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

2020 ◽  
Vol 21 (24) ◽  
pp. 9618
Author(s):  
Lin Yang ◽  
Feng Xing ◽  
Qin He ◽  
Muhammad Tahir ul Qamar ◽  
Ling-Ling Chen ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Seed Development ◽  
Genomic Imprinting ◽  
Gene Editing ◽  
Grain Filling ◽  
Imprinted Genes ◽  
Rt Pcr ◽  
Reciprocal Crosses ◽  
Reciprocal Hybrids ◽  
Epigenetic Phenomenon

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.

scholarly journals Paternally expressed imprinted genes establish postzygotic hybridization barriers in Arabidopsis thaliana

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Philip Wolff ◽  
Hua Jiang ◽  
Guifeng Wang ◽  
Juan Santos-González ◽  
Claudia Köhler
Keyword(s):  
Arabidopsis Thaliana ◽  
Differential Expression ◽  
Seed Development ◽  
Genomic Imprinting ◽  
Imprinted Genes ◽  
Functional Requirement ◽  
Functional Roles ◽  
Epigenetic Phenomenon ◽  
Parent Of Origin

Genomic imprinting is an epigenetic phenomenon causing parent-of-origin specific differential expression of maternally and paternally inherited alleles. While many imprinted genes have been identified in plants, the functional roles of most of them are unknown. In this study, we systematically examine the functional requirement of paternally expressed imprinted genes (PEGs) during seed development in Arabidopsis thaliana. While none of the 15 analyzed peg mutants has qualitative or quantitative abnormalities of seed development, we identify three PEGs that establish postzygotic hybridization barriers in the endosperm, revealing that PEGs have a major role as speciation genes in plants. Our work reveals that a subset of PEGs maintains functional roles in the inbreeding plant Arabidopsis that become evident upon deregulated expression.

scholarly journals Canonical and Non-canonical Genomic Imprinting in Rodents

2021 ◽  
Vol 9 ◽  
Author(s):  
Hisato Kobayashi
Keyword(s):  
Dna Methylation ◽  
Genomic Imprinting ◽  
Mouse Genome ◽  
Genetic Regulation ◽  
Imprinted Genes ◽  
Evolutionary Divergence ◽  
Chromatin Modifications ◽  
Allele Specific ◽  
Epigenetic Phenomenon ◽  
Parent Of Origin

Genomic imprinting is an epigenetic phenomenon that results in unequal expression of homologous maternal and paternal alleles. This process is initiated in the germline, and the parental epigenetic memories can be maintained following fertilization and induce further allele-specific transcription and chromatin modifications of single or multiple neighboring genes, known as imprinted genes. To date, more than 260 imprinted genes have been identified in the mouse genome, most of which are controlled by imprinted germline differentially methylated regions (gDMRs) that exhibit parent-of-origin specific DNA methylation, which is considered primary imprint. Recent studies provide evidence that a subset of gDMR-less, placenta-specific imprinted genes is controlled by maternal-derived histone modifications. To further understand DNA methylation-dependent (canonical) and -independent (non-canonical) imprints, this review summarizes the loci under the control of each type of imprinting in the mouse and compares them with the respective homologs in other rodents. Understanding epigenetic systems that differ among loci or species may provide new models for exploring genetic regulation and evolutionary divergence.

scholarly journals Genomic imprinting in marsupial placentation

Reproduction ◽  
2008 ◽  
Vol 136 (5) ◽  
pp. 523-531 ◽  
Author(s):  
Marilyn B Renfree ◽  
Eleanor I Ager ◽  
Geoff Shaw ◽  
Andrew J Pask
Keyword(s):  
Genomic Imprinting ◽  
Direct Evidence ◽  
Egg Laying ◽  
Common Mechanism ◽  
Parental Conflict ◽  
Imprinted Genes ◽  
Nutrient Transfer ◽  
Epigenetic Phenomenon ◽  
Selection For ◽  
Shed Light

