1
|
Bente H, Köhler C. Molecular basis and evolutionary drivers of endosperm-based hybridization barriers. PLANT PHYSIOLOGY 2024; 195:155-169. [PMID: 38298124 PMCID: PMC11060687 DOI: 10.1093/plphys/kiae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/05/2024] [Accepted: 01/06/2024] [Indexed: 02/02/2024]
Abstract
The endosperm, a transient seed tissue, plays a pivotal role in supporting embryo growth and germination. This unique feature sets flowering plants apart from gymnosperms, marking an evolutionary innovation in the world of seed-bearing plants. Nevertheless, the importance of the endosperm extends beyond its role in providing nutrients to the developing embryo by acting as a versatile protector, preventing hybridization events between distinct species and between individuals with different ploidy. This phenomenon centers on growth and differentiation of the endosperm and the speed at which both processes unfold. Emerging studies underscore the important role played by type I MADS-box transcription factors, including the paternally expressed gene PHERES1. These factors, along with downstream signaling pathways involving auxin and abscisic acid, are instrumental in regulating endosperm development and, consequently, the establishment of hybridization barriers. Moreover, mutations in various epigenetic regulators mitigate these barriers, unveiling a complex interplay of pathways involved in their formation. In this review, we discuss the molecular underpinnings of endosperm-based hybridization barriers and their evolutionary drivers.
Collapse
Affiliation(s)
- Heinrich Bente
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Claudia Köhler
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| |
Collapse
|
2
|
Yang K, Tang Y, Li Y, Guo W, Hu Z, Wang X, Berger F, Li J. Two imprinted genes primed by DEMETER in the central cell and activated by WRKY10 in the endosperm. J Genet Genomics 2024:S1673-8527(24)00072-9. [PMID: 38599515 DOI: 10.1016/j.jgg.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
The early development of the endosperm is crucial for balancing the allocation of maternal nutrients to offspring. This process is believed to be evolutionarily associated with genomic imprinting, resulting in parentally biased allelic gene expression. Beyond FertilizationIndependentSeed (FIS) genes, the number of imprinted genes involved in early endosperm development and seed size determination remains limited. This study introduces two early endosperm-expressed HAIKU (IKU) downstream Candidate F-box 1 (ICF1) and ICF2, as maternally expressed imprinted genes (MEGs). Although these genes are also demethylated by DEMETER (DME) in the central cell, their activation differs from the direct DME-mediated activation seen in classical MEGs such as the FIS genes. Instead, ICF maternal alleles carry pre-established hypomethylation in their promoters, priming them for activation by the WRKY10 transcription factor in the endosperm. On the contrary, paternal alleles are predominantly suppressed by CG methylation. Furthermore, we find that ICF genes partially contribute to the small seed size observed in iku mutants. Our discovery reveals a two-step regulatory mechanism that highlights the important role of conventional transcription factors in the activation of imprinted genes, which was previously not fully recognized. Therefore, the mechanism provides a new dimension to understand the transcriptional regulation of imprinting in plant reproduction and development.
Collapse
Affiliation(s)
- Ke Yang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, Hainan 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Yuling Tang
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, Hainan 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Yue Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Wenbin Guo
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zhengdao Hu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xuanpeng Wang
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, Hainan 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, 1030 Vienna, Austria
| | - Jing Li
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, Hainan 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China.
| |
Collapse
|
3
|
Liu B, Yang D, Wang D, Liang C, Wang J, Lisch D, Zhao M. Heritable changes of epialleles near genes in maize can be triggered in the absence of CHH methylation. PLANT PHYSIOLOGY 2024; 194:2511-2532. [PMID: 38109503 PMCID: PMC10980416 DOI: 10.1093/plphys/kiad668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 12/20/2023]
Abstract
Trans-chromosomal interactions resulting in changes in DNA methylation during hybridization have been observed in several plant species. However, little is known about the causes or consequences of these interactions. Here, we compared DNA methylomes of F1 hybrids that are mutant for a small RNA biogenesis gene, Mop1 (Mediator of paramutation1), with that of their parents, wild-type siblings, and backcrossed progeny in maize (Zea mays). Our data show that hybridization triggers global changes in both trans-chromosomal methylation (TCM) and trans-chromosomal demethylation (TCdM), most of which involved changes in CHH methylation. In more than 60% of these TCM differentially methylated regions (DMRs) in which small RNAs are available, no significant changes in the quantity of small RNAs were observed. Methylation at the CHH TCM DMRs was largely lost in the mop1 mutant, although the effects of this mutant varied depending on the location of these DMRs. Interestingly, an increase in CHH at TCM DMRs was associated with enhanced expression of a subset of highly expressed genes and suppressed expression of a small number of lowly expressed genes. Examination of the methylation levels in backcrossed plants demonstrates that both TCM and TCdM can be maintained in the subsequent generation, but that TCdM is more stable than TCM. Surprisingly, although increased CHH methylation in most TCM DMRs in F1 plants required Mop1, initiation of a new epigenetic state of these DMRs did not require a functional copy of this gene, suggesting that initiation of these changes is independent of RNA-directed DNA methylation.
Collapse
Affiliation(s)
- Beibei Liu
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Diya Yang
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Dafang Wang
- Biology Department, Hofstra University, Hempstead, NY 11549, USA
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL 32610, USA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Meixia Zhao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| |
Collapse
|
4
|
Soliman HK, Coughlan JM. United by Conflict: Convergent Signatures of Parental Conflict in Angiosperms and Placental Mammals. J Hered 2024:esae009. [PMID: 38366852 DOI: 10.1093/jhered/esae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Indexed: 02/18/2024] Open
Abstract
Endosperm in angiosperms and placenta in eutherians are convergent innovations for efficient embryonic nutrient transfer. Despite advantages, this reproductive strategy incurs metabolic costs that maternal parents disproportionately shoulder, leading to potential inter-parental conflict over optimal offspring investment. Genomic imprinting-parent-of-origin-biased gene expression-is fundamental for endosperm and placenta development and has convergently evolved in angiosperms and mammals, in part, to resolve parental conflict. Here, we review the mechanisms of genomic imprinting in these taxa. Despite differences in the timing and spatial extent of imprinting, these taxa exhibit remarkable convergence in the molecular machinery and genes governing imprinting. We then assess the role of parental conflict in shaping evolution within angiosperms and eutherians using four criteria: (1) Do differences in the extent of sibling relatedness cause differences in the inferred strength of parental conflict? (2) Do reciprocal crosses between taxa with different inferred histories of parental conflict exhibit parent-of-origin growth effects? (3) Are these parent-of-origin growth effects caused by dosage-sensitive mechanisms and do these loci exhibit signals of positive selection? (4) Can normal development be restored by genomic perturbations that restore stoichiometric balance in the endosperm/placenta? Although we find evidence for all criteria in angiosperms and eutherians, suggesting that parental conflict may help shape their evolution, many questions remain. Additionally, myriad differences between the two taxa suggest that their respective biologies may shape how/when/where/to what extent parental conflict manifests. Lastly, we discuss outstanding questions, highlighting the power of comparative work in quantifying the role of parental conflict in evolution.
Collapse
Affiliation(s)
- Hagar K Soliman
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, 06511, United States
- Department of Biotechnology, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Jenn M Coughlan
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, 06511, United States
| |
Collapse
|
5
|
Montgomery SA, Berger F. Paternal imprinting in Marchantia polymorpha. THE NEW PHYTOLOGIST 2024; 241:1000-1006. [PMID: 37936346 DOI: 10.1111/nph.19377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/09/2023] [Indexed: 11/09/2023]
Abstract
We are becoming aware of a growing number of organisms that do not express genetic information equally from both parents as a result of an epigenetic phenomenon called genomic imprinting. Recently, it was shown that the entire paternal genome is repressed during the diploid phase of the life cycle of the liverwort Marchantia polymorpha. The deposition of the repressive epigenetic mark H3K27me3 on the male pronucleus is responsible for the imprinted state, which is reset by the end of meiosis. Here, we put these recent reports in perspective of other forms of imprinting and discuss the potential mechanisms of imprinting in bryophytes and the causes of its evolution.
Collapse
Affiliation(s)
- Sean A Montgomery
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), C/ del Dr Aiguader, 88, 08003, Barcelona, Spain
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr Bohr-Gasse 3, 1030, Vienna, Austria
| |
Collapse
|
6
|
Han B, Li Y, Wu D, Li DZ, Liu A, Xu W. Dynamics of imprinted genes and their epigenetic mechanisms in castor bean seed with persistent endosperm. THE NEW PHYTOLOGIST 2023; 240:1868-1882. [PMID: 37717216 DOI: 10.1111/nph.19265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/25/2023] [Indexed: 09/19/2023]
Abstract
Genomic imprinting refers to parent-of-origin-dependent gene expression and primarily occurs in the endosperm of flowering plants, but its functions and epigenetic mechanisms remain to be elucidated in eudicots. Castor bean, a eudicot with large and persistent endosperm, provides an excellent system for studying the imprinting. Here, we identified 131 imprinted genes in developing endosperms and endosperm at seed germination phase of castor bean, involving into the endosperm development, accumulation of storage compounds and specially seed germination. Our results showed that the transcriptional repression of maternal allele of DNA METHYLTRANSFERASE 1 (MET1) may be required for maternal genome demethylation in the endosperm. DNA methylation analysis showed that only a small fraction of imprinted genes was associated with allele-specific DNA methylation, and most of them were closely associated with constitutively unmethylated regions (UMRs), suggesting a limited role for DNA methylation in controlling genomic imprinting. Instead, histone modifications can be asymmetrically deposited in maternal and paternal genomes in a DNA methylation-independent manner to control expression of most imprinted genes. These results expanded our understanding of the occurrence and biological functions of imprinted genes and showed the evolutionary flexibility of the imprinting machinery and mechanisms in plants.
Collapse
Affiliation(s)
- Bing Han
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Yelan Li
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Di Wu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Aizhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Wei Xu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| |
Collapse
|
7
|
Bresnahan ST, Galbraith D, Ma R, Anton K, Rangel J, Grozinger CM. Beyond conflict: Kinship theory of intragenomic conflict predicts individual variation in altruistic behaviour. Mol Ecol 2023; 32:5823-5837. [PMID: 37746895 DOI: 10.1111/mec.17145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/26/2023]
Abstract
Behavioural variation is essential for animals to adapt to different social and environmental conditions. The Kinship Theory of Intragenomic Conflict (KTIC) predicts that parent-specific alleles can support different behavioural strategies to maximize allele fitness. Previous studies, including in honey bees (Apis mellifera), supported predictions of the KTIC for parent-specific alleles to promote selfish behaviour. Here, we test the KTIC prediction that for altruism-promoting genes (i.e. those that promote behaviours that support the reproductive fitness of kin), the allele with the higher altruism optimum should be selected to be expressed while the other is silenced. In honey bee colonies, workers act altruistically when tending to the queen by performing a 'retinue' behaviour, distributing the queen's mandibular pheromone (QMP) throughout the hive. Workers exposed to QMP do not activate their ovaries, ensuring they care for the queen's brood instead of competing to lay unfertilized eggs. Due to the haplodiploid genetics of honey bees, the KTIC predicts that response to QMP is favoured by the maternal genome. We report evidence for parent-of-origin effects on the retinue response behaviour, ovarian development and gene expression in brains of worker honey bees exposed to QMP, consistent with the KTIC. Additionally, we show enrichment for genes with parent-of-origin expression bias within gene regulatory networks associated with variation in bees' response to QMP. Our study demonstrates that intragenomic conflict can shape diverse social behaviours and influence expression patterns of single genes as well as gene networks.
