Conserved Imprinted Genes between Intra-Subspecies and Inter-Subspecies Are Involved in Energy Metabolism and Seed Development in Rice.

Lin Yang,Qin He,Muhammad Tahir Ul Qamar,Feng Xing,Yongzhong Xing,Ling-Ling Chen

doi:10.3390/ijms21249618

Abstract

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, japonica intra-subspecies, and indica intra-subspecies reciprocal hybrids. A total of 914 imprinted genes, including 546 in inter-subspecies hybrids, 211 in japonica intra-subspecies hybrids, and 286 in indica 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 (Os01g0151700, Os07g0103100, Os10g0340600, Os11g0679700, and Os12g0632800) 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.

Highlights

Genomic imprinting, known as genetic imprinting, is an epigenetic phenomenon in which a subset of genes is expressed dependent on the origin of their parents [1]
We identified the imprinted genes by analyzing the transcriptome data of embryo and endosperm in three pairs of reciprocal crosses including two intra-subspecies crosses and one inter-subspecies cross between indica and japonica
The least number of genes were expressed in the indica intra-subspecies hybrid reciprocal crosses between 9311 and Zhenshan97 (R9Z) in both organs, 20% less than the other two sets of reciprocal hybrids (Table 1)

Summary

Introduction

Known as genetic imprinting, is an epigenetic phenomenon in which a subset of genes is expressed dependent on the origin of their parents [1]. Genomic imprinting was firstly discovered by Kermicle in maize in 1970, which proved that R pigmentation gene prefers to express maternal allele [2]. Genomic imprinting existed in embryo and placenta in animals, but most imprinting genes were found in the endosperm of flowering plants [3]. Endosperm is one of the products of plant double fertilization, and provided resources for the development of embryo, which contains two maternal genomes and one paternal genome. The expression of imprinted genes is deviated from 2:1. Some of them prefer to express maternal alleles called maternally expressed genes (MEGs). The others prefer to express paternal alleles, called paternally expressed genes (PEGs)

Methods

Results

Conclusion