Detailed observation on expression dynamics of Polycomb group genes during rice early endosperm development in subspecies hybridization reveals their characteristics of parent-of-origin genes

Abstract

Background Parent-of-origin gene expression and its role in seed development have drown a great attention in recent years. Genome-wide analysis has identified hundreds of candidate imprinted genes, a major type of parent-of-origin genes, in rice hybrid endosperms at the stage of 5 days after pollination (dap). However, the expression of these genes in early endosperm have been never confirmed due to technique limitations and the behavior of the imprinted genes in different rice hybridizations are still largely unknown. Results Here, based on our elaborate technique established previously, the expression patterns of PcG genes in the early stages of endosperm development (within 3 dap), were comprehensively analyzed. We revealed that the free nucleus stage of endosperm development is critical for parent-of-origin gene analysis. The expression of the imprinted genes are highly dynamic, likely corresponding to the critical developmental events during this period. Hybridizations between Oryza sativa japonica and indica showed that the expression patterns of the same imprinted gene could be varied by crossing with different parental cultivars, indicative of their parent-dependent character. There are strong alleles that often showed predominant expression over other alleles regardless of the parental origin, which provides a possible explanation for the cultivar-dependent predominant phenotype in crop hybridizations. In addition, we found that the transcripts of the same gene behave differently, with imprinting or non-imprinting patterns, suggesting the existence of not only imprinted and non-imprinted genes but also imprinted or non-imprinted transcripts, which reveals new aspects of the genomic imprinting. Conclusions These findings on the characters of parent-of-origin genes shed light on the understanding the real role of gene imprinting in endosperm development. Electronic supplementary material The online version of this article (10.1186/s12284-019-0306-x) contains supplementary material, which is available to authorized users.

Mutation of the imprinted geneOsEMF2ainduces autonomous endosperm development and delayed cellularization in rice

“…Luo et al reported that OsEMF2a was not imprinted, whereas Chen et al provided evidence for imprinting at this locus (Luo et al, 2009;Chen et al, 2018). Expression of the paternal allele seems to depend on developmental timing and subspecies combination (Kuang et al, 2019;Cheng et al, 2020a). These issues may explain the phenotypic variation of emf2a mutants in the endosperm in our analysis.…”

SDG711 is Involved in Rice Seed Development Through Regulation of Starch Metabolism Gene Expression in Coordination With Other Histone Modifications

“…In rice, OsFIE1, the homologs of FIS2 expressed only in endosperm, is a maternally expressed imprinting gene, other ve PRC2 genes (OsFIE2, OsEMF1, OsEMF2, OsCLF and OsiZE1) are expressed in a wide range of tissues and are not imprinted (Luo et al 2009). However, recent research showed that except for OsCLF (SDG711) being a non-imprinted gene, other four genes those previous studies considered as non-imprinted genes showed the characteristics of imprinted genes at different stages of endosperm development in rice (Kuang et al 2019). In addition, our resent research suggested that the CLF homologous gene OSCLF (SDG711) regulates endosperm development by directly binding to the gene body region of several starch synthesis genes and amylase genes to mediate H3K27me3 enrichment on them in rice.…”

SDG711 Is Involved in Rice Seed Development through Regulation of Starch Metabolism Gene Expression in Coordination with Other Histone Modifications

“…The other five PRC2 genes ( OsFIE2 , OsEMF1 , OsEMF2 , OsCLF and OsiZE1 ) are expressed in a wide range of tissues and are not imprinted (Luo et al 2009 ). However, recent research showed that except for OsCLF (SDG711) being a non-imprinted gene, four other genes that were considered as non-imprinted genes showed the characteristics of imprinted genes at different stages of endosperm development in rice (Kuang et al 2019 ). In addition, our recent research suggested that the CLF homologous gene OsCLF (SDG711) regulates endosperm development by directly binding to the gene body region of several starch synthesis genes and amylase genes to mediate H3K27me3 enrichment in rice.…”