Collapse
Affiliation(s)
- Sean T Bresnahan
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in Molecular, Cellular, and Integrative Biosciences, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - David Galbraith
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Rong Ma
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kate Anton
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Juliana Rangel
- Department of Entomology, Texas A&M University, College Station, Texas, USA
| | - Christina M Grozinger
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| |
Collapse
|
8
|
Liu B, Zhao M. How transposable elements are recognized and epigenetically silenced in plants? CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102428. [PMID: 37481986 DOI: 10.1016/j.pbi.2023.102428] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/25/2023]
Abstract
Plant genomes are littered with transposable elements (TEs). Because TEs are potentially highly mutagenic, host organisms have evolved a set of defense mechanisms to recognize and epigenetically silence them. Although the maintenance of TE silencing is well studied, our understanding of the initiation of TE silencing is limited, but it clearly involves small RNAs and DNA methylation. Once TEs are silent, the silent state can be maintained to subsequent generations. However, under some circumstances, such inheritance is unstable, leading to the escape of TEs to the silencing machinery, resulting in the transcriptional activation of TEs. Epigenetic control of TEs has been found to be closely linked to many other epigenetic phenomena, such as genomic imprinting, and is known to contribute to regulation of genes, especially those near TEs. Here we review and discuss the current models of TE silencing, its unstable inheritance after hybridization, and the effects of epigenetic regulation of TEs on genomic imprinting.
Collapse
Affiliation(s)
- Beibei Liu
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Meixia Zhao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.
| |
Collapse
|
9
|
Yadav S, Kalwan G, Meena S, Gill SS, Yadava YK, Gaikwad K, Jain PK. Unravelling the due importance of pseudogenes and their resurrection in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108062. [PMID: 37778114 DOI: 10.1016/j.plaphy.2023.108062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023]
Abstract
The complexities of a genome are underpinned to the vast expanses of the intergenic region, which constitutes ∼97-98% of the genome. This region is essentially composed of what is colloquially referred to as the "junk DNA" and is composed of various elements like transposons, repeats, pseudogenes, etc. The latter have long been considered as dead elements merely contributing to transcriptional noise in the genome. Many studies now describe the previously unknown regulatory functions of these genes. Recent advances in the Next-generation sequencing (NGS) technologies have allowed unprecedented access to these regions. With the availability of whole genome sequences of more than 788 different plant species in past 20 years, genome annotation has become feasible like never before. Different bioinformatic pipelines are available for the identification of pseudogenes. However, still little is known about their biological functions. The functional validation of these genes remains challenging and research in this area is still in infancy, particularly in plants. CRISPR/Cas-based genome editing could provide solutions to understand the biological roles of these genes by allowing creation of precise edits within these genes. The possibility of pseudogene reactivation or resurrection as has been demonstrated in a few studies might open new avenues of genetic manipulation to yield a desirable phenotype. This review aims at comprehensively summarizing the progress made with regards to the identification of pseudogenes and understanding their biological functions in plants.
Collapse
Affiliation(s)
- Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India; PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India; Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Gopal Kalwan
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India; PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Shashi Meena
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India; Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sarvajeet Singh Gill
- Stress Physiology & Molecular Biology Lab, Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124 001, Haryana, India
| | - Yashwant K Yadava
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - P K Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
| |
Collapse
|
10
|
Rojek J, Ohad N. The phenomenon of autonomous endosperm in sexual and apomictic plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4324-4348. [PMID: 37155961 PMCID: PMC10433939 DOI: 10.1093/jxb/erad168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023]
Abstract
Endosperm is a key nutritive tissue that supports the developing embryo or seedling, and serves as a major nutritional source for human and livestock feed. In sexually-reproducing flowering plants, it generally develops after fertilization. However, autonomous endosperm (AE) formation (i.e. independent of fertilization) is also possible. Recent findings of AE loci/ genes and aberrant imprinting in native apomicts, together with a successful initiation of parthenogenesis in rice and lettuce, have enhanced our understanding of the mechanisms bridging sexual and apomictic seed formation. However, the mechanisms driving AE development are not well understood. This review presents novel aspects related to AE development in sexual and asexual plants underlying stress conditions as the primary trigger for AE. Both application of hormones to unfertilized ovules and mutations that impair epigenetic regulation lead to AE development in sexual Arabidopsis thaliana, which may point to a common pathway for both phenomena. Apomictic-like AE development under experimental conditions can take place due to auxin-dependent gene expression and/or DNA methylation.
Collapse
Affiliation(s)
- Joanna Rojek
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Nir Ohad
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
11
|
Zhao Z, Wang Y, Peng Z, Luo Z, Zhao M, Wang J. Allelic expression of AhNSP2-B07 due to parent of origin affects peanut nodulation. FRONTIERS IN PLANT SCIENCE 2023; 14:1193465. [PMID: 37426991 PMCID: PMC10325728 DOI: 10.3389/fpls.2023.1193465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/19/2023] [Indexed: 07/11/2023]
Abstract
Legumes are well-known for establishing a symbiotic relationship with rhizobia in root nodules to fix nitrogen from the atmosphere. The nodulation signaling pathway 2 (NSP2) gene plays a critical role in the symbiotic signaling pathway. In cultivated peanut, an allotetraploid (2n = 4x = 40, AABB) legume crop, natural polymorphisms in a pair of NSP2 homoeologs (Na and Nb) located on chromosomes A08 and B07, respectively, can cause loss of nodulation. Interestingly, some heterozygous (NBnb) progeny produced nodules, while some others do not, suggesting non-Mendelian inheritance in the segregating population at the Nb locus. In this study, we investigated the non-Mendelian inheritance at the NB locus. Selfing populations were developed to validate the genotypical and phenotypical segregating ratios. Allelic expression was detected in roots, ovaries, and pollens of heterozygous plants. Bisulfite PCR and sequencing of the Nb gene in gametic tissue were performed to detect the DNA methylation variations of this gene in different gametic tissues. The results showed that only one allele at the Nb locus expressed in peanut roots during symbiosis. In the heterozygous (Nbnb) plants, if dominant allele expressed, the plants produced nodules, if recessive allele expressed, then no nodules were produced. qRT-PCR experiments revealed that the expression of Nb gene in the ovary was extremely low, about seven times lower than that in pollen, regardless of genotypes or phenotypes of the plants at this locus. The results indicated that Nb gene expression in peanut depends on the parent of origin and is imprinted in female gametes. However, no significant differences of DNA methylation level were detected between these two gametic tissues by bisulfite PCR and sequencing. The results suggested that the remarkable low expression of Nb in female gametes may not be caused by DNA methylation. This study provided a unique genetic basis of a key gene involved in peanut symbiosis, which could facilitate understanding the regulation of gene expression in symbiosis in polyploid legumes.
Collapse
Affiliation(s)
- Zifan Zhao
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Yichun Wang
- Agronomy Department, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
| | - Ze Peng
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Ziliang Luo
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Meixia Zhao
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
| |
Collapse
|
12
|
Liu B, Yang D, Wang D, Liang C, Wang J, Lisch D, Zhao M. Heritable changes of epialleles in maize can be triggered in the absence of DNA methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.15.537008. [PMID: 37131670 PMCID: PMC10153178 DOI: 10.1101/2023.04.15.537008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Trans-chromosomal interactions resulting in changes in DNA methylation during hybridization have been observed in several plant species. However, very little is known about the causes or consequences of these interactions. Here, we compared DNA methylomes of F1 hybrids that are mutant for a small RNA biogenesis gene, Mop1 (mediator of paramutation1) with that of their parents, wild type siblings, and backcrossed progeny in maize. Our data show that hybridization triggers global changes in both trans-chromosomal methylation (TCM) and trans-chromosomal demethylation (TCdM), most of which involved changes in CHH methylation. In more than 60% of these TCM differentially methylated regions (DMRs) in which small RNAs are available, no significant changes in the quantity of small RNAs were observed. Methylation at the CHH TCM DMRs was largely lost in the mop1 mutant, although the effects of this mutant varied depending on the location of the CHH DMRs. Interestingly, an increase in CHH at TCM DMRs was associated with enhanced expression of a subset of highly expressed genes and suppressed expression of a small number of lowly expressed genes. Examination of the methylation levels in backcrossed plants demonstrates that TCM and TCdM can be maintained in the subsequent generation, but that TCdM is more stable than TCM. Surprisingly, although increased CHH methylation in F1 plants did require Mop1, initiation of the changes in the epigenetic state of TCM DMRs did not require a functional copy of this gene, suggesting that initiation of these changes is not dependent on RNA-directed DNA methylation.
Collapse
Affiliation(s)
- Beibei Liu
- Department of Biology, Miami University, Oxford, OH 45056
| | - Diya Yang
- Department of Biology, Miami University, Oxford, OH 45056
| | - Dafang Wang
- Biology Department, Hofstra University, Hempstead, NY 11549
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH 45056
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL 32610
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Meixia Zhao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| |
Collapse
|
13
|
Szala K, Dmochowska-Boguta M, Bocian J, Orczyk W, Nadolska-Orczyk A. Transgenerational Paternal Inheritance of TaCKX GFMs Expression Patterns Indicate a Way to Select Wheat Lines with Better Parameters for Yield-Related Traits. Int J Mol Sci 2023; 24:ijms24098196. [PMID: 37175902 PMCID: PMC10179260 DOI: 10.3390/ijms24098196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Members of the TaCKX gene family (GFMs) encode the cytokinin oxygenase/dehydrogenase enzyme (CKX), which irreversibly degrades cytokinins in the organs of wheat plants; therefore, these genes perform a key role in the regulation of yield-related traits. The purpose of the investigation was to determine how expression patterns of these genes, together with the transcription factor-encoding gene TaNAC2-5A, and yield-related traits are inherited to apply this knowledge to speed up breeding processes. The traits were tested in 7 days after pollination (DAP) spikes and seedling roots of maternal and paternal parents and their F2 progeny. The expression levels of most of them and the yield were inherited in F2 from the paternal parent. Some pairs or groups of genes cooperated, and some showed opposite functions. Models of up- or down-regulation of TaCKX GFMs and TaNAC2-5A in low-yielding maternal plants crossed with higher-yielding paternal plants and their high-yielding F2 progeny reproduced gene expression and yield of the paternal parent. The correlation coefficients between TaCKX GFMs, TaNAC2-5A, and yield-related traits in high-yielding F2 progeny indicated which of these genes were specifically correlated with individual yield-related traits. The most common was expressed in 7 DAP spikes TaCKX2.1, which positively correlated with grain number, grain yield, spike number, and spike length, and seedling root mass. The expression levels of TaCKX1 or TaNAC2-5A in the seedling roots were negatively correlated with these traits. In contrast, the thousand grain weight (TGW) was negatively regulated by TaCKX2.2.2, TaCKX2.1, and TaCKX10 in 7 DAP spikes but positively correlated with TaCKX10 and TaNAC2-5A in seedling roots. Transmission of TaCKX GFMs and TaNAC2-5A expression patterns and yield-related traits from parents to the F2 generation indicate their paternal imprinting. These newly shown data of nonmendelian epigenetic inheritance shed new light on crossing strategies to obtain a high-yielding F2 generation.