Genomic imprinting is a widespread epigenetic phenomenon in eutherian mammals, which regulates many aspects of growth and development. Parental conflict over the degree of maternal nutrient transfer is the favoured hypothesis for the evolution of imprinting. Marsupials, like eutherian mammals, are viviparous but deliver an altricial young after a short gestation supported by a fully functional placenta, so can shed light on the evolution and time of acquisition of genomic imprinting. All orthologues of eutherian imprinted genes examined have a conserved expression in the marsupial placenta regardless of their imprint status. Differentially methylated regions (DMRs) are the most common mechanism controlling genomic imprinting in eutherian mammals, but none were found in the marsupial imprinted orthologues of IGF2 receptor (IGF2R), INS or mesoderm-specific transcript (MEST). Instead, histone modification appears to be the mechanism used to silence these genes. At least three genes in marsupials have DMRs: H19, IGF2 and PEG10. PEG10 is particularly interesting as it is derived from a retrotransposon, providing the first direct evidence that retrotransposon insertion can drive the evolution of an imprinted region and of a DMR in mammals. The insertion occurred after the prototherian–therian mammal divergence, suggesting that there may have been strong selection for the retention of imprinted regions that arose during the evolution of placentation. There is currently no evidence for genomic imprinting in the egg-laying monotreme mammals. However, since these mammals do have a short-lived placenta, imprinting appears to be correlated with viviparity but not placentation.

scholarly journals Paternal inheritance of egg traits in mice: a case of genomic imprinting

1989 ◽  
Vol 54 (3) ◽  
pp. 213-219 ◽  
Author(s):  
S. A. A. Bander ◽  
S. C. Watson ◽  
J. G. M. Shire
Keyword(s):  
Genomic Imprinting ◽  
Recombinant Inbred ◽  
Inbred Strains ◽  
Recombinant Inbred Strains ◽  
Paternal Inheritance ◽  
Reciprocal Crosses ◽  
Reciprocal Hybrids ◽  
Reciprocal Differences ◽  
Cross Fostering ◽  
Increased Susceptibility

SummaryEggs from reciprocal hybrids between the C57BL/6By and BALB/cBy strains were tested for their susceptibility to attack by hyaluronidase and pronase. There were significant reciprocal differences between the F1 females in the responses of their unfertilized eggs to both enzymes. The F1 hybrids from BALB mothers showed the increased susceptibility characteristic of C57BL whilst the F1 hybrids with C57BL mothers were more resistant to both enzymes, like BALB mice. Eggs from the four kinds of reciprocal F2 hybrid females also showed patroclinous patterns of susceptibility. A patroclinous difference was found between reciprocal crosses of the CXBD and CXBE recombinant inbred strains but not in crosses between recombinant inbred strains with similar phenotypes. Cross fostering did not alter the phenotypes of the C57BL and BALB females or those of their reciprocal F1 hybrids. The findings are interpreted in terms of differential genomic imprinting of paternally inherited information. The possible general usefulness of patroclinous differences between reciprocal F1 females in revealing differences in imprinting is noted.

scholarly journals Epigenetic modifications potentially controlling the allelic expression of imprinted genes in sunflower endosperm

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhichao Zhang ◽  
Shuai Yu ◽  
Jing Li ◽  
Yanbin Zhu ◽  
Siqi Jiang ◽  
...  
Keyword(s):  
Genomic Imprinting ◽  
Noncoding Rnas ◽  
Methylation Pattern ◽  
Flowering Plants ◽  
Imprinted Genes ◽  
Genome Wide ◽  
Allelic Gene ◽  
Potential Basis ◽  
Epigenetic Phenomenon ◽  
Global Patterns

Abstract Background Genomic imprinting is an epigenetic phenomenon mainly occurs in endosperm of flowering plants. Genome-wide identification of imprinted genes have been completed in several dicot Cruciferous plant and monocot crops. Results Here, we analyzed global patterns of allelic gene expression in developing endosperm of sunflower which belongs to the composite family. Totally, 691 imprinted loci candidates were identified in 12 day-after-pollination sunflower endosperm including 79 maternally expressed genes (MEG) and 596 paternally expressed genes (PEG), 6 maternally expressed noncoding RNAs (MNC) and 10 paternally expressed noncoding RNAs (PNC). And a clear clustering of imprinted genes throughout the rapeseed genome was identified. Generally, imprinting in sunflower is conserved within a species, but intraspecific variation also was detected. Limited loci in sunflower are imprinted in other several different species. The DNA methylation pattern around imprinted genes were investigated in embryo and endosperm tissues. In CG context, the imprinted genes were significantly associated with differential methylated regions exhibiting hypomethylation in endosperm and hypermethylation in embryo, which indicated that the maternal demethylation in CG context potentially induce the genomic imprinting in endosperm. Conclusion Our study would be helpful for understanding of genomic imprinting in plants and provide potential basis for further research in imprinting in sunflower.

scholarly journals Genome-wide screen of genomic imprinting in endosperm and population-level analysis reveal allelic variation for imprinting in flax

