1
|
Del Toro-De León G, van Boven J, Santos-González J, Jiao WB, Peng H, Schneeberger K, Köhler C. Epigenetic and transcriptional consequences in the endosperm of chemically induced transposon mobilization in Arabidopsis. Nucleic Acids Res 2024; 52:8833-8848. [PMID: 38967011 PMCID: PMC11347142 DOI: 10.1093/nar/gkae572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 07/06/2024] Open
Abstract
Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently evolved in the endosperm of flowering plants and the placenta of mammals-tissues crucial for nurturing embryos. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct investigations of the impact of de novo TE transposition on genomic imprinting remain scarce. In this study, we explored the effects of chemically induced transposition of the Copia element ONSEN on genomic imprinting in Arabidopsis thaliana. Through the combination of chemical TE mobilization and doubled haploid induction, we generated a line with 40 new ONSEN copies. Our findings reveal a preferential targeting of maternally expressed genes (MEGs) for transposition, aligning with the colocalization of H2A.Z and H3K27me3 in MEGs-both previously identified as promoters of ONSEN insertions. Additionally, we demonstrate that chemically-induced DNA hypomethylation induces global transcriptional deregulation in the endosperm, leading to the breakdown of MEG imprinting. This study provides insights into the consequences of chemically induced TE remobilization in the endosperm, revealing that chemically-induced epigenome changes can have long-term consequences on imprinted gene expression.
Collapse
Affiliation(s)
- Gerardo Del Toro-De León
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Joram van Boven
- 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
| | - Wen-Biao Jiao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Haoran Peng
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Faculty for Biology, LMU Munich, Planegg-Martinsried 82152, Germany
- Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Düsseldorf 40225, Germany
| | - Claudia Köhler
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala 75007, Sweden
| |
Collapse
|
2
|
Zhang S, Mohanty D, Muzaffar A, Ni M. Two MADS-box proteins, AGL9 and AGL15, recruit the FIS-PRC2 complex to trigger the phase transition from endosperm proliferation to embryo development in Arabidopsis. MOLECULAR PLANT 2024; 17:1110-1128. [PMID: 38825830 DOI: 10.1016/j.molp.2024.05.011] [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: 11/12/2023] [Revised: 03/31/2024] [Accepted: 05/29/2024] [Indexed: 06/04/2024]
Abstract
Spatiotemporal regulation of gene expression by polycomb repressive complex 2 (PRC2) is critical for animal and plant development. The Arabidopsis fertilization independent seed (FIS)-PRC2 complex functions specifically during plant reproduction from gametogenesis to seed development. After a double fertilization event, triploid endosperm proliferates early, followed by the growth of a diploid embryo, which replaces the endosperm in Arabidopsis and many dicots. Key genes critical for endosperm proliferation such as IKU2 and MINI3 are activated after fertilization. Here we report that two MADS-box AGAMOUS-LIKE (AGL) proteins associate with the key endosperm proliferation loci and recruit the FIS-PRC2 repressive complex at 4-5 days after pollination (DAP). Interestingly, AGL9 and AGL15 only accumulate toward the end of endosperm proliferation at 4-5 DAP and promote the deposition of H3K27me3 marks at key endosperm proliferation loci. Disruption of AGL9 and AGL15 or overexpression of AGL9 or AGL15 significantly influence endosperm proliferation and cellularization. Genome-wide analysis with cleavage Under Targets and tagmentation (CUT&Tag) sequencing and RNA sequencing revealed the landscape of endosperm H3K27me3 marks and gene expression profiles in Col-0 and agl9 agl15. CUT&Tag qPCR also demonstrated the occupancy of the two MADS-box proteins and FIS-PRC2 on a few representative target loci. Our studies suggest that MADS-box proteins could potentially recruit PRC2 to regulate many other developmental processes in plants or even in fungi and animals.
Collapse
Affiliation(s)
- Shen Zhang
- Department of Plant and Microbial Biology, University of Minnesota at Twin Cities, Saint Paul, Minnesota MN 55108, United States of AmericaUSA
| | - Devasantosh Mohanty
- Department of Plant and Microbial Biology, University of Minnesota at Twin Cities, Saint Paul, Minnesota MN 55108, United States of AmericaUSA
| | - Adnan Muzaffar
- Department of Plant and Microbial Biology, University of Minnesota at Twin Cities, Saint Paul, Minnesota MN 55108, United States of AmericaUSA
| | - Min Ni
- Department of Plant and Microbial Biology, University of Minnesota at Twin Cities, Saint Paul, Minnesota MN 55108, United States of AmericaUSA.
| |
Collapse
|
3
|
Khouider S, Gehring M. Parental dialectic: Epigenetic conversations in endosperm. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102591. [PMID: 38944896 DOI: 10.1016/j.pbi.2024.102591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/21/2024] [Accepted: 06/07/2024] [Indexed: 07/02/2024]
Abstract
Endosperm is a major evolutionary innovation of flowering plants, and its proper development critically impacts seed growth and viability. Epigenetic regulators have a key function in parental control of endosperm development. Notably, epigenetic regulation of parental genome dosage is a major determinant of seed development success, and disruption of this balance can produce inviable seed, as observed in some interploidy and interspecific crosses. These postzygotic reproduction barriers are also a potent driver of speciation. The molecular machinery and regulatory architecture governing endosperm development is proposed to have evolved under parental conflict. In this review, we emphasize parental conflict as a dialectic conflict and discuss recent findings about the epigenetic molecular machinery that mediates parental conflict in the endosperm.
Collapse
Affiliation(s)
- Souraya Khouider
- Whitehead Institute for Biomedical Research, Cambridge MA 02142, USA
| | - Mary Gehring
- Whitehead Institute for Biomedical Research, Cambridge MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge MA 02139, USA.
| |
Collapse
|
4
|
Kuznetsova X, Dodueva I, Afonin A, Gribchenko E, Danilov L, Gancheva M, Tvorogova V, Galynin N, Lutova L. Whole-Genome Sequencing and Analysis of Tumour-Forming Radish ( Raphanus sativus L.) Line. Int J Mol Sci 2024; 25:6236. [PMID: 38892425 PMCID: PMC11172632 DOI: 10.3390/ijms25116236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Spontaneous tumour formation in higher plants can occur in the absence of pathogen invasion, depending on the plant genotype. Spontaneous tumour formation on the taproots is consistently observed in certain inbred lines of radish (Raphanus sativus var. radicula Pers.). In this paper, using Oxford Nanopore and Illumina technologies, we have sequenced the genomes of two closely related radish inbred lines that differ in their ability to spontaneously form tumours. We identified a large number of single nucleotide variants (amino acid substitutions, insertions or deletions, SNVs) that are likely to be associated with the spontaneous tumour formation. Among the genes involved in the trait, we have identified those that regulate the cell cycle, meristem activity, gene expression, and metabolism and signalling of phytohormones. After identifying the SNVs, we performed Sanger sequencing of amplicons corresponding to SNV-containing regions to validate our results. We then checked for the presence of SNVs in other tumour lines of the radish genetic collection and found the ERF118 gene, which had the SNVs in the majority of tumour lines. Furthermore, we performed the identification of the CLAVATA3/ESR (CLE) and WUSCHEL (WOX) genes and, as a result, identified two unique radish CLE genes which probably encode proteins with multiple CLE domains. The results obtained provide a basis for investigating the mechanisms of plant tumour formation and also for future genetic and genomic studies of radish.
Collapse
Affiliation(s)
- Xenia Kuznetsova
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
| | - Irina Dodueva
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
| | - Alexey Afonin
- All-Russia Research Institute for Agricultural Microbiology, 190608 Saint Petersburg, Russia (E.G.)
| | - Emma Gribchenko
- All-Russia Research Institute for Agricultural Microbiology, 190608 Saint Petersburg, Russia (E.G.)
| | - Lavrentii Danilov
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
| | - Maria Gancheva
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
| | - Varvara Tvorogova
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, 354340 Sochi, Russia
| | - Nikita Galynin
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
| | - Lyudmila Lutova
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (I.D.); (L.D.); (V.T.); (N.G.); (L.L.)
