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Open Access Research article

Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background

Fan Zhang12, Liyu Huang12, Wensheng Wang12, Xiuqin Zhao12, Linghua Zhu12, Binying Fu12* and Zhikang Li123*

Author Affiliations

1 Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China

2 Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural Sciences, Shenzhen 518083, China

3 International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines

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BMC Genomics 2012, 13:461  doi:10.1186/1471-2164-13-461

Published: 7 September 2012

Additional files

Additional file 1:

Phenotypic performance between C418 and K354 in different experiments. Excel file containing the phenotypic performance of C418 and K354 under both control and abiotic stress conditions in different experiments.

Format: XLS Size: 32KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 2:

Phenotype and physiological changes of K354 and C418 under control and cold stress conditions. A PowerPoint file containing photographs of growth status and physiological conditions of K354 and C418 under control conditions (25°C) and cold stress treatment (4°C) for 48 h.

Format: PPT Size: 375KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

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Additional file 3:

Total number of expressed transcripts. Word file containing the total number of transcripts expressed in the two genotypes at different times under control and cold stress conditions.

Format: DOC Size: 30KB Download file

This file can be viewed with: Microsoft Word Viewer

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Additional file 4:

Expression patterns of differentially expressed transcripts in K354 and C418. A PowerPoint file containing expression patterns of 3184 differentially expressed probes based on log-transformed and normalized expression values from control conditions to 48 h under cold stress in (A) K354 and (B) C418. Green, blue, yellow, cyan, red, and black lines indicate clusters I–VI with the same color in Figure 2, respectively.

Format: PPT Size: 938KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

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Additional file 5:

Detailed list of DEGs in the six clusters of Figure2 Excel file containing a list of the transcripts used in the cluster analysis in Figure 2.

Format: XLS Size: 247KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

Validation of gene expression by qRT-PCR. A PowerPoint file containing correlation analysis results between microarray and qRT-RCR experiments based on 15 selected genes representing the OsDREB1 regulon and candidate genes of introgressed segments. Gene expression values were transformed to a log2 scale. The microarray data log2-value (X-axis) were plotted against the qRT-PCR log2-value (Y-axis).

Format: PPT Size: 376KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

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Additional file 7:

Comparative diagram of the total number of differentially regulated genes between C418 and K354 under cold stress. A PowerPoint file containing (A) Cold-induced genes; (B) Cold-repressed genes. Blue, red, and green bars indicate K354-specific (blue bar), common (red bar), and C418-specific (green bar) regulated genes by cold stress at phase I (2–6 h), phase II (12 h), and phase III (24–48 h) of cold-response, respectively.

Format: PPT Size: 128KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

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Additional file 8:

Common genes regulated by cold in both genotypes at all cold-responsive stages. Word file containing 130 and 21 genes commonly induced and repressed by cold in both genotypes at all cold-responsive stages.

Format: DOC Size: 222KB Download file

This file can be viewed with: Microsoft Word Viewer

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Additional file 9:

K354-specific cold-induced genes. Excel file containing a list of K354-specific cold-induced genes at all time points.

Format: XLS Size: 122KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 10:

K354-specific cold-repressed genes. Excel file containing a list of K354-specific cold-repressed genes at all time points.

Format: XLS Size: 56KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 11:

C418-specific cold-induced genes. Excel file containing a list of C418-specific cold-induced genes at all time points.

Format: XLS Size: 139KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 12:

C418-specific cold-repressed genes. Excel file containing a list of C418-specific cold-repressed genes at all time points.

Format: XLS Size: 119KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 13:

Constitutively highly-expressed genes in K354. Excel file containing a list of non-cold-responsive genes with constitutively higher transcriptional expression in K354 than in C418.

Format: XLS Size: 77KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 14:

TF genes detected to be differentially regulated by cold. Excel file containing a list of TF genes differentially regulated by cold in K354 and C418.

Format: XLS Size: 93KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 15:

OsDREB1s and commonly cold-induced genes including a DRE core motif. Excel file containing a list of OsDREB1s and 298 genes commonly cold-induced in both C418 and K354 with at least one DRE core motif at 1 kb up-stream.

Format: XLS Size: 163KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 16:

Genomic distribution of 17 introgression fragments in K354. A PowerPoint file containing information on introgressed fragments, polymorphic SSR markers used, and previously reported QTLs related to CT at the seedling stage near the introgressed regions.

Format: PPT Size: 214KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

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Additional file 17:

DEGs in the introgressed regions of K354. Excel file containing a list of differentially regulated genes detected by comparison of gene expression profiles of two genotypes that were within or neighboring the regions of donor introgression.

Format: XLS Size: 45KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data