scholarly journals Lack of parent-of-origin effects in Nasonia jewel wasp: A replication and extension study

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252457
Author(s):  
Kimberly C. Olney ◽  
Joshua D. Gibson ◽  
Heini M. Natri ◽  
Avery Underwood ◽  
Juergen Gadau ◽  
...  
Keyword(s):  
Genomic Imprinting ◽  
Sequence Data ◽  
Original Data ◽  
Paternal Allele ◽  
Analysis Strategy ◽  
Parent Of Origin ◽  
Origin Effects ◽  
New Processing ◽  
Diploid Cells ◽  
Origin Effect

In diploid cells, the paternal and maternal alleles are, on average, equally expressed. There are exceptions from this: a small number of genes express the maternal or paternal allele copy exclusively. This phenomenon, known as genomic imprinting, is common among eutherian mammals and some plant species; however, genomic imprinting in species with haplodiploid sex determination is not well characterized. Previous work reported no parent-of-origin effects in the hybrids of closely related haplodiploid Nasonia vitripennis and Nasonia giraulti jewel wasps, suggesting a lack of epigenetic reprogramming during embryogenesis in these species. Here, we replicate the gene expression dataset and observations using different individuals and sequencing technology, as well as reproduce these findings using the previously published RNA sequence data following our data analysis strategy. The major difference from the previous dataset is that they used an introgression strain as one of the parents and we found several loci that resisted introgression in that strain. Our results from both datasets demonstrate a species-of-origin effect, rather than a parent-of-origin effect. We present a reproducible workflow that others may use for replicating the results. Overall, we reproduced the original report of no parent-of-origin effects in the haplodiploid Nasonia using the original data with our new processing and analysis pipeline and replicated these results with our newly generated data.

scholarly journals Lack of parent-of-origin effects in Nasonia jewel wasp: a replication and extension study

2021 ◽  
Author(s):  
Kimberly C. Olney ◽  
Joshua D. Gibson ◽  
Heini M. Natri ◽  
Avery Underwood ◽  
Juergen Gadau ◽  
...  
Keyword(s):  
Genomic Imprinting ◽  
Sequence Data ◽  
Original Data ◽  
Paternal Allele ◽  
Analysis Strategy ◽  
Parent Of Origin ◽  
Origin Effects ◽  
New Processing ◽  
Diploid Cells ◽  
Origin Effect

AbstractIn diploid cells, the paternal and maternal alleles are, on average, equally expressed. There are exceptions from this: a small number of genes express the maternal or paternal allele copy exclusively. This phenomenon, known as genomic imprinting, is common among eutherian mammals and some plant species; however, genomic imprinting in species with haplodiploid sex determination is not well characterized. Previous work reported no parent-of-origin effects in the hybrids of closely related haplodiploid Nasonia vitripennis and Nasonia giraulti jewel wasps, suggesting a lack of epigenetic reprogramming during embryogenesis in these species. Here, we replicate the gene expression dataset and observations using different individuals and sequencing technology, as well as reproduce these findings using the previously published RNA sequence data following our data analysis strategy. The major difference from the previous dataset is that they used an introgression strain as one of the parents and we found several loci that resisted introgression in that strain. Our results from both datasets demonstrate a species-of-origin effect, rather than a parent-of-origin effect. We present a reproducible workflow that others may use for replicating the results. Overall, we reproduced the original report of no parent-of-origin effects in the haplodiploid Nasonia using the original data with our new processing and analysis pipeline and replicated these results with our newly generated data.

scholarly journals Parent-of-origin effect rough endosperm mutants in maize

2016 ◽  
Author(s):  
Fang Bai ◽  
Mary Daliberti ◽  
Alyssa Bagadion ◽  
Miaoyun Xu ◽  
Yubing Li ◽  
...  
Keyword(s):  
Female Parent ◽  
Mendelian Inheritance ◽  
Endosperm Development ◽  
Paternal Allele ◽  
Imprinted Genes ◽  
Incomplete Penetrance ◽  
Starchy Endosperm ◽  
Parent Of Origin ◽  
Origin Effects ◽  
Origin Effect

