Gene expression profiling of two related maize inbred lines with contrasting root-lodging traits

To assist breeding for increased resistance to root lodging in maize, an attempt was made to identify genes that are associated with root lodging by profiling mRNA expression from two inbreds with contrasting root-related traits. These two inbreds were derived from a common F(2) pool, selfed for several generations and showed 75% relatedness based on 106 genetic markers. Under field conditions, the two inbreds exhibited significant differences in root morphology and resistance to root lodging. Whole root tissue was collected at two developmental stages from inbred 100 and 101 grown in 2 years. RNA was isolated from both the V8 and V12 stages, a few weeks prior to flowering. The RNA samples from the 1997 growing season were analysed by GeneCalling analysis, an open-ended mRNA profiling method. From over 13 500 cDNA fragments detected from each of the V8- and V12-stage samples, 229 and 325 cDNA fragments, respectively, showed greater than 2-fold differences between the two inbred lines. A total of 69 cDNA fragments that showed 2-fold or greater differences for both inbred lines were observed at both developmental stages. The gene identity and expression differences of several cDNA fragments were determined and confirmed by RNA gel blot analysis. Two genes out of five identified were homologous to a cytochrome P450 and the impedance-induced protein, both showing high levels of expression in the roots of lodging resistant lines and low levels in the sensitive lines. These data provide the first clues of genes expressed in the roots during the formative stages of root development associated with root-lodging resistance.