Wednesday, November 15, 2006 - 10:30 AM

Gene identification in soybean through microarray analysis.

Lila Vodkin, Gracia Zabala, Delkin Orlando Gonzalez, Anne Marie Boone, Matt Hunt, and Jigyasa Tuteja. University of Illinois, Department of Crop Sciences, Urbana, IL 61801

We demonstrate that soybean microarrays can be successfully used to examine isogenic lines that differ with respect to a mutant phenotype and thereby to define a small list of candidate genes potentially encoding or modulated by the mutant phenotype.  The microarrays that we have constructed contain over 36,000 cDNAs representing soybean ESTs (BMC Genomics 5:73, 2004).  We have also developed a set of 70-mer “long oligos” that represent 38,000 unigenes.  The cDNAs and oligos represent a wide array of developmental stages and physiological conditions of the soybean plant.

We used the soybean cDNA microarrays to identify candidate genes for a stable mutation at the Wp locus in soybean, which changed a purple-flowered phenotype to pink, and found that flavanone 3-hydroxylase cDNAs were over-expressed in purple flower buds relative to the pink.  RFLP analysis and RNA blots of purple and pink flower isolines, as well as the presence of a 5.7 kb transposon insertion in the wp mutant allele, have unequivocally shown that flavanone 3-hydroxylase gene 1 (F3H1) is the Wp locus. The 5.7 kb insertion in wp represents a novel type of transposable element (termed Tgm-Express1) that contains contains four truncated cellular genes from the soybean genome (Zabala and Vodkin, Plant Cell, 17, 2005).  Thus, the ability to acquire and transport host DNA segments is extended to the CACTA family of elements to which both Tgm and the prototypical maize Spm/En elements belong.

In addition, we have also examined several other mutant lines with the soybean microarrays, including those that affect morphological traits.  We find sequences that vary in the mutant phenotype in and that are also verified by RNA blots.  We are currently investigating whether any of these candidate cDNAs are the molecular basis of the mutant phenotypes.