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, 1 Olympic Avenue, 354340 Sochi, Russia
| |
Collapse
|
5
|
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
|
6
|
Miller JR, Adjeroh DA. Machine learning on alignment features for parent-of-origin classification of simulated hybrid RNA-seq. BMC Bioinformatics 2024; 25:109. [PMID: 38475727 DOI: 10.1186/s12859-024-05728-3] [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: 07/28/2023] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Parent-of-origin allele-specific gene expression (ASE) can be detected in interspecies hybrids by virtue of RNA sequence variants between the parental haplotypes. ASE is detectable by differential expression analysis (DEA) applied to the counts of RNA-seq read pairs aligned to parental references, but aligners do not always choose the correct parental reference. RESULTS We used public data for species that are known to hybridize. We measured our ability to assign RNA-seq read pairs to their proper transcriptome or genome references. We tested software packages that assign each read pair to a reference position and found that they often favored the incorrect species reference. To address this problem, we introduce a post process that extracts alignment features and trains a random forest classifier to choose the better alignment. On each simulated hybrid dataset tested, our machine-learning post-processor achieved higher accuracy than the aligner by itself at choosing the correct parent-of-origin per RNA-seq read pair. CONCLUSIONS For the parent-of-origin classification of RNA-seq, machine learning can improve the accuracy of alignment-based methods. This approach could be useful for enhancing ASE detection in interspecies hybrids, though RNA-seq from real hybrids may present challenges not captured by our simulations. We believe this is the first application of machine learning to this problem domain.
Collapse
Affiliation(s)
- Jason R Miller
- Department of Computer Science, Mathematics, Engineering, Shepherd University, Shepherdstown, WV, USA.
- EVOGENE, Department of Biosciences, University of Oslo, Oslo, Norway.
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, USA.
| | - Donald A Adjeroh
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, USA
| |
Collapse
|
7
|
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
|
8
|
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
|
9
|
Lobanova YV, Zhenilo SV. Genomic Imprinting and Random Monoallelic Expression. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:84-96. [PMID: 38467547 DOI: 10.1134/s000629792401005x] [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: 10/21/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 03/13/2024]
Abstract
The review discusses the mechanisms of monoallelic expression, such as genomic imprinting, in which gene transcription depends on the parental origin of the allele, and random monoallelic transcription. Data on the regulation of gene activity in the imprinted regions are summarized with a particular focus on the areas controlling imprinting and factors influencing the variability of the imprintome. The prospects of studies of the monoallelic expression are discussed.
Collapse
Affiliation(s)
- Yaroslava V Lobanova
- Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Svetlana V Zhenilo
- Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
| |
Collapse
|
10
|
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
|
11
|
Yang G, Feng M, Yu K, Cui G, Zhou Y, Sun L, Gao L, Zhang Y, Peng H, Yao Y, Hu Z, Rossi V, De Smet I, Ni Z, Sun Q, Xin M. Paternally imprinted LATE-FLOWERING2 transcription factor contributes to paternal-excess interploidy hybridization barriers in wheat. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2587-2603. [PMID: 37846823 DOI: 10.1111/jipb.13574] [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: 09/20/2023] [Accepted: 10/16/2023] [Indexed: 10/18/2023]
Abstract
Interploidy hybridization between hexaploid and tetraploid genotypes occurred repeatedly during genomic introgression events throughout wheat evolution, and is commonly employed in wheat breeding programs. Hexaploid wheat usually serves as maternal parent because the reciprocal cross generates progeny with severe defects and poor seed germination, but the underlying mechanism is poorly understood. Here, we performed detailed analysis of phenotypic variation in endosperm between two interploidy reciprocal crosses arising from tetraploid (Triticum durum, AABB) and hexaploid wheat (Triticum aestivum, AABBDD). In the paternal- versus the maternal-excess cross, the timing of endosperm cellularization was delayed and starch granule accumulation in the endosperm was repressed, causing reduced germination percentage. The expression profiles of genes involved in nutrient metabolism differed strongly between these endosperm types. Furthermore, expression patterns of parental alleles were dramatically disturbed in interploidy versus intraploidy crosses, leading to increased number of imprinted genes. The endosperm-specific TaLFL2 showed a paternally imprinted expression pattern in interploidy crosses partially due to allele-specific DNA methylation. Paternal TaLFL2 binds to and represses a nutrient accumulation regulator TaNAC019, leading to reduced storage protein and starch accumulation during endosperm development in paternal-excess cross, as confirmed by interploidy crosses between tetraploid wild-type and clustered regularly interspaced palindromic repeats (CRISPR) - CRISPR-associated protein 9 generated hexaploid mutants. These findings reveal a contribution of genomic imprinting to paternal-excess interploidy hybridization barriers during wheat evolution history and explains why experienced breeders preferentially exploit maternal-excess interploidy crosses in wheat breeding programs.
Collapse
Affiliation(s)
- Guanghui Yang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Man Feng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Kuohai Yu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Guangxian Cui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yan Zhou
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Lv Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Lulu Gao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yumei Zhang
- Qingdao Agricultural University, Qingdao, 266109, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Vincenzo Rossi
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Bergamo, 24126, Italy
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
12
|
Zumajo-Cardona C, Gabrieli F, Anire J, Albertini E, Ezquer I, Colombo L. Evolutionary studies of the bHLH transcription factors belonging to MBW complex: their role in seed development. ANNALS OF BOTANY 2023; 132:383-400. [PMID: 37467144 PMCID: PMC10667011 DOI: 10.1093/aob/mcad097] [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: 06/19/2023] [Accepted: 07/17/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND AND AIMS The MBW complex consist of proteins belonging to three major families (MYB, bHLH and WDR) involved in various processes throughout plant development: epidermal cell development, mucilage secretory cells and flavonoid biosynthesis. Recently, it has been reported that TT8, encoding a bHLH transcription factor, is involved in the biosynthesis of flavonoids in the seed coat and it also plays a role in bypassing the postzygotic barrier resulting from an unbalance in genetic loads of the parental lines. Here, we focus on the functional evolution, in seed development, of the bHLH proteins that are part of the MBW complex, complemented with a literature review. METHODS Phylogenetic analyses performed across seed plants and expression analyses in the reproductive tissues of four selected angiosperms (Arabidopsis thaliana, Brassica napus, Capsella rubella and Solanum lycopersicum) allow us to hypothesize on the evolution of its functions. KEY RESULTS TT8 expression in the innermost layer of the seed coat is conserved in the selected angiosperms. However, except for Arabidopsis, TT8 is also expressed in ovules, carpels and fruits. The homologues belonging to the sister clade of TT8, EGL3/GL3, involved in trichome development, are expressed in the outermost layer of the seed coat, suggesting potential roles in mucilage. CONCLUSIONS The ancestral function of these genes appears to be flavonoid biosynthesis, and the conservation of TT8 expression patterns in the innermost layer of the seed coat in angiosperms suggests that their function in postzygotic barriers might also be conserved. Moreover, the literature review and the results of the present study suggest a sophisticated association, linking the mechanisms of action of these genes to the cross-communication activity between the different tissues of the seed. Thus, it provides avenues to study the mechanisms of action of TT8 in the postzygotic triploid block, which is crucial because it impacts seed development in unbalanced crosses.
Collapse
Affiliation(s)
- Cecilia Zumajo-Cardona
- Department of BioScience, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Flavio Gabrieli
- Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, Perugia, Italy
- Dipartimento di Ingegneria Industriale DII, University of Padua, via Gradenigo, 6/a, Padova, Italy
| | - Jovannemar Anire
- Department of BioScience, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
- National Coconut Research Center – Visayas, Visayas State University, Baybay City, Leyte, Philippines
| | - Emidio Albertini
- Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, Perugia, Italy
| | - Ignacio Ezquer
- Department of BioScience, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Lucia Colombo
- Department of BioScience, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| |
Collapse
|
13
|
Wu X, Xie L, Sun X, Wang N, Finnegan EJ, Helliwell C, Yao J, Zhang H, Wu X, Hands P, Lu F, Ma L, Zhou B, Chaudhury A, Cao X, Luo M. Mutation in Polycomb repressive complex 2 gene OsFIE2 promotes asexual embryo formation in rice. NATURE PLANTS 2023; 9:1848-1861. [PMID: 37814022 PMCID: PMC10654051 DOI: 10.1038/s41477-023-01536-4] [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: 11/16/2021] [Accepted: 09/06/2023] [Indexed: 10/11/2023]
Abstract
Prevention of autonomous division of the egg apparatus and central cell in a female gametophyte before fertilization ensures successful reproduction in flowering plants. Here we show that rice ovules of Polycomb repressive complex 2 (PRC2) Osfie1 and Osfie2 double mutants exhibit asexual embryo and autonomous endosperm formation at a high frequency, while ovules of single Osfie2 mutants display asexual pre-embryo-like structures at a lower frequency without fertilization. Earlier onset, higher penetrance and better development of asexual embryos in the double mutants compared with those in Osfie2 suggest that the autonomous endosperm facilitated asexual embryo development. Transcriptomic analysis showed that male genome-expressed OsBBM1 and OsWOX8/9 were activated in the asexual embryos. Similarly, the maternal alleles of the paternally expressed imprinted genes were activated in the autonomous endosperm, suggesting that the egg apparatus and central cell convergently adopt PRC2 to maintain the non-dividing state before fertilization, possibly through silencing of the maternal alleles of male genome-expressed genes.
