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Sajeev N, Koornneef M, Bentsink L. A commitment for life: Decades of unraveling the molecular mechanisms behind seed dormancy and germination. THE PLANT CELL 2024; 36:1358-1376. [PMID: 38215009 PMCID: PMC11062444 DOI: 10.1093/plcell/koad328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/19/2023] [Indexed: 01/14/2024]
Abstract
Seeds are unique time capsules that can switch between 2 complex and highly interlinked stages: seed dormancy and germination. Dormancy contributes to the survival of plants because it allows to delay germination to optimal conditions. The switch between dormancy and germination occurs in response to developmental and environmental cues. In this review we provide a comprehensive overview of studies that have helped to unravel the molecular mechanisms underlying dormancy and germination over the last decades. Genetic and physiological studies provided a strong foundation for this field of research and revealed the critical role of the plant hormones abscisic acid and gibberellins in the regulation of dormancy and germination, and later natural variation studies together with quantitative genetics identified previously unknown genetic components that control these processes. Omics technologies like transcriptome, proteome, and translatomics analysis allowed us to mechanistically dissect these processes and identify new components in the regulation of seed dormancy and germination.
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Affiliation(s)
- Nikita Sajeev
- Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Maarten Koornneef
- Laboratory of Genetics, Wageningen University, 6708PB Wageningen, the Netherlands
- Max Planck Institute for Plant Breeding Research, Former Department of Plant Breeding and Genetics, Koeln 50829, Germany
| | - Leónie Bentsink
- Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, 6708PB Wageningen, the Netherlands
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Gao Y, Qiao L, Mei C, Nong L, Li Q, Zhang X, Li R, Gao W, Chen F, Chang L, Zhang S, Guo H, Cheng T, Wen H, Chang Z, Li X. Mapping of a Major-Effect Quantitative Trait Locus for Seed Dormancy in Wheat. Int J Mol Sci 2024; 25:3681. [PMID: 38612492 PMCID: PMC11011268 DOI: 10.3390/ijms25073681] [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: 02/24/2024] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
The excavation and utilization of dormancy loci in breeding are effective endeavors for enhancing the resistance to pre-harvest sprouting (PHS) of wheat varieties. CH1539 is a wheat breeding line with high-level seed dormancy. To clarify the dormant loci carried by CH1539 and obtain linked molecular markers, in this study, a recombinant inbred line (RIL) population derived from the cross of weak dormant SY95-71 and strong dormant CH1539 was genotyped using the Wheat17K single-nucleotide polymorphism (SNP) array, and a high-density genetic map covering 21 chromosomes and consisting of 2437 SNP markers was constructed. Then, the germination percentage (GP) and germination index (GI) of the seeds from each RIL were estimated. Two QTLs for GP on chromosomes 5A and 6B, and four QTLs for GI on chromosomes 5A, 6B, 6D and 7A were identified. Among them, the QTL on chromosomes 6B controlling both GP and GI, temporarily named QGp/Gi.sxau-6B, is a major QTL for seed dormancy with the maximum phenotypic variance explained of 17.66~34.11%. One PCR-based diagnostic marker Ger6B-3 for QGp/Gi.sxau-6B was developed, and the genetic effect of QGp/Gi.sxau-6B on the RIL population and a set of wheat germplasm comprising 97 accessions was successfully confirmed. QGp/Gi.sxau-6B located in the 28.7~30.9 Mbp physical position is different from all the known dormancy loci on chromosomes 6B, and within the interval, there are 30 high-confidence annotated genes. Our results revealed a novel QTL QGp/Gi.sxau-6B whose CH1539 allele had a strong and broad effect on seed dormancy, which will be useful in further PHS-resistant wheat breeding.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Xin Li
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (Y.G.)
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3
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Smolikova G, Krylova E, Petřík I, Vilis P, Vikhorev A, Strygina K, Strnad M, Frolov A, Khlestkina E, Medvedev S. Involvement of Abscisic Acid in Transition of Pea ( Pisum sativum L.) Seeds from Germination to Post-Germination Stages. PLANTS (BASEL, SWITZERLAND) 2024; 13:206. [PMID: 38256760 PMCID: PMC10819913 DOI: 10.3390/plants13020206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/30/2023] [Accepted: 01/07/2024] [Indexed: 01/24/2024]
Abstract
The transition from seed to seedling represents a critical developmental step in the life cycle of higher plants, dramatically affecting plant ontogenesis and stress tolerance. The release from dormancy to acquiring germination ability is defined by a balance of phytohormones, with the substantial contribution of abscisic acid (ABA), which inhibits germination. We studied the embryonic axis of Pisum sativum L. before and after radicle protrusion. Our previous work compared RNA sequencing-based transcriptomics in the embryonic axis isolated before and after radicle protrusion. The current study aims to analyze ABA-dependent gene regulation during the transition of the embryonic axis from the germination to post-germination stages. First, we determined the levels of abscisates (ABA, phaseic acid, dihydrophaseic acid, and neo-phaseic acid) using ultra-high-performance liquid chromatography-tandem mass spectrometry. Second, we made a detailed annotation of ABA-associated genes using RNA sequencing-based transcriptome profiling. Finally, we analyzed the DNA methylation patterns in the promoters of the PsABI3, PsABI4, and PsABI5 genes. We showed that changes in the abscisate profile are characterized by the accumulation of ABA catabolites, and the ABA-related gene profile is accompanied by the upregulation of genes controlling seedling development and the downregulation of genes controlling water deprivation. The expression of ABI3, ABI4, and ABI5, which encode crucial transcription factors during late maturation, was downregulated by more than 20-fold, and their promoters exhibited high levels of methylation already at the late germination stage. Thus, although ABA remains important, other regulators seems to be involved in the transition from seed to seedling.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.K.); (S.M.)
