found on 11 of 12 tomato chromosomes. The clustered TAGEMs had a combination of positive and negative associations with late blight resistance. No obvious patterns of functions of the TAGEMs were found based on the annotations. However, a few disease resistance-associated genes were identified among the TAGEMs. The TAGEM clustering regions identified in this study can be targeted for genetic marker identification to support tomato late blight resistance QTL mapping in this segregating population. The discovery of multiple TAGEM clusters indicates that this late blight resistance is probably controlled by more than one single QTL locus. Some of the TAGEM clusters might represent minor QTLs that play a role in late blight resistance.