Date of Award
Master of Science
Randy C Shoemaker
Silvia R Cianzio
Iron plays a significant role in numerous cellular functions. Improved uptake and efficiency of use can have strong positive effects on the health of plants, animals and humans. Major players in iron homeostasis are the Iron-Regulated Transporters (IRT). The purpose of this research is to identify putative Iron-Regulated Transporter genes in soybean, structurally characterize these genes and examine their relational phylogeny. Additionally, gene sequence data and gene expression patterns will be considered to differentiate each gene's potential role in iron homeostasis of soybean. In this study, we identified fourteen soybean gene models with significant predicted protein similarity to A. thaliana IRT genes by comparing translated amino acid sequences from nucleotide sequences. Two gene models are most similar to AtIRT1/AtIRT2, while a third protein sequence is most similar to AtIRT3. Predicted protein similarity between soybean IRT1-like genes and those in four other plant species was also determined. The gene models with the best soybean- A. thaliana similarity to IRT1 were also the best matches in these species. Examination of genomic regions in which the genes reside revealed that ten of the fourteen gene models are found in five homoeologous syntenic regions indicative of large-scale genome duplication events. The fourteen IRT1-like gene models were aligned using ClustalW2 (Thompson et al., 1994). Upon alignment, we identified four gene models with point mutation at the 103rd residue, which suggests they lack zinc transport function. Two sets of RNASeq data from iron replete Glycine max plants at various growth stages and plant tissues were examined to evaluate the fourteen gene models. Two of the three gene models with the highest root transcript accumulation also have the highest sequence similarity to AtIRT1 and AtIRT3, respectively. One of the gene models is most analogous to AtIRT1 in that it has the highest sequence similarity and minimal root transcript accumulation under iron-sufficient conditions. In lieu of iron-deficient transcript accumulation data, one could reasonably conclude that that gene model is the IRT1 ortholog in soybean. The ensemble of these data provides a comprehensive view of the IRT gene family in the soybean genome.
Stribe, Dan, "Analysis of iron transporters in the soybean (Glycine max (L.) Merr.) genome" (2012). Graduate Theses and Dissertations. 12478.