Collapse
Affiliation(s)
- Karolina Szala
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, 05-870 Blonie, Poland
| | - Marta Dmochowska-Boguta
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, 05-870 Blonie, Poland
| | - Joanna Bocian
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, 05-870 Blonie, Poland
| | - Waclaw Orczyk
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, 05-870 Blonie, Poland
| | - Anna Nadolska-Orczyk
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, 05-870 Blonie, Poland
| |
Collapse
|
14
|
Ando A, Kirkbride RC, Qiao H, Chen ZJ. Endosperm and Maternal-specific expression of EIN2 in the endosperm affects endosperm cellularization and seed size in Arabidopsis. Genetics 2023; 223:iyac161. [PMID: 36282525 PMCID: PMC9910398 DOI: 10.1093/genetics/iyac161] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/05/2022] [Indexed: 11/13/2022] Open
Abstract
Seed size is related to plant evolution and crop yield and is affected by genetic mutations, imprinting, and genome dosage. Imprinting is a widespread epigenetic phenomenon in mammals and flowering plants. ETHYLENE INSENSITIVE2 (EIN2) encodes a membrane protein that links the ethylene perception to transcriptional regulation. Interestingly, during seed development EIN2 is maternally expressed in Arabidopsis and maize, but the role of EIN2 in seed development is unknown. Here, we show that EIN2 is expressed specifically in the endosperm, and the maternal-specific EIN2 expression affects temporal regulation of endosperm cellularization. As a result, seed size increases in the genetic cross using the ein2 mutant as the maternal parent or in the ein2 mutant. The maternal-specific expression of EIN2 in the endosperm is controlled by DNA methylation but not by H3K27me3 or by ethylene and several ethylene pathway genes tested. RNA-seq analysis in the endosperm isolated by laser-capture microdissection show upregulation of many endosperm-expressed genes such as AGAMOUS-LIKEs (AGLs) in the ein2 mutant or when the maternal EIN2 allele is not expressed. EIN2 does not interact with DNA and may act through ETHYLENE INSENSITIVE3 (EIN3), a DNA-binding protein present in sporophytic tissues, to activate target genes like AGLs, which in turn mediate temporal regulation of endosperm cellularization and seed size. These results provide mechanistic insights into endosperm and maternal-specific expression of EIN2 on endosperm cellularization and seed development, which could help improve seed production in plants and crops.
Collapse
Affiliation(s)
- Atsumi Ando
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ryan C Kirkbride
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hong Qiao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
15
|
Zumajo-Cardona C, Aguirre M, Castillo-Bravo R, Mizzotti C, Di Marzo M, Banfi C, Mendes MA, Spillane C, Colombo L, Ezquer I. Maternal control of triploid seed development by the TRANSPARENT TESTA 8 (TT8) transcription factor in Arabidopsis thaliana. Sci Rep 2023; 13:1316. [PMID: 36693864 PMCID: PMC9873634 DOI: 10.1038/s41598-023-28252-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/16/2023] [Indexed: 01/25/2023] Open
Abstract
The balance between parental genome dosage is critical to offspring development in both animals and plants. In some angiosperm species, despite the imbalance between maternally and paternally inherited chromosome sets, crosses between parental lines of different ploidy may result in viable offspring. However, many plant species, like Arabidopsis thaliana, present a post-zygotic reproductive barrier, known as triploid block which results in the inability of crosses between individuals of different ploidy to generate viable seeds but also, in defective development of the seed. Several paternal regulators have been proposed as active players in establishing the triploid block. Maternal regulators known to be involved in this process are some flavonoid biosynthetic (FB) genes, expressed in the innermost layer of the seed coat. Here we explore the role of selected flavonoid pathway genes in triploid block, including TRANSPARENT TESTA 4 (TT4), TRANSPARENT TESTA 7 (TT7), SEEDSTICK (STK), TRANSPARENT TESTA 16 (TT16), TT8 and TRANSPARENT TESTA 13 (TT13). This approach allowed us to detect that TT8, a bHLH transcription factor, member of this FB pathway is required for the paternal genome dosage, as loss of function tt8, leads to complete rescue of the triploid block to seed development.
Collapse
Affiliation(s)
- Cecilia Zumajo-Cardona
- Dipartimento Di BioScienze, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Manuel Aguirre
- Dipartimento Di BioScienze, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milano, Italy.,Translational Plant & Microbial Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
| | - Rosa Castillo-Bravo
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Chiara Mizzotti
- Dipartimento Di BioScienze, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Maurizio Di Marzo
- Dipartimento Di BioScienze, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Camilla Banfi
- Dipartimento Di BioScienze, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Marta A Mendes
- Dipartimento Di BioScienze, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Lucia Colombo
- Dipartimento Di BioScienze, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Ignacio Ezquer
- Dipartimento Di BioScienze, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milano, Italy.
| |
Collapse
|
16
|
Li T, Yin L, Stoll CE, Lisch D, Zhao M. Conserved noncoding sequences and de novo Mutator insertion alleles are imprinted in maize. PLANT PHYSIOLOGY 2023; 191:299-316. [PMID: 36173333 PMCID: PMC9806621 DOI: 10.1093/plphys/kiac459] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 08/30/2022] [Indexed: 05/20/2023]
Abstract
Genomic imprinting is an epigenetic phenomenon in which differential allele expression occurs in a parent-of-origin-dependent manner. Imprinting in plants is tightly linked to transposable elements (TEs), and it has been hypothesized that genomic imprinting may be a consequence of demethylation of TEs. Here, we performed high-throughput sequencing of ribonucleic acids from four maize (Zea mays) endosperms that segregated newly silenced Mutator (Mu) transposons and identified 110 paternally expressed imprinted genes (PEGs) and 139 maternally expressed imprinted genes (MEGs). Additionally, two potentially novel paternally suppressed MEGs are associated with de novo Mu insertions. In addition, we find evidence for parent-of-origin effects on expression of 407 conserved noncoding sequences (CNSs) in maize endosperm. The imprinted CNSs are largely localized within genic regions and near genes, but the imprinting status of the CNSs are largely independent of their associated genes. Both imprinted CNSs and PEGs have been subject to relaxed selection. However, our data suggest that although MEGs were already subject to a higher mutation rate prior to their being imprinted, imprinting may be the cause of the relaxed selection of PEGs. In addition, although DNA methylation is lower in the maternal alleles of both the maternally and paternally expressed CNSs (mat and pat CNSs), the difference between the two alleles in H3K27me3 levels was only observed in pat CNSs. Together, our findings point to the importance of both transposons and CNSs in genomic imprinting in maize.
Collapse
Affiliation(s)
- Tong Li
- Department of Biology, Miami University, Oxford, Ohio 45056, USA
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P.R. China
| | - Liangwei Yin
- Department of Biology, Miami University, Oxford, Ohio 45056, USA
| | - Claire E Stoll
- Department of Biology, Miami University, Oxford, Ohio 45056, USA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Meixia Zhao
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611, USA
| |
Collapse
|
17
|
Jia Z, Gao P, Yin F, Quilichini TD, Sheng H, Song J, Yang H, Gao J, Chen T, Yang B, Kochian LV, Zou J, Patterson N, Yang Q, Gillmor CS, Datla R, Li Q, Xiang D. Asymmetric gene expression in grain development of reciprocal crosses between tetraploid and hexaploid wheats. Commun Biol 2022; 5:1412. [PMID: 36564439 PMCID: PMC9789062 DOI: 10.1038/s42003-022-04374-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Production of viable progeny from interploid crosses requires precise regulation of gene expression from maternal and paternal chromosomes, yet the transcripts contributed to hybrid seeds from polyploid parent species have rarely been explored. To investigate the genome-wide maternal and paternal contributions to polyploid grain development, we analyzed the transcriptomes of developing embryos, from zygote to maturity, alongside endosperm in two stages of development, using reciprocal crosses between tetraploid and hexaploid wheats. Reciprocal crosses between species with varied levels of ploidy displayed broad impacts on gene expression, including shifts in alternative splicing events in select crosses, as illustrated by active splicing events, enhanced protein synthesis and chromatin remodeling. Homoeologous gene expression was repressed on the univalent D genome in pentaploids, but this suppression was attenuated in crosses with a higher ploidy maternal parent. Imprinted genes were identified in endosperm and early embryo tissues, supporting predominant maternal effects on early embryogenesis. By systematically investigating the complex transcriptional networks in reciprocal-cross hybrids, this study presents a framework for understanding the genomic incompatibility and transcriptome shock that results from interspecific hybridization and uncovers the transcriptional impacts on hybrid seeds created from agriculturally-relevant polyploid species.
