Identification by suppression subtractive hybridization of genes that are differentially expressed between near-isogenic maize lines in association with sugarcane mosaic virus resistance.

The molecular mechanisms underlying the development and progression of sugarcane mosaic virus (SCMV) infection in maize are poorly understood. A study of differential expression was conducted to identify genes involved in resistance to SCMV. In this study, we combined suppression subtractive hybridization and macroarray hybridization to identify genes that are differently expressed in the near isogenic lines F7+ (SCMV resistant) and F7 (susceptible). Altogether, 302 differentially expressed genes were identified in four comparisons based on constitutively expressed and inducible genes, and on compatible and incompatible plant-virus interactions. Apart from genes related to metabolism, most of the functionally classified genes identified belonged to three pathogenesis-related categories: cell rescue, defense, cell death and ageing, signal transduction, and transcription. The latter three groups accounted for 56-66% of the genes classified. Some 19% (60 of 302) of the identified genes had previously been assigned to 29 bins distributed over all ten maize chromosomes. Among the mapped genes, 31% (18 of 58) were located within the Scmv2 and Scmv1 regions on chromosomes 3 and 6, respectively, which have been associated with resistance to SCMV. Promising candidate genes for Scmv1 have been identified, such as AA661457 (receptor-like kinase Xa21-binding protein 3). The implications of the genomic distribution of differentially expressed genes identified by this isogenic comparison are discussed in the context of breeding for resistance.