Collapse
Affiliation(s)
- Xiaoba Wu
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia.
| | - Liqiong Xie
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, School of Life Science and Technology, Xinjiang University, Urumqi, P. R. China
| | - Xizhe Sun
- The State Key Laboratory of North China Crop Improvement and Regulation, College of Horticulture, Hebei Agricultural University, Baoding, P. R. China
- Division of Plant Science, Research School of Biology, the Australian National University, Canberra, Australian Capital Territory, Australia
| | - Ningning Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, P. R. China
| | - E Jean Finnegan
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Chris Helliwell
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Jialing Yao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, P. R. China
| | - Hongyu Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, P. R. China
| | - Xianjun Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, P. R. China
| | - Phil Hands
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Lisong Ma
- The State Key Laboratory of North China Crop Improvement and Regulation, College of Horticulture, Hebei Agricultural University, Baoding, P. R. China
- Division of Plant Science, Research School of Biology, the Australian National University, Canberra, Australian Capital Territory, Australia
| | - Bing Zhou
- Institute of Zoology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Abed Chaudhury
- Krishan Foundation Pty Ltd, Canberra, Australian Capital Territory, Australia
| | - Xiaofeng Cao
- University of Chinese Academy of Sciences, Beijing, P. R. China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Ming Luo
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia.
| |
Collapse
|
14
|
Dong X, Luo H, Bi W, Chen H, Yu S, Zhang X, Dai Y, Cheng X, Xing Y, Fan X, Zhu Y, Guo Y, Meng D. Transcriptome-wide identification and characterization of genes exhibit allele-specific imprinting in maize embryo and endosperm. BMC PLANT BIOLOGY 2023; 23:470. [PMID: 37803280 PMCID: PMC10557216 DOI: 10.1186/s12870-023-04473-8] [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: 04/18/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND Genomic imprinting refers to a subset of genes that are expressed from only one parental allele during seed development in plants. Studies on genomic imprinting have revealed that intraspecific variations in genomic imprinting expression exist in naturally genetic varieties. However, there have been few studies on the functional analysis of allele-specific imprinted genes. RESULTS Here, we generated three reciprocal crosses among the B73, Mo17 and CAU5 inbred lines. Based on the transcriptome-wide analysis of allele-specific expression using RNA sequencing technology, 305 allele-specific imprinting genes (ASIGs) were identified in embryos, and 655 ASIGs were identified in endosperms from three maize F1 hybrids. Of these ASIGs, most did not show consistent maternal or paternal bias between the same tissue from different hybrids or different tissues from one hybrid cross. By gene ontology (GO) analysis, five and eight categories of GO exhibited significantly higher functional enrichments for ASIGs identified in embryo and endosperm, respectively. These functional categories indicated that ASIGs are involved in intercellular nutrient transport, signaling pathways, and transcriptional regulation of kernel development. Finally, the mutation and overexpression of one ASIG (Zm305) affected the length and width of the kernel. CONCLUSION In this study, our data will be helpful in gaining further knowledge of genes exhibiting allele-specific imprinting patterns in seeds. The gain- and loss-of-function phenotypes of ASIGs associated with agronomically important seed traits provide compelling evidence for ASIGs as crucial targets to optimize seed traits in crop plants.
Collapse
Affiliation(s)
- Xiaomei Dong
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Haishan Luo
- College of Agronomy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Wenjing Bi
- College of Agronomy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Hanyu Chen
- College of Agronomy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Shuai Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Xiaoyu Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Yuxin Dai
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Xipeng Cheng
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Yupeng Xing
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Xiaoqin Fan
- Manas Agricultural Experimental Station of Xinjiang Academy of Agricultural Sciences, Changji, 832200, Xinjiang, China
| | - Yanbin Zhu
- National Key Laboratory of Maize Biological Breeding, Key Laboratory of Genetics and Breeding of Main Crops in Northeast Region, Ministry of Agriculture and Rural Affairs, Liaoning Dongya Seed Industry Co., Ltd, Shenyang, Liaoning, 110164, China
| | - Yanling Guo
- National Key Laboratory of Maize Biological Breeding, Key Laboratory of Genetics and Breeding of Main Crops in Northeast Region, Ministry of Agriculture and Rural Affairs, Liaoning Dongya Seed Industry Co., Ltd, Shenyang, Liaoning, 110164, China
| | - Dexuan Meng
- College of Agronomy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.
| |
Collapse
|
15
|
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
|
16
|
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
|
17
|
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
|
18
|
Luo M, Wu X, Xie L, Sun X, Wang N, Finnegan J, Helliwell C, Yao J, Zhang H, Wu X, Lu F, Ma L, Zhou B, Chaudhury A, Cao X, Hands P. Polycomb Repressive Complex 2 (PRC2) suppresses asexual embryo and autonomous endosperm formation in rice.. [DOI: 10.21203/rs.3.rs-1087314/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Abstract
Abstract
Prevention of autonomous division of the egg apparatus and central cell in a female gametophyte before fertilization ensures successful reproduction in flowering plants. Here we show that rice ovules with PRC2 Osfie1 and Osfie2 double mutations exhibit asexual embryo and autonomous endosperm formation at a high frequency, while ovules with a single Osfie2 mutation display asexual pre-embryo-like structures at a lower frequency without fertilization. Confocal microscopy images indicate that the asexual embryos were mainly derived from eggs in the double mutants, while the asexual pre-embryos likely originated from eggs or synergids. Early onsetting, higher penetrance and better development of asexual embryos in the double mutants compared with those in Osfie2 suggest that autonomous endosperm facilitated the asexual embryo development. Transcriptomic analysis showed pluripotency factors such as male genome expressed OsBBM1 and OsWOX8/9 were activated in the asexual embryos. Similarly, the maternal alleles of the paternally expressed imprinted genes were activated in the autonomous endosperm. Our results suggest that the egg apparatus and central cell convergently adopt PRC2 to suppresses asexual embryo and autonomous endosperm formation possibly through silencing male genome-expressed genes.
Collapse
Affiliation(s)
- Ming Luo
- CSIRO Agriculture and Food, Box 1700, ACT 2601, Australia
| | - Xiaoba Wu
- Institute of Botany, Chinese Academy of Sciences
| | - Liqiong Xie
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, School of Life Science and Technology, Xinjiang University, Urumqi 830046, P. R. China
| | - Xizhe Sun
- Division of Plant Science, Research School of Biology, the Australian National University, ACT 2601, Australia
| | - Ningning Wang
- Faculty of agronomy, Jilin Agricultural University, Changchun, 130118, P.R. China
| | - Jean Finnegan
- CSIRO Agriculture and Food, Box 1700, ACT 2601, Australia
| | | | | | - Hongyu Zhang
- Sate Key Laboratory of Gene Discovery and Utilization, Rice Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, P. R. China
| | | | - Falong Lu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
| | - Lisong Ma
- Division of Plant Science, Research School of Biology, the Australian National University, ACT 2601, Australia
| | - Bing Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences; Beijing
| | | | - Xiaofeng Cao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
| | - Phil Hands
- CSIRO Agriculture and Food, Box 1700, ACT 2601, Australia
| |
Collapse
|
19
|
Dong X, Luo H, Yao J, Guo Q, Yu S, Zhang X, Cheng X, Meng D. Characterization of Genes That Exhibit Genotype-Dependent Allele-Specific Expression and Its Implications for the Development of Maize Kernel. Int J Mol Sci 2023; 24:ijms24054766. [PMID: 36902194 PMCID: PMC10002780 DOI: 10.3390/ijms24054766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/19/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023] Open
Abstract
Heterosis or hybrid vigor refers to the superior phenotypic traits of hybrids relative to their parental inbred lines. An imbalance between the expression levels of two parental alleles in the F1 hybrid has been suggested as a mechanism of heterosis. Here, based on genome-wide allele-specific expression analysis using RNA sequencing technology, 1689 genes exhibiting genotype-dependent allele-specific expression (genotype-dependent ASEGs) were identified in the embryos, and 1390 genotype-dependent ASEGs in the endosperm, of three maize F1 hybrids. Of these ASEGs, most were consistent in different tissues from one hybrid cross, but nearly 50% showed allele-specific expression from some genotypes but not others. These genotype-dependent ASEGs were mostly enriched in metabolic pathways of substances and energy, including the tricarboxylic acid cycle, aerobic respiration, and energy derivation by oxidation of organic compounds and ADP binding. Mutation and overexpression of one ASEG affected kernel size, which indicates that these genotype-dependent ASEGs may make important contributions to kernel development. Finally, the allele-specific methylation pattern on genotype-dependent ASEGs indicated that DNA methylation plays a potential role in the regulation of allelic expression for some ASEGs. In this study, a detailed analysis of genotype-dependent ASEGs in the embryo and endosperm of three different maize F1 hybrids will provide an index of genes for future research on the genetic and molecular mechanism of heterosis.
