Global RNA sequencing reveals that genotype-dependent allele-specific expression contributes to differential expression in rice F1 hybrids

BMC Plant Biology

Research Article

Daiming Jiang¹  Liping Zhang¹  Daichang Yang¹  Wei Wang¹  Chuan Liu¹  Yingguo Zhu¹  Xuefeng Qu¹  Gaoyuan Song¹  Rong Chen¹  Zhibin Guo¹  Zhenwei Liu¹  Qin Cheng¹  Yunfang Sun¹ 

[1] State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, 430072, Wuhan, Hubei Province, China;

关键词: Allele-specific expression;    Complementary effects;    Differentially expressed genes;    Genotype-dependent monoallelic expression;    Rice hybrids;   

DOI  :  10.1186/1471-2229-13-221

 received in 2013-06-25, accepted in 2013-12-09,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundExtensive studies on heterosis in plants using transcriptome analysis have identified differentially expressed genes (DEGs) in F1 hybrids. However, it is not clear why yield in heterozygotes is superior to that of the homozygous parents or how DEGs are produced. Global allele-specific expression analysis in hybrid rice has the potential to answer these questions.ResultsWe report a genome-wide allele-specific expression analysis using RNA-sequencing technology of 3,637–3,824 genes from three rice F1 hybrids. Of the expressed genes, 3.7% exhibited an unexpected type of monoallelic expression and 23.8% showed preferential allelic expression that was genotype-dependent in reciprocal crosses. Those genes exhibiting allele-specific expression comprised 42.4% of the genes differentially expressed between F1 hybrids and their parents. Allele-specific expression accounted for 79.8% of the genes displaying more than a 10-fold expression level difference between an F1 and its parents, and almost all (97.3%) of the genes expressed in F1, but non-expressed in one parent. Significant allelic complementary effects were detected in the F1 hybrids of rice.ConclusionsAnalysis of the allelic expression profiles of genes at the critical stage for highest biomass production from the leaves of three different rice F1 hybrids identified genotype-dependent allele-specific expression genes. A cis-regulatory mechanism was identified that contributes to allele-specific expression, leading to differential gene expression and allelic complementary effects in F1 hybrids.

【 授权许可】

Unknown   
© Song et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.