| | - Ekaterina Krylova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.K.); (S.M.)
- Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190000 St. Petersburg, Russia;
| | - Ivan Petřík
- Laboratory of Growth Regulators, The Czech Academy of Sciences, Institute of Experimental Botany & Palacky University, Faculty of Science, Slechtitelu 27, CZ-78371 Olomouc, Czech Republic; (I.P.); (M.S.)
| | - Polina Vilis
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.K.); (S.M.)
| | - Aleksander Vikhorev
- School of Advanced Engineering Studies, Novosibirsk State University, 630090 Novosibirsk, Russia
| | | | - Miroslav Strnad
- Laboratory of Growth Regulators, The Czech Academy of Sciences, Institute of Experimental Botany & Palacky University, Faculty of Science, Slechtitelu 27, CZ-78371 Olomouc, Czech Republic; (I.P.); (M.S.)
| | - Andrej Frolov
- Laboratory of Analytical Biochemistry and Biotechnology, K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia;
| | - Elena Khlestkina
- Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190000 St. Petersburg, Russia;
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.K.); (S.M.)
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4
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Zhou H, Yuan Z, Han S, He H, Rong J, Guo D, Zhang Y, Zhang D, Liu X, Zhou C. Global Decrease in H3K9 Acetylation in Sorghum Seed Postgermination Stages. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5836-5850. [PMID: 36994885 DOI: 10.1021/acs.jafc.2c08863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Sorghum seed germination is accompanied by increases in nutrient contents and reduced levels of antinutrients and is therefore being applied to food processing. However, the characterization of acetylated histone H3 at lysine residue 9 (H3K9ac) in sorghum postgermination has lagged. In this study, we performed chromatin immunoprecipitation sequencing (ChIP-seq) to identify H3K9ac enrichment and obtained transcriptome in postgermination stages. More than 10,000 hypoacetylated genes gained H3K9ac marks in the postgermination stages. In addition, we observed that the expression of the main histone deacetylase (HDAC) genes was elevated. The application of the HDAC inhibitor trichostatin A (TSA) resulted in seed growth arrest, suggesting that the repression of the H3K9ac modification is critical for postgermination. Additionally, we obtained a comprehensive view of abundant genomic changes in H3K9ac-marked regions and transcription between the mock and TSA treatment groups, which suggested that H3K9ac was required in the late stage of autotrophic seedling establishment. Metabolic profiling, transcriptome analyses, and ChIP-seq revealed that H3K9ac is enriched at genes involved in phenylpropanoid, including lignin and flavonoid, biosynthesis. Our results suggest important roles of H3K9ac in sorghum seed postgermination stages.
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Affiliation(s)
- Hanlin Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002 Yichang, China
| | - Zhu Yuan
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002 Yichang, China
| | - Sifang Han
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002 Yichang, China
| | - Huan He
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002 Yichang, China
| | - Jiajia Rong
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002 Yichang, China
| | - Dandan Guo
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, 430056 Wuhan, China
| | - Yonghong Zhang
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Biomedical Research Institute, School of Basic Medicine, Hubei University of Medicine, 442000 Shiyan, China
| | - Dechun Zhang
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002 Yichang, China
| | - Xiaoyun Liu
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, 430056 Wuhan, China
| | - Chao Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002 Yichang, China
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Li J, Pan W, Liang J, Liu C, Li D, Yang Y, Qu L, Gazzarrini S, Yi M, Wu J. BASIC PENTACYSTEINE2 fine-tunes corm dormancy release in Gladiolus. PLANT PHYSIOLOGY 2023; 191:2489-2505. [PMID: 36659854 PMCID: PMC10069901 DOI: 10.1093/plphys/kiad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Bud dormancy is an important trait in geophytes that largely affects their flowering process and vegetative growth after dormancy release. Compared with seed dormancy, the regulation of bud dormancy is still largely unclear. Abscisic acid (ABA) acts as the predominant hormone that regulates the whole dormancy process. In Gladiolus (Gladiolus hybridus), cold storage promotes corm dormancy release (CDR) by repressing ABA biosynthesis and signaling. However, the mechanisms governing ABA-related processes during CDR via epigenetics are poorly understood. Here, we show that class I BASIC PENTACYSTEINE2, (GhBPC2) directly binds to 9-CIS-EPOXYCAROTENOID DIOXYGENASE (GhNCED) and ABA INSENSITIVE5 (GhABI5) loci and down-regulates their expression to accelerate CDR. During CDR, histone modifications change dramatically at the GhBPC2-binding loci of GhABI5 with an increase in H3K27me3 and a decrease in H3K4me3. GhBPC2 is involved in both H3K27me3 and H3K4me3 and fine-tunes GhABI5 expression by recruiting polycomb repressive complex 2 (PRC2) and the chromatin remodeling factor EARLY BOLTING IN SHORT DAYS (GhEBS). These results show GhBPC2 epigenetically regulates CDR in Gladiolus by mediating GhABI5 expression with PRC2 and GhEBS.