ABSTRACTParent-of-origin effect loci have non-Mendelian inheritance in which phenotypes are determined by either the maternal or paternal allele alone. In angiosperms, parent-of-origin effects can be caused by loci required for gametophyte development or by imprinted genes needed for seed development. Few parent-of-origin effect loci have been identified in maize (Zea mays) even though there are a large number of imprinted genes known from transcriptomics. We screened rough endosperm (rgh) mutants for parent-of-origin effects using reciprocal crosses with inbred parents. Six maternal rough endosperm (mre) and three paternal rough endosperm (pre) mutants were identified with three mre loci mapped. When inherited from the female parent, mre/+ seeds reduce grain-fill with a rough, etched, or pitted endosperm surface. Pollen transmission of pre mutants results in rgh endosperm as well as embryo lethality. Eight of the loci had significant distortion from the expected one-to-one ratio for parent-of-origin effects. Linked markers for mre1, mre2, and mre3 indicated that the mutant alleles have no bias in transmission. Histological analysis of mre1, mre2, mre3, and pre*-949 showed altered timing of starch grain accumulation and basal endosperm transfer cell layer (BETL) development. The mre1 locus delays BETL and starchy endosperm development, while mre2 and pre*-949 cause ectopic starchy endosperm differentiation. We conclude that many parent-of-origin effects in maize have incomplete penetrance of kernel phenotypes and that there is a large diversity of endosperm developmental roles for parent-of-origin effect loci.

scholarly journals Genomic imprinting and parent-of-origin effects on complex traits

2013 ◽  
Vol 14 (9) ◽  
pp. 609-617 ◽  
Author(s):  
Heather A. Lawson ◽  
James M. Cheverud ◽  
Jason B. Wolf
Keyword(s):  
Genomic Imprinting ◽  
Complex Traits ◽  
Parent Of Origin ◽  
Origin Effects

scholarly journals DNA demethylase ROS1 negatively regulates the imprinting of DOGL4 and seed dormancy in Arabidopsis thaliana

2018 ◽  
Vol 115 (42) ◽  
pp. E9962-E9970 ◽  
Author(s):  
Haifeng Zhu ◽  
Wenxiang Xie ◽  
Dachao Xu ◽  
Daisuke Miki ◽  
Kai Tang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Seed Dormancy ◽  
Genomic Imprinting ◽  
Dna Demethylation ◽  
Paternal Allele ◽  
Maternal Allele ◽  
Imprinted Gene ◽  
Differential Gene ◽  
Parent Of Origin ◽  
Dna Demethylase

Genomic imprinting is a form of epigenetic regulation resulting in differential gene expression that reflects the parent of origin. In plants, imprinted gene expression predominantly occurs in the seed endosperm. Maternal-specific DNA demethylation by the DNA demethylase DME frequently underlies genomic imprinting in endosperm. Whether other more ubiquitously expressed DNA demethylases regulate imprinting is unknown. Here, we found that the DNA demethylase ROS1 regulates the imprinting of DOGL4. DOGL4 is expressed from the maternal allele in endosperm and displays preferential methylation and suppression of the paternal allele. We found that ROS1 negatively regulates imprinting by demethylating the paternal allele, preventing its hypermethylation and complete silencing. Furthermore, we found that DOGL4 negatively affects seed dormancy and response to the phytohormone abscisic acid and that ROS1 controls these processes by regulating DOGL4. Our results reveal roles for ROS1 in mitigating imprinted gene expression and regulating seed dormancy.

scholarly journals Parent-of-origin effects, allele-specific expression, genomic imprinting and paternal manipulation in social insects

2021 ◽  
Vol 376 (1826) ◽  
Author(s):  
Benjamin P. Oldroyd ◽  
Boris Yagound
Keyword(s):  
Gene Expression ◽  
Genomic Imprinting ◽  
Social Insects ◽  
Social Insect ◽  
Specific Gene ◽  
Specific Expression ◽  
Rna Molecules ◽  
Parent Of Origin ◽  
Origin Effects ◽  
Gene Expression Studies

Haplo-diploidy and the relatedness asymmetries it generates mean that social insects are prime candidates for the evolution of genomic imprinting. In single-mating social insect species, some genes may be selected to evolve genomic mechanisms that enhance reproduction by workers when they are inherited from a female. This situation reverses in multiple mating species, where genes inherited from fathers can be under selection to enhance the reproductive success of daughters. Reciprocal crosses between subspecies of honeybees have shown strong parent-of-origin effects on worker reproductive phenotypes, and this could be evidence of such genomic imprinting affecting genes related to worker reproduction. It is also possible that social insect fathers directly affect gene expression in their daughters, for example, by placing small interfering RNA molecules in semen. Gene expression studies have repeatedly found evidence of parent-specific gene expression in social insects, but it is unclear at this time whether this arises from genomic imprinting, paternal manipulation, an artefact of cyto-nuclear interactions, or all of these. This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’

Parent-of-origin effect and genomic imprinting of the HTR2A receptor gene T102C polymorphism in psychosis

2007 ◽  
Vol 151 (3) ◽  
pp. 243-248 ◽  
Author(s):  
Vincenzo De Luca ◽  
Olga Likhodi ◽  
James L. Kennedy ◽  
Albert H.C. Wong
Keyword(s):  
Genomic Imprinting ◽  
Receptor Gene ◽  
Parent Of Origin ◽  
T102c Polymorphism ◽  
Origin Effect