Collapse
Affiliation(s)
- Zhen Jia
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Peng Gao
- grid.25152.310000 0001 2154 235XGlobal Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8 Canada
| | - Feifan Yin
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China ,grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, 430070 Wuhan, China
| | - Teagen D. Quilichini
- grid.24433.320000 0004 0449 7958Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Huajin Sheng
- grid.25152.310000 0001 2154 235XGlobal Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8 Canada
| | - Jingpu Song
- grid.24433.320000 0004 0449 7958Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Hui Yang
- grid.24433.320000 0004 0449 7958Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Jie Gao
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Ting Chen
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Bo Yang
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Leon V. Kochian
- grid.25152.310000 0001 2154 235XGlobal Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8 Canada
| | - Jitao Zou
- grid.24433.320000 0004 0449 7958Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Nii Patterson
- grid.24433.320000 0004 0449 7958Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Qingyong Yang
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China ,grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, 430070 Wuhan, China
| | - C. Stewart Gillmor
- grid.512574.0Langebio, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV-IPN), Irapuato, Guanajuato, 36821 México
| | - Raju Datla
- grid.25152.310000 0001 2154 235XGlobal Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8 Canada
| | - Qiang Li
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Daoquan Xiang
- grid.24433.320000 0004 0449 7958Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| |
Collapse
|
18
|
Kloc M, Kubiak JZ, Zdanowski R, Ghobrial RM. Memory Macrophages. Int J Mol Sci 2022; 24:ijms24010038. [PMID: 36613481 PMCID: PMC9819859 DOI: 10.3390/ijms24010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/12/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Immunological memory is a crucial part of the immune defense that allows organisms to respond against previously encountered pathogens or other harmful factors. Immunological memory is based on the establishment of epigenetic modifications of the genome. The ability to memorize encounters with pathogens and other harmful factors and mount enhanced defense upon subsequent encounters is an evolutionarily ancient mechanism operating in all animals and plants. However, the term immunological memory is usually restricted to the organisms (invertebrates and vertebrates) possessing the immune system. The mammalian immune system, with innate and adaptive branches, is the most sophisticated among vertebrates. The concept of innate memory and memory macrophages is relatively new and thus understudied. We introduce the concept of immunological memory and describe types of memory in different species and their evolutionary status. We discuss why the traditional view of innate immune cells as the first-line defenders is too restrictive and how the innate immune cells can accumulate and retain immunologic memory. We describe how the initial priming leads to chromatin remodeling and epigenetic changes, which allow memory macrophage formation. We also summarize what is currently known about the mechanisms underlying development of memory macrophages; their molecular and metabolic signature and surface markers; and how they may contribute to immune defense, diseases, and organ transplantation.
Collapse
Affiliation(s)
- Malgorzata Kloc
- The Houston Methodist Research Institute, Transplant Immunology, Houston, TX 77030, USA
- Department of Surgery, The Houston Methodist Hospital, Houston, TX 77030, USA
- Department of Genetics, MD Anderson Cancer Center, The University of Texas, Houston, TX 77030, USA
- Correspondence:
| | - Jacek Z. Kubiak
- Dynamics and Mechanics of Epithelia Group, Faculty of Medicine, Institute of Genetics and Development of Rennes, University of Rennes, CNRS, UMR 6290, 35043 Rennes, France
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine National Research Institute, Szaserow 128, 04-141 Warsaw, Poland
| | - Robert Zdanowski
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine National Research Institute, Szaserow 128, 04-141 Warsaw, Poland
| | - Rafik M. Ghobrial
- The Houston Methodist Research Institute, Transplant Immunology, Houston, TX 77030, USA
- Department of Surgery, The Houston Methodist Hospital, Houston, TX 77030, USA
| |
Collapse
|
19
|
Sato H, Köhler C. Genomic imprinting regulates establishment and release of seed dormancy. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102264. [PMID: 35872392 DOI: 10.1016/j.pbi.2022.102264] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/12/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Seed dormancy enables plant seeds to time germination until environmental conditions become favorable for seedling survival. This trait has high adaptive value and is of great agricultural relevance. The endosperm is a reproductive tissue formed after fertilization that in addition to support embryo growth has major roles in establishing seed dormancy. Many genes adopt parent-of-origin specific expression patterns in the endosperm, a phenomenon that has been termed genomic imprinting. Imprinted genes are targeted by epigenetic mechanisms acting before and after fertilization. Recent studies revealed that imprinted genes are involved in establishing seed dormancy, highlighting a new mechanism of parental control over this adaptive trait. Here, we review the regulatory mechanisms establishing genomic imprinting and their effect on seed dormancy.
Collapse
Affiliation(s)
- Hikaru Sato
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala, Sweden; Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
| |
Collapse
|
20
|
Iwasaki M, Penfield S, Lopez-Molina L. Parental and Environmental Control of Seed Dormancy in Arabidopsis thaliana. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:355-378. [PMID: 35138879 DOI: 10.1146/annurev-arplant-102820-090750] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Seed dormancy-the absence of seed germination under favorable germination conditions-is a plant trait that evolved to enhance seedling survival by avoiding germination under unsuitable environmental conditions. In Arabidopsis, dormancy levels are influenced by the seed coat composition, while the endosperm is essential to repress seed germination of dormant seeds upon their imbibition. Recent research has shown that the mother plant modulates its progeny seed dormancy in response to seasonal temperature changes by changing specific aspects of seed coat and endosperm development. This process involves genomic imprinting by means of epigenetic marks deposited in the seed progeny and regulators previously known to regulate flowering time. This review discusses and summarizes these discoveries and provides an update on our present understanding of the role of DOG1 and abscisic acid, two key contributors to dormancy.
Collapse
Affiliation(s)
- Mayumi Iwasaki
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland;
| | - Steven Penfield
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Luis Lopez-Molina
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland;
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| |
Collapse
|
21
|
Kumari P, Khan S, Wani IA, Gupta R, Verma S, Alam P, Alaklabi A. Unravelling the Role of Epigenetic Modifications in Development and Reproduction of Angiosperms: A Critical Appraisal. Front Genet 2022; 13:819941. [PMID: 35664328 PMCID: PMC9157814 DOI: 10.3389/fgene.2022.819941] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/14/2022] [Indexed: 12/28/2022] Open
Abstract
Epigenetics are the heritable changes in gene expression patterns which occur without altering DNA sequence. These changes are reversible and do not change the sequence of the DNA but can alter the way in which the DNA sequences are read. Epigenetic modifications are induced by DNA methylation, histone modification, and RNA-mediated mechanisms which alter the gene expression, primarily at the transcriptional level. Such alterations do control genome activity through transcriptional silencing of transposable elements thereby contributing toward genome stability. Plants being sessile in nature are highly susceptible to the extremes of changing environmental conditions. This increases the likelihood of epigenetic modifications within the composite network of genes that affect the developmental changes of a plant species. Genetic and epigenetic reprogramming enhances the growth and development, imparts phenotypic plasticity, and also ensures flowering under stress conditions without changing the genotype for several generations. Epigenetic modifications hold an immense significance during the development of male and female gametophytes, fertilization, embryogenesis, fruit formation, and seed germination. In this review, we focus on the mechanism of epigenetic modifications and their dynamic role in maintaining the genomic integrity during plant development and reproduction.
Collapse
Affiliation(s)
- Priyanka Kumari
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Sajid Khan
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Ishfaq Ahmad Wani
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Renu Gupta
- Division of Soil Sciences & Agricultural Chemistry, Faculty of Agriculture Sher e Kashmir University of Agricultural Sciences and Technology, Chatha, India
| | - Susheel Verma
- Department of Botany, University of Jammu, Jammu, India
- *Correspondence: Susheel Verma,
| | - Pravej Alam
- Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University (PSAU), Alkharj, Saudi Arabia
| | - Abdullah Alaklabi
- Department of Biology, College of Science, University of Bisha, Bisha, Saudi Arabia
| |
Collapse
|
22
|
Huc J, Dziasek K, Pachamuthu K, Woh T, Köhler C, Borges F. Bypassing reproductive barriers in hybrid seeds using chemically induced epimutagenesis. THE PLANT CELL 2022; 34:989-1001. [PMID: 34792584 PMCID: PMC8894923 DOI: 10.1093/plcell/koab284] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/09/2021] [Indexed: 05/13/2023]
Abstract
The triploid block, which prevents interploidy hybridizations in flowering plants, is characterized by a failure in endosperm development, arrest in embryogenesis, and seed collapse. Many genetic components of triploid seed lethality have been successfully identified in the model plant Arabidopsis thaliana, most notably the paternally expressed genes (PEGs), which are upregulated in tetraploid endosperm with paternal excess. Previous studies have shown that the paternal epigenome is a key determinant of the triploid block response, as the loss of DNA methylation in diploid pollen suppresses the triploid block almost completely. Here, we demonstrate that triploid seed collapse is bypassed in Arabidopsis plants treated with the DNA methyltransferase inhibitor 5-Azacytidine during seed germination and early growth. We identified strong suppressor lines showing stable transgenerational inheritance of hypomethylation in the CG context, as well as normalized expression of PEGs in triploid seeds. Importantly, differentially methylated loci segregate in the progeny of "epimutagenized" plants, which may allow epialleles involved in the triploid block response to be identified in future studies. Finally, we demonstrate that chemically induced epimutagenesis facilitates hybridization between different Capsella species, thus potentially emerging as a strategy for producing triploids and interspecific hybrids with high agronomic interest.
Collapse
Affiliation(s)
- Jonathan Huc
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Katarzyna Dziasek
- Department of Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Linnean Center of Plant Biology, Uppsala, Sweden
| | - Kannan Pachamuthu
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Tristan Woh
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Claudia Köhler
- Department of Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Linnean Center of Plant Biology, Uppsala, Sweden
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Filipe Borges
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
- Author for correspondence:
| |
Collapse
|
23
|
Wu H, Becraft PW, Dannenhoffer JM. Maize Endosperm Development: Tissues, Cells, Molecular Regulation and Grain Quality Improvement. FRONTIERS IN PLANT SCIENCE 2022; 13:852082. [PMID: 35330868 PMCID: PMC8940253 DOI: 10.3389/fpls.2022.852082] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/11/2022] [Indexed: 05/12/2023]
Abstract
Maize endosperm plays important roles in human diet, animal feed and industrial applications. Knowing the mechanisms that regulate maize endosperm development could facilitate the improvement of grain quality. This review provides a detailed account of maize endosperm development at the cellular and histological levels. It features the stages of early development as well as developmental patterns of the various individual tissues and cell types. It then covers molecular genetics, gene expression networks, and current understanding of key regulators as they affect the development of each tissue. The article then briefly considers key changes that have occurred in endosperm development during maize domestication. Finally, it considers prospects for how knowledge of the regulation of endosperm development could be utilized to enhance maize grain quality to improve agronomic performance, nutrition and economic value.
Collapse
Affiliation(s)
- Hao Wu
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, United States
| | - Philip W. Becraft
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, United States
- *Correspondence: Philip W. Becraft,
| | | |
Collapse
|
24
|
Zhang Z, Liu J, Sun Y, Wang S, Xing X, Feng X, Pérez-Pérez JM, Li Y. Genome-wide high-resolution mapping of DNA methylation reveals epigenetic variation in the offspring of sexual and asexual propagation in Robinia pseudoacacia. PLANT CELL REPORTS 2021; 40:2435-2447. [PMID: 34524479 DOI: 10.1007/s00299-021-02787-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
We detected the genome-wide pattern of DNA methylation and its association with gene expression in sexual and asexual progenies of mature Robinia pseudoacacia trees. DNA methylation plays an important role in plant reproduction and development. Although some studies on sexual reproduction have been carried out in model plants, little is known about the dynamic changes in DNA methylation and their effect on gene expression in sexual and asexual progeny of woody plants. Here, through whole-genome bisulfite sequencing, we revealed DNA methylation patterns in the sexual and asexual progenies of mature Robinia pseudoacacia to understand the regulation of gene expression by DNA methylation in juvenile seedlings. An average of 53% CG, 34% CHG and 5% CHH contexts was methylated in the leaves of mature and juvenile individuals. The CHH methylation level of asexually propagated seedlings was significantly lower than that of seed-derived seedlings and mature trees. The intergenic regions had the highest methylation level. Analysis of differentially methylated regions (DMRs) showed that most of them were hypermethylated and located in the gene upstream and introns. A total of 24, 108 and 162 differentially expressed genes containing DMRs were identified in root sprouts (RSs), root cuttings (RCs) and seed-derived seedlings (SSs), respectively, and a large proportion of them showed hypermethylation. In addition, DMRs were enriched within GO subcategories including catalytic activity, metabolic process and cellular process. The results reveal widespread DNA methylation changes between mature plants and their progenies through sexual/asexual reproduction, which provides novel insights into DNA methylation reprogramming and the regulation of gene expression in woody plants.