Collapse
Affiliation(s)
- Xiaomei Dong
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang 110866, China
| | - Haishan Luo
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Jiabin Yao
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Qingfeng Guo
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Shuai Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang 110866, China
| | - Xiaoyu Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang 110866, China
| | - Xipeng Cheng
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang 110866, China
| | - Dexuan Meng
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
- Correspondence:
| |
Collapse
|
20
|
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
|
21
|
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
|
22
|
Dai D, Mudunkothge JS, Galli M, Char SN, Davenport R, Zhou X, Gustin JL, Spielbauer G, Zhang J, Barbazuk WB, Yang B, Gallavotti A, Settles AM. Paternal imprinting of dosage-effect defective1 contributes to seed weight xenia in maize. Nat Commun 2022; 13:5366. [PMID: 36100609 PMCID: PMC9470594 DOI: 10.1038/s41467-022-33055-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Historically, xenia effects were hypothesized to be unique genetic contributions of pollen to seed phenotype, but most examples represent standard complementation of Mendelian traits. We identified the imprinted dosage-effect defective1 (ded1) locus in maize (Zea mays) as a paternal regulator of seed size and development. Hypomorphic alleles show a 5–10% seed weight reduction when ded1 is transmitted through the male, while homozygous mutants are defective with a 70–90% seed weight reduction. Ded1 encodes an R2R3-MYB transcription factor expressed specifically during early endosperm development with paternal allele bias. DED1 directly activates early endosperm genes and endosperm adjacent to scutellum cell layer genes, while directly repressing late grain-fill genes. These results demonstrate xenia as originally defined: Imprinting of Ded1 causes the paternal allele to set the pace of endosperm development thereby influencing grain set and size. Xenia effects describe the genetic contribution of pollen to seed phenotypes. Here the authors show that paternal imprinting of Ded1 contributes to the xenia effect in maize by setting the pace of endosperm development.
Collapse
Affiliation(s)
- Dawei Dai
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Janaki S Mudunkothge
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Mary Galli
- Waksman Institute, Rutgers University, Piscataway, NJ, 08854, USA
| | - Si Nian Char
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Ruth Davenport
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Xiaojin Zhou
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jeffery L Gustin
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA.,United States Department of Agriculture, Urbana, IL, 61801, USA
| | - Gertraud Spielbauer
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Junya Zhang
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - W Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.,Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Andrea Gallavotti
- Waksman Institute, Rutgers University, Piscataway, NJ, 08854, USA.,Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - A Mark Settles
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA. .,Bioengineering Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA.
| |
Collapse
|
23
|
Bolt CC, Lopez-Delisle L, Hintermann A, Mascrez B, Rauseo A, Andrey G, Duboule D. Context-dependent enhancer function revealed by targeted inter-TAD relocation. Nat Commun 2022; 13:3488. [PMID: 35715427 PMCID: PMC9205857 DOI: 10.1038/s41467-022-31241-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 06/09/2022] [Indexed: 11/08/2022] Open
Abstract
The expression of some genes depends on large, adjacent regions of the genome that contain multiple enhancers. These regulatory landscapes frequently align with Topologically Associating Domains (TADs), where they integrate the function of multiple similar enhancers to produce a global, TAD-specific regulation. We asked if an individual enhancer could overcome the influence of one of these landscapes, to drive gene transcription. To test this, we transferred an enhancer from its native location, into a nearby TAD with a related yet different functional specificity. We used the biphasic regulation of Hoxd genes during limb development as a paradigm. These genes are first activated in proximal limb cells by enhancers located in one TAD, which is then silenced when the neighboring TAD activates its enhancers in distal limb cells. We transferred a distal limb enhancer into the proximal limb TAD and found that its new context suppresses its normal distal specificity, even though it is bound by HOX13 transcription factors, which are responsible for the distal activity. This activity can be rescued only when a large portion of the surrounding environment is removed. These results indicate that, at least in some cases, the functioning of enhancer elements is subordinated to the host chromatin context, which can exert a dominant control over its activity.
Collapse
Affiliation(s)
- Christopher Chase Bolt
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
- Department of Genetics and Evolution, Faculty of Sciences, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva, Switzerland.
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Aurélie Hintermann
- Department of Genetics and Evolution, Faculty of Sciences, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva, Switzerland
| | - Bénédicte Mascrez
- Department of Genetics and Evolution, Faculty of Sciences, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva, Switzerland
| | - Antonella Rauseo
- Department of Medical Genetics, Faculty of Medicine, University of Geneva, Rue Michel Servet 1, 1211, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Guillaume Andrey
- Department of Medical Genetics, Faculty of Medicine, University of Geneva, Rue Michel Servet 1, 1211, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Denis Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
- Department of Genetics and Evolution, Faculty of Sciences, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva, Switzerland.
- Collège de France, 11 Place Marcelin Berthelot, 75231, Paris, France.
| |
Collapse
|
24
|
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: 17] [Impact Index Per Article: 8.5] [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
|
25
|
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
|
26
|
Lu D, Zhai J, Xi M. Regulation of DNA Methylation During Plant Endosperm Development. Front Genet 2022; 13:760690. [PMID: 35222527 PMCID: PMC8867698 DOI: 10.3389/fgene.2022.760690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/17/2022] [Indexed: 11/21/2022] Open
Abstract
The endosperm is a vital storage tissue in plant seeds. It provides nutrients to the embryos or the seedlings during seed development and germination. Although the genetic information in the endosperm cannot be passed directly to the next generation, its inherited epigenetic marks affect gene expression and its development and, consequently, embryo and seed growth. DNA methylation is a major form of epigenetic modification that can be investigated to understand the epigenome changes during reproductive development. Therefore, it is of great significance to explore the effects of endosperm DNA methylation on crop yield and traits. In this review, we discuss the changes in DNA methylation and the resulting imprinted gene expression levels during plant endosperm development, as well as their effects on seed development.
Collapse
Affiliation(s)
- Dongdong Lu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Jixian Zhai
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
- *Correspondence: Jixian Zhai, ; Mengli Xi,
| | - Mengli Xi
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- *Correspondence: Jixian Zhai, ; Mengli Xi,
| |
Collapse
|
27
|
Gawarecka K, Siwinska J, Poznanski J, Onysk A, Surowiecki P, Sztompka K, Surmacz L, Ahn JH, Korte A, Swiezewska E, Ihnatowicz A. cis-prenyltransferase 3 and α/β-hydrolase are new determinants of dolichol accumulation in Arabidopsis. PLANT, CELL & ENVIRONMENT 2022; 45:479-495. [PMID: 34778961 PMCID: PMC9300173 DOI: 10.1111/pce.14223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 11/06/2021] [Accepted: 11/07/2021] [Indexed: 06/13/2023]
Abstract
Dolichols (Dols), ubiquitous components of living organisms, are indispensable for cell survival. In plants, as well as other eukaryotes, Dols are crucial for post-translational protein glycosylation, aberration of which leads to fatal metabolic disorders in humans and male sterility in plants. Until now, the mechanisms underlying Dol accumulation remain elusive. In this study, we have analysed the natural variation of the accumulation of Dols and six other isoprenoids among more than 120 Arabidopsis thaliana accessions. Subsequently, by combining QTL and GWAS approaches, we have identified several candidate genes involved in the accumulation of Dols, polyprenols, plastoquinone and phytosterols. The role of two genes implicated in the accumulation of major Dols in Arabidopsis-the AT2G17570 gene encoding a long searched for cis-prenyltransferase (CPT3) and the AT1G52460 gene encoding an α/β-hydrolase-is experimentally confirmed. These data will help to generate Dol-enriched plants which might serve as a remedy for Dol-deficiency in humans.
