IC4R019-RNA-Seq-2013-23324257

Project Title

• Transcriptome analysis of rice root heterosis by RNA-Seq

The Background of This Project

• Heterosis is a phenomenon in which hybrids exhibit superior performance relative to parental phenotypes. In addition to the heterosis of above-ground agronomic traits on which most existing studies have focused, root heterosis is also an indispensable component of heterosis in the entire plant and of major importance to plant breeding. Consequently, systematic investigations of root heterosis, particularly in reproductive-stage rice,are needed. The recent advent of RNA sequencing technology (RNA-Seq) provides an opportunity to conduct in-depth transcript profiling for heterosis studies.

Plant Culture & Treatment

• In this study, the researchers focused our heterosis research on the late-stage high-vigor trr super-hybrid rice variety, Xieyou 9308,which has a grain yield of up to 12.23 × 103 kg ⋅ hm-2 and was designated as “super rice” by the Chinese Ministry of Agriculture in 2005. Xieyou 9308 was bred by crossing the restorer line R9308 (with 25% japonica genetic components) to the maternal line Xieqingzao B (indica).
• The researchers used RNA-Seq to investigate the global transcriptomes of roots from Xieyou 9308 and its parents at tillering and heading stages. Differentially expressed transcripts and their expression patterns were analyzed, and several potential candidate transcripts were found to be involved in carbohydrate metabolism and plant hormone signal transduction pathways.
• The researchers expect this genome-wide transcriptome comparison to provide a starting point to understand the causative mechanism of the altered gene expression in the hybrid and the molecular mechanism underlying rice root heterosis.

Illumina sequencing

• Using the Illumina HiSeq 2000 platform, the root transcriptomes of the super-hybrid rice variety Xieyou 9308 and its parents were analyzed at tillering and heading stages.

Research Findings

• The researchers used RNA-Seq to investigate gene expression and function in a heterotic cross involving Xieyou 9308, a super-hybrid rice variety with superior yield performance,its maternal line Xieqingzao B, and its paternal line R9308.As suggested by Pickett [29], other yield-related traits might also show heterosis. In this study, the researchers found that the roots and aerial parts of Xieyou 9308 were more vigorous than those of either parent (Figure 1).

'Figure 1 Comparisons of heterosis in the super-hybrid rice combination Xieyou 9308. (A) The upper panel illustrates the cross between Xieqingzao B and R9308 at the tillering stage. Left, Xieqingzao B; middle, Xieyou 9308; right, R9308. The lower panel shows the cross at the heading stage. Left, R9308; middle, Xieyou 9308; right, Xieqingzao B. (B) Root traits of Xieyou 9308, Xieqingzao B, and R9308 at tillering and heading stages.'

• Correlations between the hybrid and its parents at tillering and heading stages were investigated using cluster analysis with Cluster 3.0 software. Xieqingzao B had smaller differences in gene expression between the two stages than did R9308 and Xieyou 9308(Figure 2).

'Figure 2 Hierarchical cluster analysis of all transcripts. The color key represents RPKM normalized log2 transformed counts. R, X, and F denote R9308, Xieqingzao B, and Xieyou 9308, respectively.Numbers 12 and 34 denote samples from roots at tillering and heading stages, respectively.'

• DGHP may be relevant to heterosis because differences in expression between the hybrid and its parents should underlie their phenotypic differences, while DGPP only represents the differences between the two parental lines. In total, 829 and 4186 DGHP were identified at tillering and heading stages, respectively (Table 3, Figure 3A and B).

'Figure 3 DEGs in the rice heterotic crosses. Venn diagram of DEGs between the hybrid and its parents at (A) tillering and (B) heading stages.'

Labs working on this Project

• State Key Laboratory of Rice Biology, China National Rice Research Institute,Hangzhou 310006, China.
• College of Agronomy, Shenyang Agricultural University, Shenyang 110161, China.
• Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
• Rice Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China.

Corresponding Author

• caolycgf@mail.hz.zj.cn; & shcheng@mail.hz.zj.cn