Collapse
Affiliation(s)
- Zijie Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Jie Liu
- National Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Yuhan Sun
- National Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Shaoming Wang
- State-Owned Quanbaoshan Forestry Station in Luoning County of He'nan Province, Luoyang, 471717, People's Republic of China
| | - Xiuxia Xing
- Agricultural Service Center of Wangfan Hui Town in Luoning County of He'nan Province, Luoyang, 471700, People's Republic of China
| | - Xiaojing Feng
- State-Owned Lvcun Forestry Station in Luoning County of He'nan Province, Luoyang, 471700, People's Republic of China
| | | | - Yun Li
- National Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, People's Republic of China.
| |
Collapse
|
25
|
Montgomery SA, Berger F. The evolution of imprinting in plants: beyond the seed. PLANT REPRODUCTION 2021; 34:373-383. [PMID: 33914165 PMCID: PMC8566399 DOI: 10.1007/s00497-021-00410-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/12/2021] [Indexed: 05/14/2023]
Abstract
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.
Collapse
Affiliation(s)
- Sean A Montgomery
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030, Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030, Vienna, Austria.
| |
Collapse
|
26
|
Fang H, Shao Y, Wu G. Reprogramming of Histone H3 Lysine Methylation During Plant Sexual Reproduction. FRONTIERS IN PLANT SCIENCE 2021; 12:782450. [PMID: 34917115 PMCID: PMC8669150 DOI: 10.3389/fpls.2021.782450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
Plants undergo extensive reprogramming of chromatin status during sexual reproduction, a process vital to cell specification and pluri- or totipotency establishment. As a crucial way to regulate chromatin organization and transcriptional activity, histone modification can be reprogrammed during sporogenesis, gametogenesis, and embryogenesis in flowering plants. In this review, we first introduce enzymes required for writing, recognizing, and removing methylation marks on lysine residues in histone H3 tails, and describe their differential expression patterns in reproductive tissues, then we summarize their functions in the reprogramming of H3 lysine methylation and the corresponding chromatin re-organization during sexual reproduction in Arabidopsis, and finally we discuss the molecular significance of histone reprogramming in maintaining the pluri- or totipotency of gametes and the zygote, and in establishing novel cell fates throughout the plant life cycle. Despite rapid achievements in understanding the molecular mechanism and function of the reprogramming of chromatin status in plant development, the research in this area still remains a challenge. Technological breakthroughs in cell-specific epigenomic profiling in the future will ultimately provide a solution for this challenge.
Collapse
|
27
|
Jiang H, Guo D, Ye J, Gao Y, Liu H, Wang Y, Xue M, Yan Q, Chen J, Duan L, Li G, Li X, Xie L. Genome-wide analysis of genomic imprinting in the endosperm and allelic variation in flax. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1697-1710. [PMID: 34228847 DOI: 10.1111/tpj.15411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Genomic imprinting is an epigenetic phenomenon that causes biased expression of maternally and paternally inherited alleles. In flowering plants, genomic imprinting predominantly occurs in the triploid endosperm and plays a vital role in seed development. In this study, we identified 248 candidate imprinted genes including 114 maternally expressed imprinted genes (MEGs) and 134 paternally expressed imprinted genes (PEGs) in flax (Linum usitatissimum L.) endosperm using deep RNA sequencing. These imprinted genes were neither clustered in specific chromosomal regions nor well conserved among flax and other plant species. MEGs tended to be expressed specifically in the endosperm, whereas the expression of PEGs was not tissue-specific. Imprinted single nucleotide polymorphisms differentiated 200 flax cultivars into the oil flax, oil-fiber dual purpose flax and fiber flax subgroups, suggesting that genomic imprinting contributed to intraspecific variation in flax. The nucleotide diversity of imprinted genes in the oil flax subgroup was significantly higher than that in the fiber flax subgroup, indicating that some imprinted genes underwent positive selection during flax domestication from oil flax to fiber flax. Moreover, imprinted genes that underwent positive selection were related to flax functions. Thirteen imprinted genes related to flax seed size and weight were identified using a candidate gene-based association study. Therefore, our study provides information for further exploration of the function and genomic variation of imprinted genes in the flax population.
Collapse
Affiliation(s)
- Haixia Jiang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Dongliang Guo
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Jiali Ye
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanfang Gao
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Huiqing Liu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Yue Wang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Min Xue
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Qingcheng Yan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Jiaxun Chen
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Lepeng Duan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Gongze Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Xiao Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Liqiong Xie
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| |
Collapse
|
28
|
Sun S, Zhu J, Guo R, Whelan J, Shou H. DNA methylation is involved in acclimation to iron-deficiency in rice (Oryza sativa). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:727-739. [PMID: 33977637 DOI: 10.1111/tpj.15318] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/27/2021] [Accepted: 05/03/2021] [Indexed: 05/24/2023]
Abstract
Iron (Fe) is an essential micronutrient in plants, and Fe limitation significantly affects plant growth, yield and food quality. While many studies have reported the transcriptomic profile and pursue molecular mechanism in response to Fe limitation, little is known if epigenetic factors play a role in response to Fe-deficiency. In this study, whole-genome bisulfite sequencing analysis, high-throughput RNA-Seq of mRNA, small RNA and transposable element (TE) expression with root and shoot organs of rice seedlings under Fe-sufficient and Fe-deficient conditions were performed. The results showed that widespread hypermethylation, especially for the CHH context, occurred after Fe-deficiency. Integrative analysis of methylation and transcriptome revealed that the transcript abundance of Fe-deficiency-induced genes was negatively correlated with nearby TEs and positively with the 24-nucleotide siRNAs. The ability of methylation to affect the physiology and molecular response to Fe-deficiency was tested using an exogenous DNA methyltransferase inhibitor (5-azacytidine), and genetically using a mutant for domains rearranged methyltransferase 2 (DRM2), that lacks CHH methylation. Both approaches resulted in decreased growth and Fe content in rice plants. Thus, alterations in specific methylation patterns, directed by siRNAs, play an important role in acclimation of rice to Fe-deficient conditions. Furthermore, comparison with other reports suggests this may be a universal mechanism to acclimate to limited nutrient availability.
Collapse
Affiliation(s)
- Shuo Sun
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, P.R. China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang, 314400, P.R. China
| | - Jiamei Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, P.R. China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang, 314400, P.R. China
| | - Runze Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, P.R. China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang, 314400, P.R. China
| | - James Whelan
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang, 314400, P.R. China
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Victoria, 3086, Australia
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, P.R. China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang, 314400, P.R. China
- Hainan Institute, Zhejiang University, Sanya, 572025, China
| |
Collapse
|
29
|
Fortuny AP, Bueno RA, Pereira da Costa JH, Zanor MI, Rodríguez GR. Tomato fruit quality traits and metabolite content are affected by reciprocal crosses and heterosis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5407-5425. [PMID: 34013312 DOI: 10.1093/jxb/erab222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/17/2021] [Indexed: 06/12/2023]
Abstract
Heterosis occurs when the F1s outperform their parental lines for a trait. Reciprocal hybrids are obtained by changing the cross direction of parental genotypes. Both biological phenomena could affect the external and internal attributes of fleshy fruits. This work aimed to detect reciprocal effects and heterosis in tomato (Solanum lycopersicum) fruit quality traits and metabolite content. Twelve agronomic traits and 28 metabolites identified and estimated by 1H-NMR were evaluated in five cultivars grown in two environments. Given that the genotype component was more important than the phenotype, the traits were evaluated following a full diallel mating design among those cultivars, in a greenhouse. Hybrids showed a higher phenotypic diversity than parental lines. Interestingly, the metabolites, mainly amino acids, displayed more reciprocal effects and heterosis. Agronomic traits were more influenced by general combining ability (GCA) and metabolites by specific combining ability (SCA). Furthermore, the genetic distance between parental lines was not causally related to the occurrence of reciprocal effects or heterosis. Hybrids with heterosis and a high content of metabolites linked to tomato flavour and nutritious components were obtained. Our results highlight the impact of selecting a cultivar as male or female in a cross to enhance the variability of fruit attributes through hybrids as well as the possibility to exploit heterosis for fruit composition.
Collapse
Affiliation(s)
- Agustina P Fortuny
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, Argentina
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Rosario, Argentina
| | - Rodrigo A Bueno
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Rosario, Argentina
| | - Javier H Pereira da Costa
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Rosario, Argentina
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Rosario, Argentina
| | - María Inés Zanor
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Gustavo R Rodríguez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Rosario, Argentina
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Rosario, Argentina
| |
Collapse
|
30
|
Valverde Caballero P, Trapero Ramírez C, Barranco Navero D, López-Escudero FJ, Gordon Bermúdez-Coronel A, Díez CM. Assessment of Maternal Effects and Genetic Variability in Resistance to Verticillium dahliae in Olive Progenies. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10081534. [PMID: 34451579 PMCID: PMC8398735 DOI: 10.3390/plants10081534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/16/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
The use of genetic resistance is likely the most efficient, economically convenient and environmentally friendly control method for plant diseases, as well as a fundamental piece in an integrated management strategy. This is particularly important for woody crops affected by diseases in which mainly horizontal resistance mechanisms are operative, such as Verticillium wilt, caused by Verticillium dahliae. In this study, we analyzed the variability in resistance to Verticillium wilt of olive trees in progenies from five crosses: 'Picual' × 'Frantoio', 'Arbosana' × 'Koroneiki', 'Sikitita' × 'Arbosana', 'Arbosana' × 'Frantoio' and 'Arbosana' × 'Arbequina' and their respective reciprocal crosses. Additionally, seedlings of 'Picual' and 'Frantoio' in open pollination were used as controls. In October 2016 and 2018, the fruits were harvested, and seeds germinated. Six-week-old seedlings were inoculated by dipping their bare roots in a conidial suspension of V. dahliae, and disease progress in terms of symptom severity and mortality was evaluated weekly. Additionally, seedling growth was evaluated every two weeks. At the end of the experiment, no significant differences were found for any of the assessed parameters when reciprocal crosses were compared. These results suggest that there is no maternal or paternal effect in regard to the heritability of resistance. In addition, this study identifies the best crosses for obtaining the highest number of resistant genotypes, highlighting the importance of the selection of specific cultivars to optimize the breeding process.
