The quest for molecular markers indicating root growth in microbially treated tomato (Solanum lycopersicum) plants.

Roots are essential plant organs for anchorage in soil, uptake of water with nutrients, storage of photosynthates, and microbial interactions. More knowledge on microorganisms stimulating root growth is needed to control root development of cultured plants. A marker-assisted approach would facilitate vast screenings of microbes for eventual effects on root development. It was aimed to select for transcripts that report on root growth stimulation at the early tomato plant growth stage upon microbial treatments. Microbially treated tomato (Solanum lycopersicum) plants were cultivated in stone wool slabs and screened for genes that increased or decreased in differential expression upon increased root growth, by RNAseq. Expression of 21 selected genes was measured by quantitative polymerase chain reaction (qPCR) in relation with stimulated root growth, recorded by X-ray microtomography, of microbially treated tomato plants cultivated in stone wool blocks. Two genes were identified of which expression significantly correlated with high measured root length, and for one also with high measured shoot wet and dry weight. The translated products, both involved in modulation of Rubisco activity, were a chloroplast-localized acetyltransferase (SlSNAT2) and a Rubisco activase (Rca). Transcripts whose translated products modulate Rubisco activity can serve as candidates for reporting on early root development upon microbial inoculation.