Collapse
Affiliation(s)
- Katarzyna Gawarecka
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarszawaPoland
- Department of Life SciencesKorea UniversitySeoulKorea
| | - Joanna Siwinska
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of GdanskUniversity of GdanskGdanskPoland
| | - Jaroslaw Poznanski
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarszawaPoland
| | - Agnieszka Onysk
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarszawaPoland
| | | | - Karolina Sztompka
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarszawaPoland
| | - Liliana Surmacz
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarszawaPoland
| | - Ji Hoon Ahn
- Department of Life SciencesKorea UniversitySeoulKorea
| | - Arthur Korte
- Center for Computational and Theoretical BiologyUniversity of WurzburgWurzburgGermany
| | - Ewa Swiezewska
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarszawaPoland
| | - Anna Ihnatowicz
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of GdanskUniversity of GdanskGdanskPoland
| |
Collapse
|
28
|
Zhang Z, Yu S, Li J, Zhu Y, Jiang S, Xia H, Zhou Y, Sun D, Liu M, Li C, Zhu Y, Ruan Y, Dong X. Epigenetic modifications potentially controlling the allelic expression of imprinted genes in sunflower endosperm. BMC PLANT BIOLOGY 2021; 21:570. [PMID: 34863098 PMCID: PMC8642925 DOI: 10.1186/s12870-021-03344-4] [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: 07/07/2021] [Accepted: 10/26/2021] [Indexed: 06/02/2023]
Abstract
BACKGROUND Genomic imprinting is an epigenetic phenomenon mainly occurs in endosperm of flowering plants. Genome-wide identification of imprinted genes have been completed in several dicot Cruciferous plant and monocot crops. RESULTS Here, we analyzed global patterns of allelic gene expression in developing endosperm of sunflower which belongs to the composite family. Totally, 691 imprinted loci candidates were identified in 12 day-after-pollination sunflower endosperm including 79 maternally expressed genes (MEG) and 596 paternally expressed genes (PEG), 6 maternally expressed noncoding RNAs (MNC) and 10 paternally expressed noncoding RNAs (PNC). And a clear clustering of imprinted genes throughout the rapeseed genome was identified. Generally, imprinting in sunflower is conserved within a species, but intraspecific variation also was detected. Limited loci in sunflower are imprinted in other several different species. The DNA methylation pattern around imprinted genes were investigated in embryo and endosperm tissues. In CG context, the imprinted genes were significantly associated with differential methylated regions exhibiting hypomethylation in endosperm and hypermethylation in embryo, which indicated that the maternal demethylation in CG context potentially induce the genomic imprinting in endosperm. CONCLUSION Our study would be helpful for understanding of genomic imprinting in plants and provide potential basis for further research in imprinting in sunflower.
Collapse
Affiliation(s)
- Zhichao Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Shuai Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Jing Li
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Yanbin Zhu
- State Key Laboratory of Maize Bio-Breeding, Shenyang, China
- State Key Laboratory of the Northeast Crop Genetics and Breeding, Shenyang, China
| | - Siqi Jiang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Haoran Xia
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Yue Zhou
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Daqiu Sun
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Meiling Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Cong Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Yanshu Zhu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Yanye Ruan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Xiaomei Dong
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China.
- State Key Laboratory of Maize Bio-Breeding, Shenyang, China.
| |
Collapse
|
29
|
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
|
30
|
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
|
31
|
Rodrigues JA, Hsieh PH, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proc Natl Acad Sci U S A 2021; 118:e2104445118. [PMID: 34272287 PMCID: PMC8307775 DOI: 10.1073/pnas.2104445118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Parent-of-origin-dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin-specific expression. To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA-producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic variation occurred at key regulatory regions-the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution.
Collapse
Affiliation(s)
- Jessica A Rodrigues
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Ping-Hung Hsieh
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Deling Ruan
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Toshiro Nishimura
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Manoj K Sharma
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Rita Sharma
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - XinYi Ye
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Nicholas D Nguyen
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Sukhranjan Nijjar
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Pamela C Ronald
- Department of Plant Pathology, University of California, Davis, CA 95616
- The Genome Center, University of California, Davis, CA 95616
| | - Robert L Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720;
| | - Daniel Zilberman
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720;
- Department of Cell and Developmental Biology, The John Innes Centre, Norwich NR4 7UH, United Kingdom
| |
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
|
Widespread imprinting of transposable elements and variable genes in the maize endosperm. PLoS Genet 2021; 17:e1009491. [PMID: 33830994 PMCID: PMC8057601 DOI: 10.1371/journal.pgen.1009491] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/20/2021] [Accepted: 03/15/2021] [Indexed: 11/19/2022] Open
Abstract
Fertilization and seed development is a critical time in the plant life cycle, and coordinated development of the embryo and endosperm are required to produce a viable seed. In the endosperm, some genes show imprinted expression where transcripts are derived primarily from one parental genome. Imprinted gene expression has been observed across many flowering plant species, though only a small proportion of genes are imprinted. Understanding how imprinted expression arises has been complicated by the reliance on single nucleotide polymorphisms between alleles to enable testing for imprinting. Here, we develop a method to use whole genome assemblies of multiple genotypes to assess for imprinting of both shared and variable portions of the genome using data from reciprocal crosses. This reveals widespread maternal expression of genes and transposable elements with presence-absence variation within maize and across species. Most maternally expressed features are expressed primarily in the endosperm, suggesting that maternal de-repression in the central cell facilitates expression. Furthermore, maternally expressed TEs are enriched for maternal expression of the nearest gene, and read alignments over maternal TE-gene pairs indicate that these are fused rather than independent transcripts.
Collapse
|
34
|
Anderson SN, Zhou P, Higgins K, Brandvain Y, Springer NM. Widespread imprinting of transposable elements and variable genes in the maize endosperm. PLoS Genet 2021. [PMID: 33830994 DOI: 10.1371/journal.pgen.100949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
Fertilization and seed development is a critical time in the plant life cycle, and coordinated development of the embryo and endosperm are required to produce a viable seed. In the endosperm, some genes show imprinted expression where transcripts are derived primarily from one parental genome. Imprinted gene expression has been observed across many flowering plant species, though only a small proportion of genes are imprinted. Understanding how imprinted expression arises has been complicated by the reliance on single nucleotide polymorphisms between alleles to enable testing for imprinting. Here, we develop a method to use whole genome assemblies of multiple genotypes to assess for imprinting of both shared and variable portions of the genome using data from reciprocal crosses. This reveals widespread maternal expression of genes and transposable elements with presence-absence variation within maize and across species. Most maternally expressed features are expressed primarily in the endosperm, suggesting that maternal de-repression in the central cell facilitates expression. Furthermore, maternally expressed TEs are enriched for maternal expression of the nearest gene, and read alignments over maternal TE-gene pairs indicate that these are fused rather than independent transcripts.
Collapse
Affiliation(s)
- Sarah N Anderson
- Department of Genetics, Development, and Cell Biology; Iowa State University; Ames, Iowa, United States of America
| | - Peng Zhou
- Department of Plant and Microbial Biology; University of Minnesota; St. Paul, Minnesota, United States of America
| | - Kaitlin Higgins
- Department of Genetics, Development, and Cell Biology; Iowa State University; Ames, Iowa, United States of America
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology; University of Minnesota; St. Paul, Minnesota, United States of America
| | - Nathan M Springer
- Department of Plant and Microbial Biology; University of Minnesota; St. Paul, Minnesota, United States of America
| |
Collapse
|
35
|
Rong H, Yang W, Zhu H, Jiang B, Jiang J, Wang Y. Genomic imprinted genes in reciprocal hybrid endosperm of Brassica napus. BMC PLANT BIOLOGY 2021; 21:140. [PMID: 33726676 PMCID: PMC7968328 DOI: 10.1186/s12870-021-02908-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 02/28/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND Genomic imprinting results in the expression of parent-of-origin-specific alleles in the offspring. Brassica napus is an oil crop with research values in polyploidization. Identification of imprinted genes in B. napus will enrich the knowledge of genomic imprinting in dicotyledon plants. RESULTS In this study, we performed reciprocal crosses between B. napus L. cultivars Yangyou 6 (Y6) and Zhongshuang 11 (ZS11) to collect endosperm at 20 and 25 days after pollination (DAP) for RNA-seq. In total, we identified 297 imprinted genes, including 283 maternal expressed genes (MEGs) and 14 paternal expressed genes (PEGs) according to the SNPs between Y6 and ZS11. Only 36 genes (35 MEGs and 1 PEG) were continuously imprinted in 20 and 25 DAP endosperm. We found 15, 2, 5, 3, 10, and 25 imprinted genes in this study were also imprinted in Arabidopsis, rice, castor bean, maize, B. rapa, and other B. napus lines, respectively. Only 26 imprinted genes were specifically expressed in endosperm, while other genes were also expressed in root, stem, leaf and flower bud of B. napus. A total of 109 imprinted genes were clustered on rapeseed chromosomes. We found the LTR/Copia transposable elements (TEs) were most enriched in both upstream and downstream of the imprinted genes, and the TEs enriched around imprinted genes were more than non-imprinted genes. Moreover, the expression of 5 AGLs and 6 pectin-related genes in hybrid endosperm were significantly changed comparing with that in parent endosperm. CONCLUSION This research provided a comprehensive identification of imprinted genes in B. napus, and enriched the gene imprinting in dicotyledon plants, which would be useful in further researches on how gene imprinting regulates seed development.
