Agrobacterium-Mediated Transformation of Tomato Elicits Unexpected Flower Phenotypes with Similar Gene Expression Profiles

Background Genetic transformation mediated by Agrobacterium tumefaciens is known to cause unexpected phenotypes. Mutations of a specific set of homeotic genes can result in alterred floral structure. Methodology/Principal Findings Previously we identified two genes ( LeTGA1 and SOLly GLB1 ) induced by nutrient availability in tomato. To further elucidate their function, we sought to knock out the genes using antisense RNAi. When antisense constructs for the two different tomato genes were each transformed into Micro-Tina tomato plants, one primary transformant with similar mutant flower phenotypes was identified from transformation of each construct. Microarray analysis shows that a similar set of genes were up- or downregulated in both mutants. Sequencing of insertion sites indicates that each is inserted into a repetitive region which could impact expression of affected genes but direct alteration of floral homeotic gene sequences was not detected. Conclusion This is the first report that dominant flower mutations could be caused by genetic transformation designed to knock out two nutrient stress related genes.