2020 ◽  
Author(s):  
Haixia Jiang ◽  
Dongliang Guo ◽  
Jiali Ye ◽  
Yanfang Gao ◽  
Huiqing Liu ◽  
...  
Keyword(s):  
Positive Selection ◽  
Genomic Imprinting ◽  
Allelic Variation ◽  
Population Level ◽  
Vital Role ◽  
Genomic Variation ◽  
Imprinted Genes ◽  
Fiber Flax ◽  
Genome Wide ◽  
Epigenetic Phenomenon

AbstractGenomic imprinting is an epigenetic phenomenon caused by the biased expression of maternally and paternally inherited alleles. In flowering plants, genomic imprinting predominantly occurs in triploid endosperm and plays a vital role in seed development. In this study, we identified 241 candidate imprinted genes including 143 maternally expressed imprinted genes (MEGs) and 98 paternally expressed imprinted genes (PEGs) in flax (Linum usitatissimum L.) endosperm using deep RNA sequencing. The conservation of imprinting in plants is very limited and imprinting clustering is not a general feature. MEGs tends to be endosperm expression specific, while PEGs are non-tissue specific. Imprinted SNPs differentiated 200 flax cultivars into oil flax, oil-fiber dual purpose flax (OF) and fiber flax subgroups, suggesting that genomic imprinting contributes to intraspecific variation in flax. The nucleotide diversity (π) of imprinted genes in oil flax subgroup is significantly higher than that in fiber flax subgroup, indicating that some imprinted genes undergo positive selection during flax domestication from oil flax to fiber flax. Imprinted genes undergo positive selection is related to the functions. Eleven imprinted genes related to seed size and weight were identified using the candidate gene-based association study. Our study provides information for further exploring the function and genomic variation of imprinted genes in flax population.

scholarly journals Leaf-derived ABA regulates rice seed development via a transporter-mediated and temperature-sensitive mechanism

2021 ◽  
Vol 7 (3) ◽  
pp. eabc8873
Author(s):  
Peng Qin ◽  
Guohua Zhang ◽  
Binhua Hu ◽  
Jie Wu ◽  
Weilan Chen ◽  
...  
Keyword(s):  
Seed Development ◽  
Starch Synthesis ◽  
Biological Significance ◽  
Grain Filling ◽  
Temperature Sensitive ◽  
Rice Seed ◽  
Dependent Manner ◽  
Long Distance ◽  
Long Distance Transport ◽  
Mechanistic Basis

Long-distance transport of the phytohormone abscisic acid (ABA) has been studied for ~50 years, yet its mechanistic basis and biological significance remain very poorly understood. Here, we show that leaf-derived ABA controls rice seed development in a temperature-dependent manner and is regulated by defective grain-filling 1 (DG1), a multidrug and toxic compound extrusion transporter that effluxes ABA at nodes and rachilla. Specifically, ABA is biosynthesized in both WT and dg1 leaves, but only WT caryopses accumulate leaf-derived ABA. Our demonstration that leaf-derived ABA activates starch synthesis genes explains the incompletely filled and floury seed phenotypes in dg1. Both the DG1-mediated long-distance ABA transport efficiency and grain-filling phenotypes are temperature sensitive. Moreover, we extended these mechanistic insights to other cereals by observing similar grain-filling defects in a maize DG1 ortholog mutant. Our study demonstrates that rice uses a leaf-to-caryopsis ABA transport–based mechanism to ensure normal seed development in response to variable temperatures.

scholarly journals Genomic imprinting in germ cells: imprints are under control

Reproduction ◽  
2010 ◽  
Vol 140 (3) ◽  
pp. 411-423 ◽  
Author(s):  
Philippe Arnaud
Keyword(s):  
Dna Methylation ◽  
Genomic Imprinting ◽  
Germ Cells ◽  
Imprinted Genes ◽  
Regulatory Sequences ◽  
Sequence Specificity ◽  
Maternal Allele ◽  
Primary Sequence ◽  
Chromatin Configuration

The cis-acting regulatory sequences of imprinted gene loci, called imprinting control regions (ICRs), acquire specific imprint marks in germ cells, including DNA methylation. These epigenetic imprints ensure that imprinted genes are expressed exclusively from either the paternal or the maternal allele in offspring. The last few years have witnessed a rapid increase in studies on how and when ICRs become marked by and subsequently maintain such epigenetic modifications. These novel findings are summarised in this review, which focuses on the germline acquisition of DNA methylation imprints and particularly on the combined role of primary sequence specificity, chromatin configuration, non-histone proteins and transcriptional events.

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