Identification and Comparison of Imprinted Genes Across Plant Species

Picard, Colette L.; Gehring, Mary

doi:10.1007/978-1-0716-0179-2_13

Cited by 16 publications

(13 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Regardless of whether whole tissues or single cells are collected, special care must be taken to prevent contamination of transcriptomes by RNA from surrounding maternal tissues (Schon and Nodine 2017 ). Finally, assuming that parental genomic imprinting is found in ferns, lycophytes, and bryophytes, a bioinformatic comparison of imprinted genes across all land plant groups using a recently published pipeline (Picard and Gehring 2020 ) may help uncover if common pathways are affected.…”

Section: Perspectivesmentioning

confidence: 99%

The evolution of imprinting in plants: beyond the seed

Montgomery

Berger

2021

Plant Reprod

View full text Add to dashboard Cite

Genomic imprinting results in the biased expression of alleles depending on if the allele was inherited from the mother or the father. Despite the prevalence of sexual reproduction across eukaryotes, imprinting is only found in placental mammals, flowering plants, and some insects, suggesting independent evolutionary origins. Numerous hypotheses have been proposed to explain the selective pressures that favour the innovation of imprinted gene expression and each differs in their experimental support and predictions. Due to the lack of investigation of imprinting in land plants, other than angiosperms with triploid endosperm, we do not know whether imprinting occurs in species lacking endosperm and with embryos developing on maternal plants. Here, we discuss the potential for uncovering additional examples of imprinting in land plants and how these observations may provide additional support for one or more existing imprinting hypotheses.

show abstract

Section: Perspectivesmentioning

confidence: 99%

The evolution of imprinting in plants: beyond the seed

Montgomery

Berger

2021

Plant Reprod

View full text Add to dashboard Cite

show abstract

“…The identification of imprinted genes in the endosperm and embryo can be confounded by maternal tissues [ 38 , 39 ] and parent-of-origin effects [ 40 ]. The seed coat, a maternal tissue that surrounds and protects the seed, can lead to false-positive MEGs.…”

Section: Discussionmentioning

confidence: 99%

Identification of Imprinted Genes Based on Homology: An Example of Fragaria vesca

Liu

Jing

Zhang

et al. 2021

Genes

View full text Add to dashboard Cite

Genomic imprinting has drawn increasing attention in plant biology in recent years. At present, hundreds of imprinted genes have been identified in various plants, and some of them have been reported to be evolutionarily conserved in plant species. In this research, 17 candidate genes in Fragaria vesca were obtained based on the homologous imprinted genes in Arabidopsis thaliana and other species. We further constructed reciprocal crosses of diploid strawberry (F. vesca) using the varieties 10-41 and 18-86 as the parents to investigate the conservation of these imprinted genes. Potentially informative single nucleotide polymorphisms (SNPs) were used as molecular markers of two parents obtained from candidate imprinted genes which have been cloned and sequenced. Meanwhile, we analyzed the SNP site variation ratios and parent-of-origin expression patterns of candidate imprinted genes at 10 days after pollination (DAP) endosperm and embryo for the hybrids of reciprocal cross, respectively. A total of five maternally expressed genes (MEGs), i.e., FvARI8, FvKHDP-2, FvDRIP2, FvBRO1, and FvLTP3, were identified in the endosperm, which did not show imprinting in the embryo. Finally, tissues expression analysis indicated that the five imprinted genes excluding FvDRIP2 mainly expressed in the endosperm. This is the first report on imprinted genes of Fragaria, and we provide a simple and rapid method based on homologous conservation to screen imprinted genes. The present study will provide a basis for further study of function and mechanism of genomic imprinting in F. vesca.

show abstract

“…Translational research on imprinted genes from model species to crops, or between crops, will require conservation of any functions arising from the imprinted state. A key challenge for the plant genomic imprinting community has been the use of common protocols and bioinformatic protocols to identify which endosperm-expressed genes are imprinted across different species (Picard & Gehring, 2020;Wyder, Raissig, & Grossniklaus, 2019).…”

Section: Epigenetic Control Of Seed Development and Seed Traitsmentioning

confidence: 99%

First the seed: Genomic advances in seed science for improved crop productivity and food security

Dwivedi¹,

Spillane

Lopez

et al. 2021

Crop Science

View full text Add to dashboard Cite

Seeds are valuable sources of carbohydrates, lipids, proteins, fibers, minerals, and vitamins. They provide energy and nutrition to germinating seedlings, food to humans, feed to livestock and feedstocks to industry. High-throughput analyses of gene expression in crops has identified many candidate genes associated with seed dormancy, longevity, germination, and vigor. In this review, we cover the latest research focusing on such key seed traits. Transcriptome analyses of time-courses of seed filling have identified sets of genes expressed at different stages of this process. The potential role of epigenetics (including seed-endosperm imprinted genes) in regulating seed development and chemistry is highlighted herein. We also discuss how advances in genomics and seed biology are facilitating the unravelling of associations between seed traits with genebank accessions and gene sequences, including how functional research can accelerate the discovery of allelic variants. Such knowledge of functional effects relating to gene variants is necessary for more efficient and cost-effective management of genetic resources or for redesigning crops with specific seed characteristics. For instance, genebank curators may assess seed viability by monitoring changes in gene expression of biomarker genes in dry seed samples to decide germplasm regeneration and assess genetic integrity of collections by monitoring changes in This article is protected by copyright. All rights reserved. diversity and allele frequencies between samples of same accession stored in genebanks. We highlight that resistance to preharvest sprouting can be enhanced through genomicsassisted breeding in otherwise nondormant rice and wheat cultivars, while pimt, another valuable marker for seed longevity, may be deployed to enhance seed vigor in crops.

show abstract

Identification and Comparison of Imprinted Genes Across Plant Species

Cited by 16 publications

References 47 publications

The evolution of imprinting in plants: beyond the seed

The evolution of imprinting in plants: beyond the seed

Identification of Imprinted Genes Based on Homology: An Example of Fragaria vesca

First the seed: Genomic advances in seed science for improved crop productivity and food security

Contact Info

Product

Resources

About