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

Li ZY, Wang N, Dong L, Bai H, Quan JZ, Liu L, Dong ZP - PLoS ONE (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of plant protect, Millet Institute, Hebei Academy of Agricultural and Forestry Sciences, National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Shijiazhuang, China.

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.

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Venn diagram showing all of the DEGs.
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pone.0123825.g002: Venn diagram showing all of the DEGs.

Mentions: To specifically identify genes related to rust inoculation in foxtail millet, the DEGs between two samples were identified. Comparison of DEGs in Shilixiang at 24 h after inoculation with rust versus Shilixiang inoculated with rust 0 h showed that 4542 genes differed significantly (FDR < 0.001, /log2 ratio/⩾1) between the two samples. Among them, 3442 genes were up-regulated and 1100 genes were down-regulated. Between Shilixiang at 48 h after inoculation with rust and Shilixiang inoculated with rust 0 h, a total of 5112 DEGs were detected, including both up-regulated (3941) and down-regulated genes (1171). We identified 968 genes that were expressed differently at 48 h post-inoculation compared to after only 24 h. Of those, 518 were up-regulated and 450 were down-regulated. A Venn diagram illustrating all of the DEGs is shown in Fig 2. A total of 267 genes were common to the 3 comparison groups, indicating that these genes are in a constant process of change. DEGs were also located on the chromosomes of foxtail millet, and physical maps were constructed; 5090 DEGs at 48 h post-inoculation were mapped to the nine chromosomes of foxtail millet (Fig 3). Among them, chromosome 9 had the most DEGs (961), followed by chromosome 5 (778), while chromosome 8 had the fewest (219; Table 1).


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

Li ZY, Wang N, Dong L, Bai H, Quan JZ, Liu L, Dong ZP - PLoS ONE (2015)

Venn diagram showing all of the DEGs.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4401669&req=5

pone.0123825.g002: Venn diagram showing all of the DEGs.
Mentions: To specifically identify genes related to rust inoculation in foxtail millet, the DEGs between two samples were identified. Comparison of DEGs in Shilixiang at 24 h after inoculation with rust versus Shilixiang inoculated with rust 0 h showed that 4542 genes differed significantly (FDR < 0.001, /log2 ratio/⩾1) between the two samples. Among them, 3442 genes were up-regulated and 1100 genes were down-regulated. Between Shilixiang at 48 h after inoculation with rust and Shilixiang inoculated with rust 0 h, a total of 5112 DEGs were detected, including both up-regulated (3941) and down-regulated genes (1171). We identified 968 genes that were expressed differently at 48 h post-inoculation compared to after only 24 h. Of those, 518 were up-regulated and 450 were down-regulated. A Venn diagram illustrating all of the DEGs is shown in Fig 2. A total of 267 genes were common to the 3 comparison groups, indicating that these genes are in a constant process of change. DEGs were also located on the chromosomes of foxtail millet, and physical maps were constructed; 5090 DEGs at 48 h post-inoculation were mapped to the nine chromosomes of foxtail millet (Fig 3). Among them, chromosome 9 had the most DEGs (961), followed by chromosome 5 (778), while chromosome 8 had the fewest (219; Table 1).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of plant protect, Millet Institute, Hebei Academy of Agricultural and Forestry Sciences, National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Shijiazhuang, China.

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.

Show MeSH
Related in: MedlinePlus