Loss of genomic imprinting in Drosophila clones

Genome ◽  
2006 ◽  
Vol 49 (8) ◽  
pp. 1043-1046 ◽  
Author(s):  
Andrew J Haigh ◽  
Vett K Lloyd
Keyword(s):  
Drosophila Melanogaster ◽  
Genomic Imprinting ◽  
X Chromosome ◽  
Chromatin Structure ◽  
Nuclear Transfer ◽  
Paternal Allele ◽  
Monoallelic Expression ◽  
C Elegans ◽  
Human Cancers ◽  
Parent Of Origin

Genomic imprinting is a process that genetically distinguishes maternal and paternal genomes, and can result in parent-of-origin-dependent monoallelic expression of a gene that is dependent on the parent of origin. As such, an otherwise functional maternally inherited allele may be silenced so that the gene is expressed exclusively from the paternal allele, or vice versa. Once thought to be restricted to mammals, genomic imprinting has been documented in angiosperm plants (J.L. Kermicle. 1970. Genetics, 66: 69–85), zebrafish (C.C. Martin and R. McGowan. 1995. Genet. Res. 65: 21–28), insects, and C. elegans (C.J. Bean, C.E. Schaner, and W.G. Kelly. 2004. Nat. Genet. 36: 100–105.). In each case, it appears to rely on differential chromatin structure. Aberrant imprinting has been implicated in various human cancers and has been detected in a number of cloned mammals, potentially limiting the usefulness of somatic nuclear transfer. Here we show that genomic imprinting associated with a mini-X chromosome is lost in Drosophila melanogaster clones.Key words: cloning, Drosophila, genomic imprinting, nuclear transfer.

scholarly journals An Introduction to Genomic Imprinting and Parent of Origin Effects

1996 ◽  
Vol 45 (1-2) ◽  
pp. 59-61
Author(s):  
J.G. Hall ◽  
E. Lopez-Rangel
Keyword(s):  
Genomic Imprinting ◽  
Protein Interactions ◽  
Uniparental Disomy ◽  
Protein Protein Interactions ◽  
Human Heredity ◽  
Expression Of Genes ◽  
Recent Developments ◽  
Genetic Mechanisms ◽  
Parent Of Origin ◽  
Origin Effects

Recent developments in molecular genetics and cytogenetics have allowed for better understanding of the inheritance and expression of genes. Many newly recognized mechanisms such as genomic imprinting, mosaicism, allelic expansion, cytoplasmic inheritance and uniparental disomy have been recognized to play an important role in human heredity.Genomic imprinting refers to differences in the phenotype which are observed depending on whether the gene was inherited from the father or from the mother. Genomic imprinting is a difficult concept to understand because imprinting has been used loosely to refer to a number of different mechanisms including psychological development, endocrinological actions of cells and protein-protein interactions. Genomic imprinting produces parent-of-origin effects. Parent-of-origin effects is a term that encompasses many of the non-traditional types of inheritance and other genetic and non-genetic mechanisms which show an effect depending on whether they were paternally or maternally derived.

scholarly journals A parent-of-origin effect on honeybee worker ovary size

2014 ◽  
Vol 281 (1775) ◽  
pp. 20132388 ◽  
Author(s):  
Benjamin P. Oldroyd ◽  
Michael H. Allsopp ◽  
Katherine M. Roth ◽  
Emily J. Remnant ◽  
Robert A. Drewell ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Reproductive Traits ◽  
Female Offspring ◽  
Apis Mellifera Capensis ◽  
Intragenomic Conflict ◽  
Size Number ◽  
Parent Of Origin ◽  
Origin Effects ◽  
Honeybee Subspecies ◽  
Origin Effect

Apis mellifera capensis is unique among honeybees in that unmated workers can produce pseudo-clonal female offspring via thelytokous parthenogenesis. Workers use this ability to compete among themselves and with their queen to be the mother of new queens. Males could therefore enhance their reproductive success by imprinting genes that enhance fertility in their daughter workers. This possibility sets the scene for intragenomic conflict between queens and drones over worker reproductive traits. Here, we show a strong parent-of-origin effect for ovary size (number of ovarioles) in reciprocal crosses between two honeybee subspecies, A. m. capensis and Apis mellifera scutellata. In this cross, workers with an A. m. capensis father had 30% more ovarioles than genotypically matched workers with an A. m. scutellata father. Other traits we measured (worker weight at emergence and the presence/absence of a spermatheca) are influenced more by rearing conditions than by parent-of-origin effects. Our study is the first to show a strong epigenetic (or, less likely, cytoplasmic maternal) effect for a reproductive trait in the honeybee and suggests that a search for parent-of-origin effects in other social insects may be fruitful.

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