Abstract
Recent advances in RNA profiling offer an opportunity to establish functional links between genotype and phenotype for complex traits such as SCMV resistance. The change of RNA profiles was monitored on a macroarray containing SSH (suppression subtractive hybridization) clones. The number of differentially expressed genes (SCMV infected vs. non-infected) in individual lines was 177, 163, 165, 62, 47, 37, and 93, for FAP1360A, D21, D32, Pa405, F7, D145, and D408, respectively. All inbreds were divided into two groups by hierarchical cluster analysis: D32, D21, FAP1360A and D408 formed one; Pa405, D145, and F7 another group. Due to the genetic structure among the seven inbreds, genetic background and resistance response are confounded. With or without the resistant U.S. inbred line Pa405, 22 and 112 genes were identified by t tests between resistant (D21, D32, and FAP1360A) and susceptible (D145, D408, and F7) inbred lines, respectively. The 112 candidate genes were divided into three clusters by K-means clustering and analyzed in more detail, e.g., five genes were in silico mapped surrounding Scmv2 QTLs. These candidate genes provide a better understanding of signal transduction pathway for SCMV resistance and have the potential to develop functional markers to distinguish resistant and susceptible genotypes.
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