Open Access Highly Accessed Research article

Transcriptome analysis of rice root heterosis by RNA-Seq

Rongrong Zhai1, Yue Feng1, Huimin Wang2, Xiaodeng Zhan1, Xihong Shen1, Weiming Wu1, Yingxin Zhang1, Daibo Chen1, Gaoxing Dai3, Zhanlie Yang4, Liyong Cao1* and Shihua Cheng1*

Author Affiliations

1 State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China

2 College of Agronomy, Shenyang Agricultural University, Shenyang, 110161, China

3 Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China

4 Rice Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China

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BMC Genomics 2013, 14:19  doi:10.1186/1471-2164-14-19

Published: 16 January 2013

Additional files

Additional file 1:

Figure S1. Scatterplots comparing gene expression scores from biological replicates of Xieyou 9308 and the two parents. Numbers12 and 34 denote biological replicates at tillering and heading stages, respectively. R, X, and F refer to R9308, Xieqingzao B, and Xieyou 9308, respectively.

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Additional file 2:

Figure S2. Comparison of the root dry weight of Xieyou 9308, Xieqingzao B, and R9308 at tillering and heading stages.

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Additional file 3:

Table S1. RPKM of RAP2-annotated transcripts at tillering and heading stages.

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Additional file 4:

Table S2. Classification of DGHP based on the dominance ratio hp.

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Additional file 5:

Figure S3. The number of DGHP in the biological process category at tillering and heading stages.

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Additional file 6:

Tables S3 and Table S4. Significant KO terms of DGHP at the tillering stage (Table S3) and the heading stage (Table S4).

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Additional file 7:

Figure S4. The number of DGHP in each KEGG pathway at tillering and heading stages.

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Additional file 8:

Table S5. Experimental validation using qRT-PCR and primer sequences for qRT-PCR expression analysis.

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Additional file 9:

Table S6. Significant differentially expressed trans-regulatory elements located in each of the QTL regions.

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