Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland.
Plant J. 2017 Dec;92(6):1044-1058. doi: 10.1111/tpj.13740. Epub 2017 Nov 28.
Genomic imprinting in the seed endosperm could be due to unequal parental-genome contribution effects in triploid endosperm tissue that trigger parent-of-origin specific activation and/or silencing of loci prone to genomic imprinting. To determine whether genomic imprinting is triggered by unequal parental-genome contribution effects, we generated a whole-genome transcriptome dataset of F1 hybrid triploid embryos (as mimics of F1 hybrid triploid endosperm). For the vast majority of genes, the parental contributions to their expression levels in the F1 triploid hybrid embryos follow a biallelic and linear expression pattern. While allele-specific expression (ASE) bias was detected, such effects were predominantly parent-of-origin independent. We demonstrate that genomic imprinting is largely absent from F1 triploid embryos, strongly suggesting that neither triploidy nor unequal parental-genome contribution are key triggers of genomic imprinting in plants. However, extensive parental-genome dosage effects on gene expression were observed between the reciprocal F1 hybrid embryos, particularly for genes involved in defence response and nutrient reservoir activity, potentially leading to the seed size differences between reciprocal triploids. We further determined that unequal parental-genome contribution in F1 triploids can lead to overexpression effects that are parent-of-origin dependent, and which are not observed in diploid or tetraploid embryos in which the parental-genome dosage is balanced. Overall, our study demonstrates that neither triploidy nor unequal parental-genome contribution is sufficient to trigger imprinting in plant tissues, suggesting that genomic imprinting is an intrinsic and unique feature of the triploid seed endosperm.
种子胚乳中的基因组印迹可能是由于三倍体胚乳组织中双亲基因组贡献不均等的影响，从而触发亲本来源特异性的激活和/或易发生基因组印迹的基因座沉默。为了确定基因组印迹是否由双亲基因组贡献不均等的影响引发，我们生成了 F1 杂种三倍体胚胎的全基因组转录组数据集（作为 F1 杂种三倍体胚乳的模拟物）。对于绝大多数基因，它们在 F1 三倍体杂种胚胎中的表达水平的双亲贡献遵循双等位基因和线性表达模式。虽然检测到等位基因特异性表达（ASE）偏倚，但这种影响主要与亲本来源无关。我们证明 F1 三倍体胚胎中基因组印迹基本不存在，这强烈表明三倍体或双亲基因组贡献不均等都不是植物中基因组印迹的关键触发因素。然而，在正反交 F1 杂种胚胎之间观察到广泛的双亲基因组剂量效应对基因表达的影响，特别是对于参与防御反应和营养库活性的基因，这可能导致正反交三倍体之间的种子大小差异。我们进一步确定 F1 三倍体中双亲基因组贡献的不均等会导致依赖亲本来源的过表达效应，而在双亲基因组剂量平衡的二倍体或四倍体胚胎中则不会观察到这种效应。总体而言，我们的研究表明，三倍体或双亲基因组贡献不均等都不足以触发植物组织中的印迹，这表明基因组印迹是三倍体种子胚乳的内在和独特特征。