Collapse
Affiliation(s)
- Hao Rong
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Wenjing Yang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Haotian Zhu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Bo Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Jinjin Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Youping Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou, 225009 China
| |
Collapse
|
36
|
Liu Y, Jing X, Zhang H, Xiong J, Qiao Y. Identification of Imprinted Genes Based on Homology: An Example of Fragaria vesca. Genes (Basel) 2021; 12:genes12030380. [PMID: 33800118 PMCID: PMC7999015 DOI: 10.3390/genes12030380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/28/2021] [Accepted: 03/04/2021] [Indexed: 01/04/2023] Open
Abstract
Genomic imprinting has drawn increasing attention in plant biology in recent years. At present, hundreds of imprinted genes have been identified in various plants, and some of them have been reported to be evolutionarily conserved in plant species. In this research, 17 candidate genes in Fragaria vesca were obtained based on the homologous imprinted genes in Arabidopsis thaliana and other species. We further constructed reciprocal crosses of diploid strawberry (F. vesca) using the varieties 10-41 and 18-86 as the parents to investigate the conservation of these imprinted genes. Potentially informative single nucleotide polymorphisms (SNPs) were used as molecular markers of two parents obtained from candidate imprinted genes which have been cloned and sequenced. Meanwhile, we analyzed the SNP site variation ratios and parent-of-origin expression patterns of candidate imprinted genes at 10 days after pollination (DAP) endosperm and embryo for the hybrids of reciprocal cross, respectively. A total of five maternally expressed genes (MEGs), i.e., FvARI8, FvKHDP-2, FvDRIP2, FvBRO1, and FvLTP3, were identified in the endosperm, which did not show imprinting in the embryo. Finally, tissues expression analysis indicated that the five imprinted genes excluding FvDRIP2 mainly expressed in the endosperm. This is the first report on imprinted genes of Fragaria, and we provide a simple and rapid method based on homologous conservation to screen imprinted genes. The present study will provide a basis for further study of function and mechanism of genomic imprinting in F. vesca.
Collapse
|
37
|
Yang L, Xing F, He Q, Tahir ul Qamar M, Chen LL, Xing Y. Conserved Imprinted Genes between Intra-Subspecies and Inter-Subspecies Are Involved in Energy Metabolism and Seed Development in Rice. Int J Mol Sci 2020; 21:ijms21249618. [PMID: 33348666 PMCID: PMC7765902 DOI: 10.3390/ijms21249618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/10/2020] [Accepted: 12/16/2020] [Indexed: 01/28/2023] Open
Abstract
Genomic imprinting is an epigenetic phenomenon in which a subset of genes express dependent on the origin of their parents. In plants, it is unclear whether imprinted genes are conserved between subspecies in rice. Here we identified imprinted genes from embryo and endosperm 5-7 days after pollination from three pairs of reciprocal hybrids, including inter-subspecies, japonica intra-subspecies, and indica intra-subspecies reciprocal hybrids. A total of 914 imprinted genes, including 546 in inter-subspecies hybrids, 211 in japonica intra-subspecies hybrids, and 286 in indica intra-subspecies hybrids. In general, the number of maternally expressed genes (MEGs) is more than paternally expressed genes (PEGs). Moreover, imprinted genes tend to be in mini clusters. The number of shared genes by R9N (reciprocal crosses between 9311 and Nipponbare) and R9Z (reciprocal crosses between 9311 and Zhenshan 97), R9N and RZN (reciprocal crosses between Zhonghua11 and Nipponbare), R9Z and RZN was 72, 46, and 16. These genes frequently involved in energy metabolism and seed development. Five imprinted genes (Os01g0151700, Os07g0103100, Os10g0340600, Os11g0679700, and Os12g0632800) are commonly detected in all three pairs of reciprocal hybrids and were validated by RT-PCR sequencing. Gene editing of two imprinted genes revealed that both genes conferred grain filling. Moreover, 15 and 27 imprinted genes with diverse functions in rice were shared with Arabidopsis and maize, respectively. This study provided valuable resources for identification of imprinting genes in rice or even in cereals.
Collapse
Affiliation(s)
- Lin Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (L.Y.); (Q.H.)
| | - Feng Xing
- College of Life Science, Xinyang Normal University, Xinyang 464000, China;
| | - Qin He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (L.Y.); (Q.H.)
| | - Muhammad Tahir ul Qamar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China;
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (L.Y.); (Q.H.)
- Correspondence: (L.-L.C.); (Y.X.)
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (L.Y.); (Q.H.)
- Correspondence: (L.-L.C.); (Y.X.)
| |
Collapse
|
38
|
Howe J, Schiøtt M, Li Q, Wang Z, Zhang G, Boomsma JJ. A novel method for using RNA-seq data to identify imprinted genes in social Hymenoptera with multiply mated queens. J Evol Biol 2020; 33:1770-1782. [PMID: 33030255 DOI: 10.1111/jeb.13716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/13/2020] [Accepted: 09/21/2020] [Indexed: 11/30/2022]
Abstract
Genomic imprinting results in parent-of-origin-dependent gene expression biased towards either the maternally or paternally derived allele at the imprinted locus. The kinship theory of genomic imprinting argues that this unusual expression pattern can be a manifestation of intra-genomic conflict between the maternally and paternally derived halves of the genome that arises because they are not equally related to the genomes of social partners. The theory thus predicts that imprinting may evolve wherever there are close interactions among asymmetrically related kin. The social Hymenoptera with permanent caste differentiation are suitable candidates for testing the kinship theory because haplodiploid sex determination creates strong relatedness asymmetries and nursing workers interact closely with kin. However, progress in the search for imprinted genes in the social Hymenoptera has been slow, in part because tests for imprinting rely on reciprocal crosses that are impossible in most species. Here, we develop a method to systematically search for imprinting in haplodiploid social insects without crosses, using instead samples of pooled individuals collected from natural colonies. We tested this protocol using data available for the leaf-cutting ant Acromyrmex echinatior, providing the first genome-wide search for imprinting in any ant. Although we identified several genes as potentially imprinted, none of the four genes tested could be verified as imprinted using digital droplet PCR, highlighting the need for higher quality genomic assemblies that accurately map duplicated genes.
Collapse
Affiliation(s)
- Jack Howe
- Department of Biology, Section for Ecology and Evolution, Centre for Social Evolution, University of Copenhagen, Copenhagen, Denmark
| | - Morten Schiøtt
- Department of Biology, Section for Ecology and Evolution, Centre for Social Evolution, University of Copenhagen, Copenhagen, Denmark
| | - Qiye Li
- BGI-Shenzhen, Shenzhen, China
| | | | - Guojie Zhang
- Department of Biology, Section for Ecology and Evolution, Centre for Social Evolution, University of Copenhagen, Copenhagen, Denmark.,BGI-Shenzhen, Shenzhen, China
| | - Jacobus J Boomsma
- Department of Biology, Section for Ecology and Evolution, Centre for Social Evolution, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
39
|
Xu L, Jiang H. Writing and Reading Histone H3 Lysine 9 Methylation in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:452. [PMID: 32435252 PMCID: PMC7218100 DOI: 10.3389/fpls.2020.00452] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/27/2020] [Indexed: 05/05/2023]
Abstract
In eukaryotes, histone H3 lysine 9 methylation (H3K9me) mediates the silencing of invasive and repetitive sequences by preventing the expression of aberrant gene products and the activation of transposition. In Arabidopsis, while it is well known that dimethylation of histone H3 at lysine 9 (H3K9me2) is maintained through a feedback loop between H3K9me2 and DNA methylation, the details of the H3K9me2-dependent silencing pathway have not been fully elucidated. Recently, the regulation and the function of H3K9 methylation have been extensively characterized. In this review, we summarize work from the recent studies regarding the regulation of H3K9me2, emphasizing the process of deposition and reading and the biological significance of H3K9me2 in Arabidopsis.
