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Transcriptome sequencing in a Tibetan barley landrace with high resistance to powdery mildew.

Zeng XQ, Luo XM, Wang YL, Xu QJ, Bai LJ, Yuan HJ, Tashi N - ScientificWorldJournal (2014)

Bottom Line: A total of 831 significant differentially expressed genes were found in the infected seedlings, covering 19 functions.In addition, 330 KEGG pathways were found using BLASTx with an E-value cut-off of <10(-5).Among them, three pathways, namely, "photosynthesis," "plant-pathogen interaction," and "photosynthesis-antenna proteins" had significant matches in the database.

View Article: PubMed Central - PubMed

Affiliation: Barley Improvement and Yak Breeding Key Laboratory, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China.

ABSTRACT
Hulless barley is an important cereal crop worldwide, especially in Tibet of China. However, this crop is usually susceptible to powdery mildew caused by Blumeria graminis f. sp. hordei. In this study, we aimed to understand the functions and pathways of genes involved in the disease resistance by transcriptome sequencing of a Tibetan barley landrace with high resistance to powdery mildew. A total of 831 significant differentially expressed genes were found in the infected seedlings, covering 19 functions. Either "cell," "cell part," and "extracellular region" in the cellular component category or "binding" and "catalytic" in the category of molecular function as well as "metabolic process" and "cellular process" in the biological process category together demonstrated that these functions may be involved in the resistance to powdery mildew of the hulless barley. In addition, 330 KEGG pathways were found using BLASTx with an E-value cut-off of <10(-5). Among them, three pathways, namely, "photosynthesis," "plant-pathogen interaction," and "photosynthesis-antenna proteins" had significant matches in the database. Significant expressions of the three pathways were detected at 24 h, 48 h, and 96 h after infection, respectively. These results indicated a complex process of barley response to powdery mildew infection.

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Euclidean distance was used to establish the distance of expression between A (C0, TR130348) and B (C24, TR130349).
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fig3: Euclidean distance was used to establish the distance of expression between A (C0, TR130348) and B (C24, TR130349).

Mentions: Gene saturation of each sample was also similar, and Sample A was illustrated in Supplementary Figure 5. Comparisons of gene expressions in each subsample to the whole sample showed less than 15% of the difference between them, indicating fine expression genes in the current size of sequencing data. The results represented an accurate dataset to detect highly expressed genes. The distribution density of gene global expressions of each sample was illustrated in Figure 2, which exhibits similar expressed gene distributions among these samples. Cuffdiff software (http://cufflinks.cbcb.umd.edu/index.html) was used to compare the gene expressions between sample pairs. Differently expressed genes were identified based on genes with q < 0.05 (q is the corrected P value). The results were listed in Supplementary Table 2. Total DEGs from each sample were clustered in Supplementary Figure 6. The first subgroup contained only A, the second one included B and C (C48, TR130350), and the last one covered the rest samples of D (C72, TR130351), E (C96, TR130352), and F. Euclidean distance was used to estimate the distance of gene expression between sample pairs. The clusters of A and B were illustrated in Figure 3. In the histogram, the red color indicates upregulation and the green color downregulation. Compared with Sample A, gene expressions of B and C were significantly different. There were similar distributions between A and D, between A and E, and between A and F.


Transcriptome sequencing in a Tibetan barley landrace with high resistance to powdery mildew.

Zeng XQ, Luo XM, Wang YL, Xu QJ, Bai LJ, Yuan HJ, Tashi N - ScientificWorldJournal (2014)

Euclidean distance was used to establish the distance of expression between A (C0, TR130348) and B (C24, TR130349).
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4284937&req=5

fig3: Euclidean distance was used to establish the distance of expression between A (C0, TR130348) and B (C24, TR130349).
Mentions: Gene saturation of each sample was also similar, and Sample A was illustrated in Supplementary Figure 5. Comparisons of gene expressions in each subsample to the whole sample showed less than 15% of the difference between them, indicating fine expression genes in the current size of sequencing data. The results represented an accurate dataset to detect highly expressed genes. The distribution density of gene global expressions of each sample was illustrated in Figure 2, which exhibits similar expressed gene distributions among these samples. Cuffdiff software (http://cufflinks.cbcb.umd.edu/index.html) was used to compare the gene expressions between sample pairs. Differently expressed genes were identified based on genes with q < 0.05 (q is the corrected P value). The results were listed in Supplementary Table 2. Total DEGs from each sample were clustered in Supplementary Figure 6. The first subgroup contained only A, the second one included B and C (C48, TR130350), and the last one covered the rest samples of D (C72, TR130351), E (C96, TR130352), and F. Euclidean distance was used to estimate the distance of gene expression between sample pairs. The clusters of A and B were illustrated in Figure 3. In the histogram, the red color indicates upregulation and the green color downregulation. Compared with Sample A, gene expressions of B and C were significantly different. There were similar distributions between A and D, between A and E, and between A and F.

Bottom Line: A total of 831 significant differentially expressed genes were found in the infected seedlings, covering 19 functions.In addition, 330 KEGG pathways were found using BLASTx with an E-value cut-off of <10(-5).Among them, three pathways, namely, "photosynthesis," "plant-pathogen interaction," and "photosynthesis-antenna proteins" had significant matches in the database.

View Article: PubMed Central - PubMed

Affiliation: Barley Improvement and Yak Breeding Key Laboratory, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China.

ABSTRACT
Hulless barley is an important cereal crop worldwide, especially in Tibet of China. However, this crop is usually susceptible to powdery mildew caused by Blumeria graminis f. sp. hordei. In this study, we aimed to understand the functions and pathways of genes involved in the disease resistance by transcriptome sequencing of a Tibetan barley landrace with high resistance to powdery mildew. A total of 831 significant differentially expressed genes were found in the infected seedlings, covering 19 functions. Either "cell," "cell part," and "extracellular region" in the cellular component category or "binding" and "catalytic" in the category of molecular function as well as "metabolic process" and "cellular process" in the biological process category together demonstrated that these functions may be involved in the resistance to powdery mildew of the hulless barley. In addition, 330 KEGG pathways were found using BLASTx with an E-value cut-off of <10(-5). Among them, three pathways, namely, "photosynthesis," "plant-pathogen interaction," and "photosynthesis-antenna proteins" had significant matches in the database. Significant expressions of the three pathways were detected at 24 h, 48 h, and 96 h after infection, respectively. These results indicated a complex process of barley response to powdery mildew infection.

Show MeSH
Related in: MedlinePlus