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. 2015 May 18;16(5):11398-416.
doi: 10.3390/ijms160511398.

Comparative Analysis of Anther Transcriptome Profiles of Two Different Rice Male Sterile Lines Genotypes under Cold Stress

Bin Bai  1   2 , Jun Wu  3   4 , Wen-Tao Sheng  5   6 , Bo Zhou  7 , Li-Jie Zhou  8   9 , Wen Zhuang  10 , Dong-Ping Yao  11   12 , Qi-Yun Deng  13   14   15
Affiliations

Comparative Analysis of Anther Transcriptome Profiles of Two Different Rice Male Sterile Lines Genotypes under Cold Stress

Bin Bai et al. Int J Mol Sci. .

Abstract

Rice is highly sensitive to cold stress during reproductive developmental stages, and little is known about the mechanisms of cold responses in rice anther. Using the HiSeq™ 2000 sequencing platform, the anther transcriptome of photo thermo sensitive genic male sterile lines (PTGMS) rice Y58S and P64S (Pei'ai64S) were analyzed at the fertility sensitive stage under cold stress. Approximately 243 million clean reads were obtained from four libraries and aligned against the oryza indica genome and 1497 and 5652 differentially expressed genes (DEGs) were identified in P64S and Y58S, respectively. Both gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted for these DEGs. Functional classification of DEGs was also carried out. The DEGs common to both genotypes were mainly involved in signal transduction, metabolism, transport, and transcriptional regulation. Most of the DEGs were unique for each comparison group. We observed that there were more differentially expressed MYB (Myeloblastosis) and zinc finger family transcription factors and signal transduction components such as calmodulin/calcium dependent protein kinases in the Y58S comparison group. It was also found that ribosome-related DEGs may play key roles in cold stress signal transduction. These results presented here would be particularly useful for further studies on investigating the molecular mechanisms of rice responses to cold stress.

Keywords: PTGMS rice; RNA-Seq; anther; cold stress; transcriptome.

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Figures

Figure 1
Figure 1
The comparison of the seed setting rates of Y58S and P64S in the control and in the cold treatment. CK indicates control treatment; CT indicates cold treatment. Vertical bar indicates standard error.
Figure 2
Figure 2
Hierarchical cluster analysis of gene expression based on the log ratio fold change data. The color scale indicates the gene expression level: red color represents increased transcript abundance and blue color represents decreased transcript abundance. TP and CP indicate cold treated P64S and control treated P64S, respectively. TY and CY indicate cold treated Y58S and control treated Y58S, respectively.
Figure 3
Figure 3
Gene ontology (GO) classifications of differentially expressed genes (DEGs) in P64S and Y58S, respectively. * indicates significantly enriched GO terms with correct p-value < 0.05.
Figure 4
Figure 4
Comparison of genes expression levels using RNA-Seq and qRT-PCR. The relative expression values were normalized to the rice actin 1 gene. Error bars indicate standard deviation. Log2FC refers to the log2 fold change.
See this image and copyright information in PMC

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