National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
College of Life Science, Xinyang Normal University, Xinyang 464000, China.
Int J Mol Sci. 2020 Dec 17;21(24):9618. doi: 10.3390/ijms21249618.
Genomic imprinting is an epigenetic phenomenon in which a subset of genes express dependent on the origin of their parents. In plants, it is unclear whether imprinted genes are conserved between subspecies in rice. Here we identified imprinted genes from embryo and endosperm 5-7 days after pollination from three pairs of reciprocal hybrids, including inter-subspecies, intra-subspecies, and intra-subspecies reciprocal hybrids. A total of 914 imprinted genes, including 546 in inter-subspecies hybrids, 211 in intra-subspecies hybrids, and 286 in intra-subspecies hybrids. In general, the number of maternally expressed genes (MEGs) is more than paternally expressed genes (PEGs). Moreover, imprinted genes tend to be in mini clusters. The number of shared genes by R9N (reciprocal crosses between 9311 and Nipponbare) and R9Z (reciprocal crosses between 9311 and Zhenshan 97), R9N and RZN (reciprocal crosses between Zhonghua11 and Nipponbare), R9Z and RZN was 72, 46, and 16. These genes frequently involved in energy metabolism and seed development. Five imprinted genes (, , , , and ) are commonly detected in all three pairs of reciprocal hybrids and were validated by RT-PCR sequencing. Gene editing of two imprinted genes revealed that both genes conferred grain filling. Moreover, 15 and 27 imprinted genes with diverse functions in rice were shared with Arabidopsis and maize, respectively. This study provided valuable resources for identification of imprinting genes in rice or even in cereals.
基因组印迹是一种表观遗传现象，其中一部分基因的表达依赖于其父母的来源。在植物中，尚不清楚印迹基因在水稻亚种间是否保守。在这里，我们从三个相互杂交的对中，包括亚种间、亚种内和亚种内相互杂交，鉴定了授粉后 5-7 天的胚和胚乳中的印迹基因。总共鉴定到 914 个印迹基因，包括亚种间杂交中的 546 个，亚种内杂交中的 211 个和亚种内杂交中的 286 个。通常，母源表达基因（MEGs）的数量多于父源表达基因（PEGs）。此外，印迹基因倾向于形成小簇。R9N（9311 与 Nipponbare 之间的相互杂交）和 R9Z（9311 与 Zhenshan 97 之间的相互杂交）、R9N 和 RZN（中华 11 与 Nipponbare 之间的相互杂交）、R9Z 和 RZN 之间共有 72、46 和 16 个基因。这些基因通常参与能量代谢和种子发育。五个印迹基因（、、、、和）在所有三对相互杂交中都被共同检测到，并通过 RT-PCR 测序进行了验证。两个印迹基因的基因编辑表明，这两个基因都能赋予籽粒灌浆。此外，水稻中有 15 个和 27 个具有不同功能的印迹基因分别与拟南芥和玉米共享。本研究为鉴定水稻甚至禾本科植物中的印迹基因提供了有价值的资源。