Collapse
Affiliation(s)
| | - Hua Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| |
Collapse
|
40
|
Botet R, Keurentjes JJB. The Role of Transcriptional Regulation in Hybrid Vigor. FRONTIERS IN PLANT SCIENCE 2020; 11:410. [PMID: 32351526 PMCID: PMC7174566 DOI: 10.3389/fpls.2020.00410] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/23/2020] [Indexed: 05/19/2023]
Abstract
The genetic basis of hybrid vigor in plants remains largely unsolved but strong evidence suggests that variation in transcriptional regulation can explain many aspects of this phenomenon. Natural variation in transcriptional regulation is highly abundant in virtually all species and thus a potential source of heterotic variability. Allele Specific Expression (ASE), which is tightly linked to parent of origin effects and modulated by complex interactions in cis and in trans, is generally considered to play a key role in explaining the differences between hybrids and parental lines. Here we discuss the recent developments in elucidating the role of transcriptional variation in a number of aspects of hybrid vigor, thereby bridging old paradigms and hypotheses with contemporary research in various species.
Collapse
Affiliation(s)
- Ramon Botet
- Laboratory of Genetics, Wageningen University & Research, Wageningen, Netherlands
| | | |
Collapse
|
41
|
Abstract
In this review, Batista and Köhler revisit the current models explaining imprinting regulation in plants, and discuss novel regulatory mechanisms that could function independently of parental DNA methylation asymmetries in the establishment of imprinting. Genomic imprinting is an epigenetic phenomenon leading to parentally biased gene expression. Throughout the years, extensive efforts have been made to characterize the epigenetic marks underlying imprinting in animals and plants. As a result, DNA methylation asymmetries between parental genomes emerged as the primary factor controlling the imprinting status of many genes. Nevertheless, the data accumulated so far suggest that this process cannot solely explain the imprinting of all genes. In this review, we revisit the current models explaining imprinting regulation in plants, and discuss novel regulatory mechanisms that could function independently of parental DNA methylation asymmetries in the establishment of imprinting.
Collapse
Affiliation(s)
- Rita A Batista
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala SE-750 07, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala SE-750 07, Sweden
| |
Collapse
|
42
|
Abstract
Genomic imprinting is a phenomenon that occurs in flowering plants and mammals, whereby a gene is expressed in a parent-of-origin-specific manner. Although imprinting has now been examined genome-wide in a number of species using RNA-seq, the analyses used to assess imprinting vary between studies, making consistent comparisons between species difficult. Here we present a simple, easy-to-use bioinformatic pipeline for imprinting analyses suitable for any tissue, including plant endosperm. All relevant scripts can be downloaded. As an illustrative example, we reanalyze published data from A. thaliana and Z. mays endosperm using the pipeline and then demonstrate how to use the results to assess the conservation of imprinting between these species. We also introduce the Plant Imprinting Database, a repository for published imprinting datasets in plants that can be used to view, compare, and download data.
Collapse
Affiliation(s)
- Colette L Picard
- Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Mary Gehring
- Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
43
|
Lafon Placette C. Endosperm genome dosage, hybrid seed failure, and parental imprinting: sexual selection as an alternative to parental conflict. AMERICAN JOURNAL OF BOTANY 2020; 107:17-19. [PMID: 31797356 DOI: 10.1002/ajb2.1401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/04/2019] [Indexed: 05/15/2023]
Affiliation(s)
- Clément Lafon Placette
- Department of Botany, Faculty of Science, Charles University, CZ-128 01, Prague, Czech Republic
| |
Collapse
|
44
|
Bjerkan KN, Hornslien KS, Johannessen IM, Krabberød AK, van Ekelenburg YS, Kalantarian M, Shirzadi R, Comai L, Brysting AK, Bramsiepe J, Grini PE. Genetic variation and temperature affects hybrid barriers during interspecific hybridization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:122-140. [PMID: 31487093 DOI: 10.1111/tpj.14523] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 07/31/2019] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
Genomic imprinting regulates parent-specific transcript dosage during seed development and is mainly confined to the endosperm. Elucidation of the function of many imprinted genes has been hampered by the lack of corresponding mutant phenotypes, and the role of imprinting is mainly associated with genome dosage regulation or allocation of resources. Disruption of imprinted genes has also been suggested to mediate endosperm-based post-zygotic hybrid barriers depending on genetic variation and gene dosage. Here, we have analyzed the conservation of a clade from the MADS-box type I class transcription factors in the closely related species Arabidopsis arenosa, A. lyrata, and A. thaliana, and show that AGL36-like genes are imprinted and maternally expressed in seeds of Arabidopsis species and in hybrid seeds between outbreeding species. In hybridizations between outbreeding and inbreeding species the paternally silenced allele of the AGL36-like gene is reactivated in the hybrid, demonstrating that also maternally expressed imprinted genes are perturbed during hybridization and that such effects on imprinted genes are specific to the species combination. Furthermore, we also demonstrate a quantitative effect of genetic diversity and temperature on the strength of the post-zygotic hybridization barrier. Markedly, a small decrease in temperature during seed development increases the survival of hybrid F1 seeds, suggesting that abiotic and genetic parameters play important roles in post-zygotic species barriers, pointing at evolutionary scenarios favoring such effects. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA562212. All sequences generated in this study have been deposited in the National Center for Biotechnology Information Sequence Read Archive (https://www.ncbi.nlm.nih.gov/sra/) with project number PRJNA562212.
Collapse
Affiliation(s)
- Katrine N Bjerkan
- EVOGENE, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
- CEES, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Karina S Hornslien
- EVOGENE, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Ida M Johannessen
- EVOGENE, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Anders K Krabberød
- EVOGENE, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | | | - Maryam Kalantarian
- EVOGENE, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Reza Shirzadi
- EVOGENE, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Luca Comai
- Plant Biology and Genome Center, University of California, Davis, Davis, CA, 95616, USA
| | - Anne K Brysting
- EVOGENE, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
- CEES, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Jonathan Bramsiepe
- EVOGENE, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
- CEES, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Paul E Grini
- EVOGENE, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| |
Collapse
|
45
|
Flores-Vergara MA, Oneal E, Costa M, Villarino G, Roberts C, De Luis Balaguer MA, Coimbra S, Willis J, Franks RG. Developmental Analysis of Mimulus Seed Transcriptomes Reveals Functional Gene Expression Clusters and Four Imprinted, Endosperm-Expressed Genes. FRONTIERS IN PLANT SCIENCE 2020; 11:132. [PMID: 32161609 PMCID: PMC7052496 DOI: 10.3389/fpls.2020.00132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/28/2020] [Indexed: 05/15/2023]
Abstract
The double fertilization of the female gametophyte initiates embryogenesis and endosperm development in seeds via the activation of genes involved in cell differentiation, organ patterning, and growth. A subset of genes expressed in endosperm exhibit imprinted expression, and the correct balance of gene expression between parental alleles is critical for proper endosperm and seed development. We use a transcriptional time series analysis to identify genes that are associated with key shifts in seed development, including genes associated with secondary cell wall synthesis, mitotic cell cycle, chromatin organization, auxin synthesis, fatty acid metabolism, and seed maturation. We relate these genes to morphological changes in Mimulus seeds. We also identify four endosperm-expressed transcripts that display imprinted (paternal) expression bias. The imprinted status of these four genes is conserved in other flowering plants, suggesting that they are functionally important in endosperm development. Our study explores gene regulatory dynamics in a species with ab initio cellular endosperm development, broadening the taxonomic focus of the literature on gene expression in seeds. Moreover, it is the first to validate genes with imprinted endosperm expression in Mimulus guttatus, and will inform future studies on the genetic causes of seed failure in this model system.
Collapse
Affiliation(s)
- Miguel A. Flores-Vergara
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Elen Oneal
- Department of Biology, Duke University, Durham, NC, United States
- *Correspondence: Elen Oneal,
| | - Mario Costa
- GreenUPorto, Sustainable Agrifood Production Research Centre, Biology Department, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Gonzalo Villarino
- Biology Department, San Diego State University, San Diego, CA, United States
| | - Caitlyn Roberts
- Department of Biology, Berea College, Berea, KY, United States
| | | | - Sílvia Coimbra
- GreenUPorto, Sustainable Agrifood Production Research Centre, Biology Department, Faculty of Sciences, University of Porto, Porto, Portugal
| | - John Willis
- Department of Biology, Duke University, Durham, NC, United States
| | - Robert G. Franks
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| |
Collapse
|
46
|
Batista RA, Moreno-Romero J, Qiu Y, van Boven J, Santos-González J, Figueiredo DD, Köhler C. The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons. eLife 2019; 8:50541. [PMID: 31789592 PMCID: PMC6914339 DOI: 10.7554/elife.50541] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/30/2019] [Indexed: 12/31/2022] Open
Abstract
MADS-box transcription factors (TFs) are ubiquitous in eukaryotic organisms and play major roles during plant development. Nevertheless, their function in seed development remains largely unknown. Here, we show that the imprinted Arabidopsis thaliana MADS-box TF PHERES1 (PHE1) is a master regulator of paternally expressed imprinted genes, as well as of non-imprinted key regulators of endosperm development. PHE1 binding sites show distinct epigenetic modifications on maternal and paternal alleles, correlating with parental-specific transcriptional activity. Importantly, we show that the CArG-box-like DNA-binding motifs that are bound by PHE1 have been distributed by RC/Helitron transposable elements. Our data provide an example of the molecular domestication of these elements which, by distributing PHE1 binding sites throughout the genome, have facilitated the recruitment of crucial endosperm regulators into a single transcriptional network.
