Differential gene expression in foxtail millet during incompatible interaction with Uromyces setariae-italicae

Abstract

Foxtail millet (Setaria italica) is an important food and fodder grain crop that is grown for human consumption. Production of this species is affected by several plant diseases, such as rust. The cultivar Shilixiang has been identified as resistant to the foxtail millet rust pathogen, Uromyces setariae-italicae. In order to identify signaling pathways and genes related to the plant's defense mechanisms against rust, the Shilixiang cultivar was used to construct a digital gene expression (DGE) library during the interaction of foxtail millet with U. setariae-italicae. In this study, we determined the most abundant differentially expressed signaling pathways of up-regulated genes in foxtail millet and identified significantly up-regulated genes. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) analysis was used to analyze the expression of nine selected genes, and the patterns observed agreed well with DGE analysis. Expression levels of the genes were also compared between a resistant cultivar Shilixiang and a susceptible cultivar Yugu-1, and the result indicated that expression level of Shilixiang is higher than that of Yugu-1. This study reveals the relatively comprehensive mechanisms of rust-responsive transcription in foxtail millet.

Fig 1. Distribution of total clean tags and distinct clean tags in each sample.

The numbers in square brackets indicate the range of copy numbers of each tag category. The data in parentheses indicate the percentage of corresponding tags among the total clean tags and distinct clean tags. (A) Distribution of total clean tags. (B) Distribution of distinct clean tags.

Fig 2. Venn diagram showing all of the DEGs.

Fig 3. A physical map of foxtail millet 48h post-inoculation based on 5090 DEGs.

Red lines represent up-regulated genes and green lines represent down-regulated genes.

Fig 4. Change in gene expression of the plant-pathogen interaction pathway in foxtail millet 48h post-inoculation.

Genes that up-regulated are marked with red borders while Genes that down-regulated are marked with green borders. Genes that did not change are marked with black borders.

Fig 5. Change in gene expression of the phenylpropanoid biosynthesis pathway in foxtail millet 48h post-inoculation.

Genes that up-regulated are marked with red borders while Genes that down-regulated are marked with green borders. Genes that did not change are marked with black borders.

Fig 6. Quantitative RT-PCR validation of DGE analysis.

TPM, transcription per million mapped reads. Relative quantification was carried out to measure changes in target gene expression in foxtail millet leaf samples relative to an endogenous reference gene; 18S rRNA was used as a reference gene. The X axis indicates the inoculation time. The Y axis indicates the fold change of target gene in qRT-PCR and TPM in DGE analysis. Bars represent standard errors of the means.

Fig 7. Gene expression level comparison between resistant cultivar Shilixiang and susceptible cultivar Yugu 1.

The X axis indicates the inoculation time. The Y axis indicates the fold change of target gene in qRT-PCR. SLX represent resistant cultivar Shilixiang and YG-1 represent susceptible cultivar Yugu 1. Bars represent standard errors of the means.