Collapse
|
31
|
Auboeuf D. The Physics-Biology continuum challenges darwinism: Evolution is directed by the homeostasis-dependent bidirectional relation between genome and phenotype. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:121-139. [PMID: 34097984 DOI: 10.1016/j.pbiomolbio.2021.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/19/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
The physics-biology continuum relies on the fact that life emerged from prebiotic molecules. Here, I argue that life emerged from the coupling between nucleic acid and protein synthesis during which proteins (or proto-phenotypes) maintained the physicochemical parameter equilibria (or proto-homeostasis) in the proximity of their encoding nucleic acids (or proto-genomes). This protected the proto-genome physicochemical integrity (i.e., atomic composition) from environmental physicochemical constraints, and therefore increased the probability of reproducing the proto-genome without variation. From there, genomes evolved depending on the biological activities they generated in response to environmental fluctuations. Thus, a genome maintaining homeostasis (i.e., internal physicochemical parameter equilibria), despite and in response to environmental fluctuations, maintains its physicochemical integrity and has therefore a higher probability to be reproduced without variation. Consequently, descendants have a higher probability to share the same phenotype than their parents. Otherwise, the genome is modified during replication as a consequence of the imbalance of the internal physicochemical parameters it generates, until new mutation-deriving biological activities maintain homeostasis in offspring. In summary, evolution depends on feedforward and feedback loops between genome and phenotype, as the internal physicochemical conditions that a genome generates ─ through its derived phenotype in response to environmental fluctuations ─ in turn either guarantee its stability or direct its variation. Evolution may not be explained by the Darwinism-derived, unidirectional principle (random mutations-phenotypes-natural selection) but rather by the bidirectional relationship between genome and phenotype, in which the phenotype in interaction with the environment directs the evolution of the genome it derives from.
Collapse
Affiliation(s)
- Didier Auboeuf
- ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée D'Italie, Site Jacques Monod, F-69007, Lyon, France.
| |
Collapse
|
32
|
Yadav VK, Santos-González J, Köhler C. INT-Hi-C reveals distinct chromatin architecture in endosperm and leaf tissues of Arabidopsis. Nucleic Acids Res 2021; 49:4371-4385. [PMID: 33744975 PMCID: PMC8096224 DOI: 10.1093/nar/gkab191] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/10/2021] [Accepted: 03/06/2021] [Indexed: 12/13/2022] Open
Abstract
Higher-order chromatin structure undergoes striking changes in response to various developmental and environmental signals, causing distinct cell types to adopt specific chromatin organization. High throughput chromatin conformation capture (Hi-C) allows studying higher-order chromatin structure; however, this technique requires substantial amounts of starting material, which has limited the establishment of cell type-specific higher-order chromatin structure in plants. To overcome this limitation, we established a protocol that is applicable to a limited amount of nuclei by combining the INTACT (isolation of nuclei tagged in specific cell types) method and Hi-C (INT-Hi-C). Using this INT-Hi-C protocol, we generated Hi-C data from INTACT purified endosperm and leaf nuclei. Our INT-Hi-C data from leaf accurately reiterated chromatin interaction patterns derived from conventional leaf Hi-C data. We found that the higher-order chromatin organization of mixed leaf tissues and endosperm differs and that DNA methylation and repressive histone marks positively correlate with the chromatin compaction level. We furthermore found that self-looped interacting genes have increased expression in leaves and endosperm and that interacting intergenic regions negatively impact on gene expression in the endosperm. Last, we identified several imprinted genes involved in long-range and trans interactions exclusively in endosperm. Our study provides evidence that the endosperm adopts a distinct higher-order chromatin structure that differs from other cell types in plants and that chromatin interactions influence transcriptional activity.
Collapse
Affiliation(s)
- Vikash Kumar Yadav
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala 75007, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala 75007, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala 75007, Sweden
| |
Collapse
|
33
|
Brodie ED, Gregory B, Lisch D, Riddle NC. The epigenome and beyond: How does non-genetic inheritance change our view of evolution? Integr Comp Biol 2021; 61:2199-2207. [PMID: 34028538 DOI: 10.1093/icb/icab084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Evidence from across the tree of life suggests that epigenetic inheritance is more common than previously thought. If epigenetic inheritance is indeed as common as the data suggest, this finding has potentially important implications for evolutionary theory and our understanding of how evolution and adaptation progress. However, we currently lack an understanding of how common various epigenetic inheritance types are, and how they impact phenotypes. In this perspective, we review the open questions that need to be addressed to fully integrate epigenetic inheritance into evolutionary theory and to develop reliable predictive models for phenotypic evolution. We posit that addressing these challenges will require the collaboration of biologists from different disciplines and a focus on the exploration of data and phenomena without preconceived limits on potential mechanisms or outcomes.
Collapse
Affiliation(s)
- Edmund D Brodie
- Department of Biology, University of Virginia, Charlottesville, VA
| | - Brian Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN
| | - Nicole C Riddle
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL
| |
Collapse
|
34
|
Chen B, Xu H, Guo Y, Grünhofer P, Schreiber L, Lin J, Li R. Transcriptomic and epigenomic remodeling occurs during vascular cambium periodicity in Populus tomentosa. HORTICULTURE RESEARCH 2021; 8:102. [PMID: 33931595 PMCID: PMC8087784 DOI: 10.1038/s41438-021-00535-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 02/20/2021] [Accepted: 03/08/2021] [Indexed: 05/06/2023]
Abstract
Trees in temperate regions exhibit evident seasonal patterns, which play vital roles in their growth and development. The activity of cambial stem cells is the basis for regulating the quantity and quality of wood, which has received considerable attention. However, the underlying mechanisms of these processes have not been fully elucidated. Here we performed a comprehensive analysis of morphological observations, transcriptome profiles, the DNA methylome, and miRNAs of the cambium in Populus tomentosa during the transition from dormancy to activation. Anatomical analysis showed that the active cambial zone exhibited a significant increase in the width and number of cell layers compared with those of the dormant and reactivating cambium. Furthermore, we found that differentially expressed genes associated with vascular development were mainly involved in plant hormone signal transduction, cell division and expansion, and cell wall biosynthesis. In addition, we identified 235 known miRNAs and 125 novel miRNAs. Differentially expressed miRNAs and target genes showed stronger negative correlations than other miRNA/target pairs. Moreover, global methylation and transcription analysis revealed that CG gene body methylation was positively correlated with gene expression, whereas CHG exhibited the opposite trend in the downstream region. Most importantly, we observed that the number of CHH differentially methylated region (DMR) changes was the greatest during cambium periodicity. Intriguingly, the genes with hypomethylated CHH DMRs in the promoter were involved in plant hormone signal transduction, phenylpropanoid biosynthesis, and plant-pathogen interactions during vascular cambium development. These findings improve our systems-level understanding of the epigenomic diversity that exists in the annual growth cycle of trees.
Collapse
Affiliation(s)
- Bo Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, 100083, China
| | - Huimin Xu
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yayu Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, 100083, China
| | - Paul Grünhofer
- Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Lukas Schreiber
- Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, 100083, China
| | - Ruili Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, 100083, China.
| |
Collapse
|
35
|
Arabidopsis thaliana Mature Endosperm Dissection and Isolation of Genomic DNA from Mature Seed Tissues. Methods Mol Biol 2021. [PMID: 33900609 DOI: 10.1007/978-1-0716-1134-0_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
We describe methods to separate endosperms and embryos from Arabidopsis thaliana mature seeds in large amounts and to isolate high-quality genomic DNA from those tissues. The resulting materials are suitable for analysis of DNA methylation by bisulfite sequencing or histone modifications by chromatin immunoprecipitation (ChIP).
Collapse
|
36
|
Köhler C, Dziasek K, Del Toro-De León G. Postzygotic reproductive isolation established in the endosperm: mechanisms, drivers and relevance. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200118. [PMID: 33866810 DOI: 10.1098/rstb.2020.0118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The endosperm is a developmental innovation of angiosperms that supports embryo growth and germination. Aside from this essential reproductive function, the endosperm fuels angiosperm evolution by rapidly establishing reproductive barriers between incipient species. Specifically, the endosperm prevents hybridization of newly formed polyploids with their non-polyploid progenitors, a phenomenon termed the triploid block. Furthermore, recently diverged diploid species are frequently reproductively isolated by endosperm-based hybridization barriers. Current genetic approaches have revealed a prominent role for epigenetic processes establishing these barriers. In particular, imprinted genes, which are expressed in a parent-of-origin-specific manner, underpin the interploidy barrier in the model species Arabidopsis. We will discuss the mechanisms establishing hybridization barriers in the endosperm, the driving forces for these barriers and their impact for angiosperm evolution. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
Collapse
Affiliation(s)
- Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Katarzyna Dziasek
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Gerardo Del Toro-De León
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| |
Collapse
|
37
|
Xu X, E Z, Zhang D, Yun Q, Zhou Y, Niu B, Chen C. OsYUC11-mediated auxin biosynthesis is essential for endosperm development of rice. PLANT PHYSIOLOGY 2021; 185:934-950. [PMID: 33793908 PMCID: PMC8133553 DOI: 10.1093/plphys/kiaa057] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/18/2020] [Indexed: 05/06/2023]
Abstract
Auxin is a phytohormone essential for plant development. However, our understanding of auxin-regulated endosperm development remains limited. Here, we described rice YUCCA (YUC) flavin-containing monooxygenase encoding gene OsYUC11 as a key contributor to auxin biosynthesis in rice (Oryza sativa) endosperm. Grain filling or storage product accumulation was halted by mutation of OsYUC11, but the deficiencies could be recovered by the exogenous application of auxin. A rice transcription factor (TF) yeast library was screened, and 41 TFs that potentially bind to the OsYUC11 promoter were identified, of which OsNF-YB1, a member of the nuclear factor Y family, is predominantly expressed in the endosperm. Both osyuc11 and osnf-yb1 mutants exhibited reduced seed size and increased chalkiness, accompanied by a reduction in indole-3-acetic acid biosynthesis. OsNF-YB1 can bind the OsYUC11 promoter to induce gene expression in vivo. We also found that OsYUC11 was a dynamically imprinted gene that predominantly expressed the paternal allele in the endosperm up to 10 d after fertilization (DAF) but then became a non-imprinted gene at 15 DAF. A functional maternal allele of OsYUC11 was able to recover the paternal defects of this gene. Overall, the findings indicate that OsYUC11-mediated auxin biosynthesis is essential for endosperm development in rice.
