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

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BMC Plant Biology

, 13:221

Genetics and crop biotechnology


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.

KeywordsAllele-specific expression Complementary effects Differentially expressed genes Genotype-dependent monoallelic expression Rice hybrids AbbreviationsASEAllele-specific expression

DEGDifferentially expressed gene

FDRFalse discovery rate

GOGene ontology

RPKMReads per kb per million reads

RT-PCRReverse transcription polymerase chain reaction

SNPSingle nucleotide polymorphism.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2229-13-221 contains supplementary material, which is available to authorized users.

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Autor: Gaoyuan Song - Zhibin Guo - Zhenwei Liu - Qin Cheng - Xuefeng Qu - Rong Chen - Daiming Jiang - Chuan Liu - Wei Wang - Yun


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