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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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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.
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pone.0123825.g001: 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.

Mentions: Solexa/Illumina DGE analysis was performed to obtain a global view of the foxtail millet transcriptome after plants were inoculated with rust. Three Shilixiang millet DGE libraries were sequenced: at 0 h after inoculation with rust (SRX659703), at 24 h after inoculation (SRX659704), and at 48 h after inoculation (SRX659705)—this generated approximately three million raw tags in each library. After removing the low quality tags, the total number of clean tags for each of the three libraries ranged from 3.2 to 3.3 million and the number of tag entities with unique nucleotide sequences ranged from 80,668 to 105,050 (S2 Table). A foxtail millet Shilixiang leaf transcriptome reference gene database that included 32538 sequences (SRX800775, GBYO00000000) was preprocessed for tag mapping. Genes with a CATG site accounted for 82.88% of sequences. To obtain the reference tags, all the CATG+17 tags in the gene were taken as gene reference tags. Finally, 113,479 total reference tag sequences with 113,084 unambiguous reference tags were obtained. Among the clean tags, the number of sequences that could be mapped to unigenes ranged from 2.02 to 2.08 million, and the percentage of these clean tags ranged from 60.30 to 62.50% among the three libraries (S2 Table). To evaluate the DGE data, the distribution of the expression of clean tags were analyzed (Fig 1). The distribution of total clean tags and distinct clean tags across different tag abundance categories showed similar patterns for all three DGE libraries. In each library, the highly expressed tags dominated the total clean tags, but their distributions of distinct clean tags were small. In contrast, tags with a low level of expression among the total clean tags represented the majority of distinct clean tags. Results suggested that sequencing quality was high enough to enable the following analyses. Deep sequencing of foxtail millet during its interaction with U. setariae-italicae could facilitate the identification of signaling pathways and genes related to millet defense against rust.


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)

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.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4401669&req=5

pone.0123825.g001: 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.
Mentions: Solexa/Illumina DGE analysis was performed to obtain a global view of the foxtail millet transcriptome after plants were inoculated with rust. Three Shilixiang millet DGE libraries were sequenced: at 0 h after inoculation with rust (SRX659703), at 24 h after inoculation (SRX659704), and at 48 h after inoculation (SRX659705)—this generated approximately three million raw tags in each library. After removing the low quality tags, the total number of clean tags for each of the three libraries ranged from 3.2 to 3.3 million and the number of tag entities with unique nucleotide sequences ranged from 80,668 to 105,050 (S2 Table). A foxtail millet Shilixiang leaf transcriptome reference gene database that included 32538 sequences (SRX800775, GBYO00000000) was preprocessed for tag mapping. Genes with a CATG site accounted for 82.88% of sequences. To obtain the reference tags, all the CATG+17 tags in the gene were taken as gene reference tags. Finally, 113,479 total reference tag sequences with 113,084 unambiguous reference tags were obtained. Among the clean tags, the number of sequences that could be mapped to unigenes ranged from 2.02 to 2.08 million, and the percentage of these clean tags ranged from 60.30 to 62.50% among the three libraries (S2 Table). To evaluate the DGE data, the distribution of the expression of clean tags were analyzed (Fig 1). The distribution of total clean tags and distinct clean tags across different tag abundance categories showed similar patterns for all three DGE libraries. In each library, the highly expressed tags dominated the total clean tags, but their distributions of distinct clean tags were small. In contrast, tags with a low level of expression among the total clean tags represented the majority of distinct clean tags. Results suggested that sequencing quality was high enough to enable the following analyses. Deep sequencing of foxtail millet during its interaction with U. setariae-italicae could facilitate the identification of signaling pathways and genes related to millet defense against rust.

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