Collapse
Affiliation(s)
- Xinyu Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Zhiguo E
- Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Dongping Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Qianbin Yun
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Yong Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Baixiao Niu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Chen Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Author for communication:
| |
Collapse
|
38
|
Hernández F, Vercellino RB, Fanna I, Presotto A. Maternal control of early life history traits affects overwinter survival and seedling phenotypes in sunflower (Helianthus annuus L.). PLANT BIOLOGY (STUTTGART, GERMANY) 2021; 23:307-316. [PMID: 33222359 DOI: 10.1111/plb.13220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/07/2020] [Indexed: 06/11/2023]
Abstract
When cultivated and wild plants hybridize, hybrids often show intermediate phenotypic traits relative to their parents, which makes them unfit in natural environments. However, maternal genetic effects may affect the outcome of hybridization by controlling expression of the earliest life history traits. Here, using wild, cultivated and reciprocal crop-wild sunflower (Helianthus annuus L.) hybrids, we evaluated the maternal effects on emergence timing and seedling establishment in the field and on seedling traits under controlled conditions. In the field, we evaluated reciprocal crop-wild hybrids between two wild populations with contrasting dormancy (the high dormant BAR and the low dormant DIA) and one cultivar (CROP) with low dormancy. Under controlled conditions, we evaluated reciprocal crop-wild hybrids between two wild populations (BAR and RCU) and one CROP under three contrasting temperature treatments. In the field, BAR overwintered as dormant seeds whereas DIA and CROP showed high autumn emergence (~50% of planted seeds), resulting in differential overwinter survival and seedling establishment in the spring. Reciprocal crop-wild hybrids resembled their female parents in emergence timing and success of seedling establishment. Under controlled conditions, we observed large maternal effects on most seedling traits across temperatures. Cotyledon size explained most of the variation in seedling traits, suggesting that the maternal effects on seed size have cascading effects on seedling traits. Maternal effects on early life history traits affect early plant survival and phenotypic variation of crop-wild hybrids, thus, they should be addressed in hybridization studies, especially those involving highly divergent parents, such as cultivated species and their wild ancestors.
Collapse
Affiliation(s)
- F Hernández
- CERZOS, Dpto. Agronomía, Universidad Nacional del Sur (UNS)-CONICET, San Andrés 800, CP, 8000, Bahía Blanca, Argentina
| | - R B Vercellino
- CERZOS, Dpto. Agronomía, Universidad Nacional del Sur (UNS)-CONICET, San Andrés 800, CP, 8000, Bahía Blanca, Argentina
| | - I Fanna
- CERZOS, Dpto. Agronomía, Universidad Nacional del Sur (UNS)-CONICET, San Andrés 800, CP, 8000, Bahía Blanca, Argentina
| | - A Presotto
- CERZOS, Dpto. Agronomía, Universidad Nacional del Sur (UNS)-CONICET, San Andrés 800, CP, 8000, Bahía Blanca, Argentina
| |
Collapse
|
39
|
Genomic territories in inter-genomic hybrids: the winners and losers with hybrid fixation. THE NUCLEUS 2021. [DOI: 10.1007/s13237-021-00348-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
|
40
|
Lu Y, Song Y, Liu L, Wang T. DNA methylation dynamics of sperm cell lineage development in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:565-579. [PMID: 33249677 DOI: 10.1111/tpj.15098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 11/16/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
During the sexual reproduction of higher plants, DNA methylation and transcription are broadly changed to reshape a microspore into two sperm cells (SCs) and a vegetative cell (VC). However, when and how the DNA methylation of SCs is established remains not fully understood. Here we investigate the DNA methylation (5 mC) dynamics of SC lineage and the VC in tomato using whole-genome bisulfite sequencing. We find the asymmetric division of the microspore gives its two daughter cells differential methylome. Compared with the generative cell (GC), the VC is hypomethylated at CG sites while hypermethylated at CHG and CHH sites, with the majority of differentially methylation regions targeted to transposable elements (TEs). SCs have a nearly identical DNA methylome to the GC, suggesting that the methylation landscape in SCs may be pre-established following the asymmetric division or inherited from the GC. The random forest classifier for predicting gene and TE expression shows that methylation within the gene body is a more powerful predictor for gene expression. Among all tested samples, gene and TE expression in the microspore may be more predictable by DNA methylation. Our results depict an intact DNA methylome landscape of SC lineage in higher plants, and reveal that the impact of DNA methylation on transcription is variant in different cell types.
Collapse
Affiliation(s)
- Yunlong Lu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100093, China
| | - Yunyun Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100093, China
| | - Lingtong Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Tai Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100093, China
- Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
| |
Collapse
|
41
|
Gimenez MD, Vazquez DV, Trepat F, Cambiaso V, Rodríguez GR. Fruit quality and DNA methylation are affected by parental order in reciprocal crosses of tomato. PLANT CELL REPORTS 2021; 40:171-186. [PMID: 33079280 DOI: 10.1007/s00299-020-02624-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 10/03/2020] [Indexed: 06/11/2023]
Abstract
Reciprocal effects were found for tomato fruit quality and DNA methylation. The epigenetic identity of reciprocal hybrids indicates that DNA methylation might be one of the mechanisms involved in POEs. Crosses between different genotypes and even between different species are commonly used in plant breeding programs. Reciprocal hybrids are obtained by changing the cross direction (or the sexual role) of parental genotypes in a cross. Phenotypic differences between these hybrids constitute reciprocal effects (REs). The aim of this study was to evaluate phenotypic differences in tomato fruit traits and DNA methylation profiles in three inter- and intraspecific reciprocal crosses. REs were detected for 13 of the 16 fruit traits analyzed. The number of traits with REs was the lowest in the interspecific cross, whereas the highest was found in the cross between recombinant inbred lines (RILs) derived from the same interspecific cross. An extension of gene action analysis was proposed to incorporate parent-of-origin effects (POEs). Maternal and paternal dominance were found in four fruit traits. REs and paternal inheritance were found for epiloci located at coding and non-coding regions. The epigenetic identity displayed by the reciprocal hybrids accounts for the phenotypic differences among them, indicating that DNA methylation might be one of the mechanisms involved in POEs.
Collapse
Affiliation(s)
- Magalí Diana Gimenez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
- CIGEOBIO, (CONICET-UNSJ), Complejo Universitario "Islas Malvinas", FCEFN, Universidad de San Juan, Av. Ignacio de la Roza 590, J5402DCS, Rivadavia, San Juan, Argentina
| | - Dana Valeria Vazquez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Felipe Trepat
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Vladimir Cambiaso
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Gustavo Rubén Rodríguez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina.
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina.
| |
Collapse
|
42
|
Rougée M, Quadrana L, Zervudacki J, Hure V, Colot V, Navarro L, Deleris A. Polycomb mutant partially suppresses DNA hypomethylation-associated phenotypes in Arabidopsis. Life Sci Alliance 2020; 4:4/2/e202000848. [PMID: 33443101 PMCID: PMC7756957 DOI: 10.26508/lsa.202000848] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 11/25/2020] [Accepted: 12/01/2020] [Indexed: 12/16/2022] Open
Abstract
A mutation in Arabidopsis polycomb repressive complex 2 partially suppresses the transposon activity observed in a DNA methylation mutant, challenging expectations. In plants and mammals, DNA methylation and histone H3 lysine 27 trimethylation (H3K27me3), which is deposited by the polycomb repressive complex 2, are considered as two specialized systems for the epigenetic silencing of transposable element (TE) and genes, respectively. Nevertheless, many TE sequences acquire H3K27me3 when DNA methylation is lost. Here, we show in Arabidopsis thaliana that the gain of H3K27me3 observed at hundreds of TEs in the ddm1 mutant defective in the maintenance of DNA methylation, essentially depends on CURLY LEAF (CLF), one of two partially redundant H3K27 methyltransferases active in vegetative tissues. Surprisingly, the complete loss of H3K27me3 in ddm1 clf double mutant plants was not associated with further reactivation of TE expression nor with a burst of transposition. Instead, ddm1 clf plants exhibited less activated TEs, and a chromatin recompaction as well as hypermethylation of linker DNA compared with ddm1. Thus, a mutation in polycomb repressive complex 2 does not aggravate the molecular phenotypes linked to ddm1 but instead partially suppresses them, challenging our assumptions of the relationship between two conserved epigenetic silencing pathways.
Collapse
Affiliation(s)
- Martin Rougée
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Leandro Quadrana
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, Sciences and Lettres (PSL) Research University, Paris, France
| | - Jérôme Zervudacki
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, Sciences and Lettres (PSL) Research University, Paris, France
| | - Valentin Hure
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, Sciences and Lettres (PSL) Research University, Paris, France
| | - Lionel Navarro
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, Sciences and Lettres (PSL) Research University, Paris, France
| | - Angélique Deleris
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| |
Collapse
|
43
|
Marshall H, van Zweden JS, Van Geystelen A, Benaets K, Wäckers F, Mallon EB, Wenseleers T. Parent of origin gene expression in the bumblebee, Bombus terrestris, supports Haig's kinship theory for the evolution of genomic imprinting. Evol Lett 2020; 4:479-490. [PMID: 33312684 PMCID: PMC7719552 DOI: 10.1002/evl3.197] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 07/02/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022] Open
Abstract
Genomic imprinting is the differential expression alleles in diploid individuals, with the expression being dependent on the sex of the parent from which it was inherited. Haig's kinship theory hypothesizes that genomic imprinting is due to an evolutionary conflict of interest between alleles from the mother and father. In social insects, it has been suggested that genomic imprinting should be widespread. One recent study identified parent-of-origin expression in honey bees and found evidence supporting the kinship theory. However, little is known about genomic imprinting in insects and multiple theoretical predictions must be tested to avoid single-study confirmation bias. We, therefore, tested for parent-of-origin expression in a primitively eusocial bee. We found equal numbers of maternally and paternally biased expressed genes. The most highly biased genes were maternally expressed, offering support for the kinship theory. We also found low conservation of potentially imprinted genes with the honey bee, suggesting rapid evolution of genomic imprinting in Hymenoptera.
Collapse
Affiliation(s)
- Hollie Marshall
- Department of Genetics and Genome BiologyThe University of Leicester, Leicester LE1 7RHUnited Kingdom
| | - Jelle S. van Zweden
- Laboratory of Socioecology and Social EvolutionDepartment of Biology, KU Leuven, 3000LeuvenBelgium
| | - Anneleen Van Geystelen
- Laboratory of Socioecology and Social EvolutionDepartment of Biology, KU Leuven, 3000LeuvenBelgium
| | - Kristof Benaets
- Laboratory of Socioecology and Social EvolutionDepartment of Biology, KU Leuven, 3000LeuvenBelgium
| | - Felix Wäckers
- Biobest Belgium N.V., 2260 WesterloBelgium
- The Lancaster Environmental CentreUniversity of Lancaster, Lancaster LA1 4YWUnited Kingdom
| | - Eamonn B. Mallon
- Department of Genetics and Genome BiologyThe University of Leicester, Leicester LE1 7RHUnited Kingdom
| | - Tom Wenseleers
- Laboratory of Socioecology and Social EvolutionDepartment of Biology, KU Leuven, 3000LeuvenBelgium
| |
Collapse
|
44
|
Epigenetics and epigenomics: underlying mechanisms, relevance, and implications in crop improvement. Funct Integr Genomics 2020; 20:739-761. [PMID: 33089419 DOI: 10.1007/s10142-020-00756-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 01/21/2023]
Abstract
Epigenetics is defined as changes in gene expression that are not associated with changes in DNA sequence but due to the result of methylation of DNA and post-translational modifications to the histones. These epigenetic modifications are known to regulate gene expression by bringing changes in the chromatin state, which underlies plant development and shapes phenotypic plasticity in responses to the environment and internal cues. This review articulates the role of histone modifications and DNA methylation in modulating biotic and abiotic stresses, as well as crop improvement. It also highlights the possibility of engineering epigenomes and epigenome-based predictive models for improving agronomic traits.