Collapse
Affiliation(s)
- Rita A Batista
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jordi Moreno-Romero
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Yichun Qiu
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Joram van Boven
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Duarte D Figueiredo
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| |
Collapse
|
47
|
Ramirez-Prado JS, Latrasse D, Rodriguez-Granados NY, Huang Y, Manza-Mianza D, Brik-Chaouche R, Jaouannet M, Citerne S, Bendahmane A, Hirt H, Raynaud C, Benhamed M. The Polycomb protein LHP1 regulates Arabidopsis thaliana stress responses through the repression of the MYC2-dependent branch of immunity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1118-1131. [PMID: 31437321 DOI: 10.1111/tpj.14502] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/26/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
Polycomb repressive complexes (PRCs) have been traditionally associated with the regulation of developmental processes in various organisms, including higher plants. However, similar to other epigenetic regulators, there is accumulating evidence for their role in the regulation of stress and immune-related pathways. In the current study we show that the PRC1 protein LHP1 is required for the repression of the MYC2 branch of jasmonic acid (JA)/ethylene (ET) pathway of immunity. Loss of LHP1 induces the reduction in H3K27me3 levels in the gene bodies of ANAC019 and ANAC055, as well as some of their targets, leading to their transcriptional upregulation. Consistently, increased expression of these two transcription factors leads to the misregulation of several of their genomic targets. The lhp1 mutant mimics the MYC2, ANAC019, and ANAC055 overexpressers in several of their phenotypes, including increased aphid resistance, abscisic acid (ABA) sensitivity and drought tolerance. In addition, like the MYC2 and ANAC overexpressers, lhp1 displays reduced salicylic acid (SA) content caused by a deregulation of ICS1 and BSMT1, as well as increased susceptibility to the hemibiotrophic pathogen Pseudomonas syringae pv. tomato DC3000. Together, our results indicate that LHP1 regulates the expression of stress-responsive genes as well as the homeostasis and responses to the stress hormones SA and ABA. This protein emerges as a key chromatin player fine tuning the complex balance between developmental and stress-responsive processes.
Collapse
Affiliation(s)
- Juan Sebastian Ramirez-Prado
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Natalia Yaneth Rodriguez-Granados
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Ying Huang
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Deborah Manza-Mianza
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Rim Brik-Chaouche
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Maelle Jaouannet
- CNRS, INRA, Université Nice Sophia Antipolis, UMR 1355-7254, Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Heribert Hirt
- Desert Agriculture Initiative, King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Kingdom of Saudi Arabia
| | - Cecile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| |
Collapse
|
48
|
Abstract
The plant haploid generation is specified late in higher plant development, and post-meiotic haploid plant cells divide mitotically to produce a haploid gametophyte, in which a subset of cells differentiates into the gametes. The immediate mother of the angiosperm seed is the female gametophyte, also called the embryo sac. In most flowering plants the embryo sac is comprised of two kinds of gametes (egg and central cell) and two kinds of subsidiary cells (antipodals and synergids) all of which descend from a single haploid spore produced by meiosis. The embryo sac develops within a specialized organ of the flower called the ovule, which supports and controls many steps in the development of both the embryo sac and the seed. Double fertilization of the central cell and egg cell by the two sperm cells of a pollen grain produce the endosperm and embryo of the seed, respectively. The endosperm and embryo develop under the influence of their precursor gametes and the surrounding tissues of the ovule and the gametophyte. The final size and pattern of the angiosperm seed then is the result of complex interactions across multiple tissues of three different generations (maternal sporophyte, maternal gametophyte, and the fertilization products) and three different ploidies (haploid gametophyte, diploid parental sporophyte and embryo, and triploid endosperm).
Collapse
|
49
|
Mateo-Bonmatí E, Casanova-Sáez R, Ljung K. Epigenetic Regulation of Auxin Homeostasis. Biomolecules 2019; 9:biom9100623. [PMID: 31635281 PMCID: PMC6843323 DOI: 10.3390/biom9100623] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 12/12/2022] Open
Abstract
Epigenetic regulation involves a myriad of mechanisms that regulate the expression of loci without altering the DNA sequence. These different mechanisms primarily result in modifications of the chromatin topology or DNA chemical structure that can be heritable or transient as a dynamic response to environmental cues. The phytohormone auxin plays an important role in almost every aspect of plant life via gradient formation. Auxin maxima/minima result from a complex balance of metabolism, transport, and signaling. Although epigenetic regulation of gene expression during development has been known for decades, the specific mechanisms behind the spatiotemporal dynamics of auxin levels in plants are only just being elucidated. In this review, we gather current knowledge on the epigenetic mechanisms regulating the expression of genes for indole-3-acetic acid (IAA) metabolism and transport in Arabidopsis and discuss future perspectives of this emerging field.
Collapse
Affiliation(s)
- Eduardo Mateo-Bonmatí
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden.
| | - Rubén Casanova-Sáez
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden.
| | - Karin Ljung
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden.
| |
Collapse
|
50
|
Tuteja R, McKeown PC, Ryan P, Morgan CC, Donoghue MTA, Downing T, O'Connell MJ, Spillane C. Paternally Expressed Imprinted Genes under Positive Darwinian Selection in Arabidopsis thaliana. Mol Biol Evol 2019; 36:1239-1253. [PMID: 30913563 PMCID: PMC6526901 DOI: 10.1093/molbev/msz063] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genomic imprinting is an epigenetic phenomenon where autosomal genes display uniparental expression depending on whether they are maternally or paternally inherited. Genomic imprinting can arise from parental conflicts over resource allocation to the offspring, which could drive imprinted loci to evolve by positive selection. We investigate whether positive selection is associated with genomic imprinting in the inbreeding species Arabidopsis thaliana. Our analysis of 140 genes regulated by genomic imprinting in the A. thaliana seed endosperm demonstrates they are evolving more rapidly than expected. To investigate whether positive selection drives this evolutionary acceleration, we identified orthologs of each imprinted gene across 34 plant species and elucidated their evolutionary trajectories. Increased positive selection was sought by comparing its incidence among imprinted genes with nonimprinted controls. Strikingly, we find a statistically significant enrichment of imprinted paternally expressed genes (iPEGs) evolving under positive selection, 50.6% of the total, but no such enrichment for positive selection among imprinted maternally expressed genes (iMEGs). This suggests that maternally- and paternally expressed imprinted genes are subject to different selective pressures. Almost all positively selected amino acids were fixed across 80 sequenced A. thaliana accessions, suggestive of selective sweeps in the A. thaliana lineage. The imprinted genes under positive selection are involved in processes important for seed development including auxin biosynthesis and epigenetic regulation. Our findings support a genomic imprinting model for plants where positive selection can affect paternally expressed genes due to continued conflict with maternal sporophyte tissues, even when parental conflict is reduced in predominantly inbreeding species.
Collapse
Affiliation(s)
- Reetu Tuteja
- Genetics & Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, Ryan Institute, National University of Ireland Galway, Galway, Ireland.,Center for Genomics and Systems Biology, New York University, New York, NY
| | - Peter C McKeown
- Genetics & Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Pat Ryan
- Genetics & Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Claire C Morgan
- School of Biotechnology, Faculty of Biological Sciences, Dublin City University, Dublin, Ireland.,Division of Diabetes, Endocrinology and Metabolism, Imperial College London, London, United Kingdom
| | - Mark T A Donoghue
- Genetics & Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, Ryan Institute, National University of Ireland Galway, Galway, Ireland.,Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tim Downing
- School of Biotechnology, Faculty of Biological Sciences, Dublin City University, Dublin, Ireland
| | - Mary J O'Connell
- Computational and Molecular Evolutionary Biology Research Group, School of Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, United Kingdom.,Computational and Molecular Evolutionary Biology Group, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Charles Spillane
- Genetics & Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, Ryan Institute, National University of Ireland Galway, Galway, Ireland
| |
Collapse
|