Collapse
|
45
|
Quadrana L. The contribution of transposable elements to transcriptional novelty in plants: the FLC affair. Transcription 2020; 11:192-198. [PMID: 32783496 PMCID: PMC7714446 DOI: 10.1080/21541264.2020.1803031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are repetitive DNA sequences with the ability to replicate across genomes and generate mutations with major transcriptional effects. Epigenetic silencing mechanisms that target TEs to limit their activity, including DNA methylation, add to the range of gene expression variants generated by TEs. Here, using the iconic gene flowering locus C (FLC) as a case study I discuss the multiple ways by which TEs can affect the expression of genes and contribute to the adaptation of plants to changing environments
Collapse
Affiliation(s)
- Leandro Quadrana
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University , Paris, France
| |
Collapse
|
46
|
Wambui Mbichi R, Wang QF, Wan T. RNA directed DNA methylation and seed plant genome evolution. PLANT CELL REPORTS 2020; 39:983-996. [PMID: 32594202 DOI: 10.1007/s00299-] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/08/2020] [Indexed: 05/28/2023]
Abstract
RNA Directed DNA Methylation (RdDM) is a pathway that mediates de novo DNA methylation, an evolutionary conserved chemical modification of cytosine bases, which exists in living organisms and utilizes small interfering RNA. Plants utilize DNA methylation for transposable element (TE) repression, regulation of gene expression and developmental regulation. TE activity strongly influences genome size and evolution, therefore making DNA methylation a key component in understanding divergence in genome evolution among seed plants. Multiple proteins that have extensively been studied in model plant Arabidopsis thaliana catalyze RNA dependent DNA Methylation pathway along with small interfering RNA. Several developmental functions have also been attributed to DNA methylation. This review will highlight aspects of RdDM pathway dynamics, evolution and functions in seed plants with focus on recent findings on conserved and non-conserved attributes between angiosperms and gymnosperms to potentially explain how methylation has impacted variations in evolutionary and developmental complexity among them and advance current understanding of this crucial epigenetic pathway.
Collapse
Affiliation(s)
- R Wambui Mbichi
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, Hubei, 430074, China
- Key laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, Hubei, 430074, China.
- Sino-Africa Joint Research Center, Chinese Academy of Science, Wuhan, 430074, China.
- Center of Conservation Biology, Core Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Tao Wan
- Key laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China.
- Sino-Africa Joint Research Center, Chinese Academy of Science, Wuhan, 430074, China.
| |
Collapse
|
47
|
Wambui Mbichi R, Wang QF, Wan T. RNA directed DNA methylation and seed plant genome evolution. PLANT CELL REPORTS 2020; 39:983-996. [PMID: 32594202 PMCID: PMC7359171 DOI: 10.1007/s00299-020-02558-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/08/2020] [Indexed: 05/11/2023]
Abstract
RNA Directed DNA Methylation (RdDM) is a pathway that mediates de novo DNA methylation, an evolutionary conserved chemical modification of cytosine bases, which exists in living organisms and utilizes small interfering RNA. Plants utilize DNA methylation for transposable element (TE) repression, regulation of gene expression and developmental regulation. TE activity strongly influences genome size and evolution, therefore making DNA methylation a key component in understanding divergence in genome evolution among seed plants. Multiple proteins that have extensively been studied in model plant Arabidopsis thaliana catalyze RNA dependent DNA Methylation pathway along with small interfering RNA. Several developmental functions have also been attributed to DNA methylation. This review will highlight aspects of RdDM pathway dynamics, evolution and functions in seed plants with focus on recent findings on conserved and non-conserved attributes between angiosperms and gymnosperms to potentially explain how methylation has impacted variations in evolutionary and developmental complexity among them and advance current understanding of this crucial epigenetic pathway.
Collapse
Affiliation(s)
- R Wambui Mbichi
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, Hubei, 430074, China
- Key laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan, Hubei, 430074, China.
- Sino-Africa Joint Research Center, Chinese Academy of Science, Wuhan, 430074, China.
- Center of Conservation Biology, Core Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Tao Wan
- Key laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China.
- Sino-Africa Joint Research Center, Chinese Academy of Science, Wuhan, 430074, China.
| |
Collapse
|
48
|
N'Diaye A, Byrns B, Cory AT, Nilsen KT, Walkowiak S, Sharpe A, Robinson SJ, Pozniak CJ. Machine learning analyses of methylation profiles uncovers tissue-specific gene expression patterns in wheat. THE PLANT GENOME 2020; 13:e20027. [PMID: 33016606 DOI: 10.1002/tpg2.20027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/24/2020] [Accepted: 04/12/2020] [Indexed: 06/11/2023]
Abstract
DNA methylation is a mechanism of epigenetic modification in eukaryotic organisms. Generally, methylation within genes promoter inhibits regulatory protein binding and represses transcription, whereas gene body methylation is associated with actively transcribed genes. However, it remains unclear whether there is interaction between methylation levels across genic regions and which site has the biggest impact on gene regulation. We investigated and used the methylation patterns of the bread wheat cultivar Chinese Spring to uncover differentially expressed genes (DEGs) between roots and leaves, using six machine learning algorithms and a deep neural network. As anticipated, genes with higher expression in leaves were mainly involved in photosynthesis and pigment biosynthesis processes whereas genes that were not differentially expressed between roots and leaves were involved in protein processes and membrane structures. Methylation occurred preponderantly (60%) in the CG context, whereas 35 and 5% of methylation occurred in CHG and CHH contexts, respectively. Methylation levels were highly correlated (r = 0.7 to 0.9) between all genic regions, except within the promoter (r = 0.4 to 0.5). Machine learning models gave a high (0.81) prediction accuracy of DEGs. There was a strong correlation (p-value = 9.20×10-10 ) between all features and gene expression, suggesting that methylation across all genic regions contribute to gene regulation. However, the methylation of the promoter, the CDS and the exon in CG context was the most impactful. Our study provides more insights into the interplay between DNA methylation and gene expression and paves the way for identifying tissue-specific genes using methylation profiles.
Collapse
Affiliation(s)
- Amidou N'Diaye
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Brook Byrns
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Aron T Cory
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Kirby T Nilsen
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Sean Walkowiak
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Andrew Sharpe
- Global Institute for Food Security, Saskatoon, SK, Canada, S7N 0W9
| | - Stephen J Robinson
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
| | - Curtis J Pozniak
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| |
Collapse
|
49
|
Ginno PA, Gaidatzis D, Feldmann A, Hoerner L, Imanci D, Burger L, Zilbermann F, Peters AHFM, Edenhofer F, Smallwood SA, Krebs AR, Schübeler D. A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity. Nat Commun 2020; 11:2680. [PMID: 32471981 PMCID: PMC7260214 DOI: 10.1038/s41467-020-16354-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 04/24/2020] [Indexed: 12/21/2022] Open
Abstract
DNA methylation is considered a stable epigenetic mark, yet methylation patterns can vary during differentiation and in diseases such as cancer. Local levels of DNA methylation result from opposing enzymatic activities, the rates of which remain largely unknown. Here we developed a theoretical and experimental framework enabling us to infer methylation and demethylation rates at 860,404 CpGs in mouse embryonic stem cells. We find that enzymatic rates can vary as much as two orders of magnitude between CpGs with identical steady-state DNA methylation. Unexpectedly, de novo and maintenance methylation activity is reduced at transcription factor binding sites, while methylation turnover is elevated in transcribed gene bodies. Furthermore, we show that TET activity contributes substantially more than passive demethylation to establishing low methylation levels at distal enhancers. Taken together, our work unveils a genome-scale map of methylation kinetics, revealing highly variable and context-specific activity for the DNA methylation machinery.
Collapse
Affiliation(s)
- Paul Adrian Ginno
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Dimos Gaidatzis
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Angelika Feldmann
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Leslie Hoerner
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Dilek Imanci
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Lukas Burger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Faculty of Sciences, University of Basel, Basel, Switzerland
| | - Frank Edenhofer
- Leopold-Franzens-University Innsbruck & CMBI, Innsbruck, Austria
| | | | - Arnaud R Krebs
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- EMBL Heidelberg, Heidelberg, Germany
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- Faculty of Sciences, University of Basel, Basel, Switzerland.
| |
Collapse
|
50
|
Glombik M, Bačovský V, Hobza R, Kopecký D. Competition of Parental Genomes in Plant Hybrids. FRONTIERS IN PLANT SCIENCE 2020; 11:200. [PMID: 32158461 PMCID: PMC7052263 DOI: 10.3389/fpls.2020.00200] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/11/2020] [Indexed: 05/17/2023]
Abstract
Interspecific hybridization represents one of the main mechanisms of plant speciation. Merging of two genomes from different subspecies, species, or even genera is frequently accompanied by whole-genome duplication (WGD). Besides its evolutionary role, interspecific hybridization has also been successfully implemented in multiple breeding programs. Interspecific hybrids combine agronomic traits of two crop species or can be used to introgress specific loci of interests, such as those for resistance against abiotic or biotic stresses. The genomes of newly established interspecific hybrids (both allopolyploids and homoploids) undergo dramatic changes, including chromosome rearrangements, amplifications of tandem repeats, activation of mobile repetitive elements, and gene expression modifications. To ensure genome stability and proper transmission of chromosomes from both parental genomes into subsequent generations, allopolyploids often evolve mechanisms regulating chromosome pairing. Such regulatory systems allow only pairing of homologous chromosomes and hamper pairing of homoeologs. Despite such regulatory systems, several hybrid examples with frequent homoeologous chromosome pairing have been reported. These reports open a way for the replacement of one parental genome by the other. In this review, we provide an overview of the current knowledge of genomic changes in interspecific homoploid and allopolyploid hybrids, with strictly homologous pairing and with relaxed pairing of homoeologs.
Collapse
Affiliation(s)
- Marek Glombik
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
| | - Roman Hobza
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
| | - David Kopecký
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| |
Collapse
|