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Affiliation(s)
- Jingru Li
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China
| | - Wenqiang Pan
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China
| | - Jiahui Liang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China
- Institute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Chang Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China
| | - Danqing Li
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Institute of Landscape Architecture, Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yingdong Yang
- Institute of Floriculture, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
| | - Lianwei Qu
- Institute of Floriculture, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
| | - Sonia Gazzarrini
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON Canada
| | - Mingfang Yi
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China
| | - Jian Wu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China
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Singh KBM, Thakur JK. Endosperm ontogeny through the lens of epigenetics. MOLECULAR PLANT 2023; 16:295-297. [PMID: 36258669 DOI: 10.1016/j.molp.2022.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/15/2022] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Kajol B M Singh
- National Institute of Plant Genome Research, New Delhi 110067, India
| | - Jitendra K Thakur
- National Institute of Plant Genome Research, New Delhi 110067, India; International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India.
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Jiang K, Guo H, Zhai J. Interplay of phytohormones and epigenetic regulation: A recipe for plant development and plasticity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:381-398. [PMID: 36223083 DOI: 10.1111/jipb.13384] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Both phytohormone signaling and epigenetic mechanisms have long been known to play crucial roles in plant development and plasticity in response to ambient stimuli. Indeed, diverse signaling pathways mediated by phytohormones and epigenetic processes integrate multiple upstream signals to regulate various plant traits. Emerging evidence indicates that phytohormones and epigenetic processes interact at multiple levels. In this review, we summarize the current knowledge of the interplay between phytohormones and epigenetic processes from the perspective of phytohormone biology. We also review chemical regulators used in epigenetic studies and propose strategies for developing novel regulators using multidisciplinary approaches.
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Affiliation(s)
- Kai Jiang
- Institute of Plant and Food Science, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| | - Hongwei Guo
- Institute of Plant and Food Science, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| | - Jixian Zhai
- Institute of Plant and Food Science, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
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Huang J, Chen Z, Lin J, Guan B, Chen J, Zhang Z, Chen F, Jiang L, Zheng J, Wang T, Chen H, Xie W, Huang S, Wang H, Huang Y, Huang R. gw2.1, a new allele of GW2, improves grain weight and grain yield in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111495. [PMID: 36240912 DOI: 10.1016/j.plantsci.2022.111495] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 10/04/2022] [Accepted: 10/08/2022] [Indexed: 06/16/2023]
Abstract
Grain weight is an important characteristic of grain shape and a key contributing factor to the grain yield in rice. Here, we report that gw2.1, a new allele of the Grain Width and Weight 2 (GW2) gene, regulates grain size and grain weight. A single nucleotide substitution in the coding sequence (CDS) of gw2.1 resulted in the change of glutamate to lysine (E128K) in GW2.1 protein. Complementation tests and GW2 overexpression experiments demonstrated that the missense mutation in gw2.1 was responsible for the phenotype of enlarged grain size in the mutant line jf42. The large grain trait of the near-isogenic line NIL-gw2.1 was found to result from increased cell proliferation during flower development. Meanwhile, NIL-gw2.1 was shown to increase grain yield without compromising the grain quality. The GW2 protein was localized to the cell nucleus and membrane, and interacted with CHB705, a subunit of the chromatin remodeling complex. Finally, the F1 hybrids from crosses of NIL-gw2.1 with 7 cytoplasmic male-sterile lines exhibited large grains and desirable grain appearance. Thus, gw2.1 is a promising allele that could be applied to improve grain yield and grain appearance in rice. AVAILABILITY OF DATA AND MATERIALS: The datasets generated and/or analyzed in the study are available from the corresponding author on reasonable request.
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Affiliation(s)
- Jinpeng Huang
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Zhiming Chen
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jiajia Lin
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Binbin Guan
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jinwen Chen
- Quanzhou Agricultural Science Institute, Quanzhou 362212, China
| | - Zesen Zhang
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Fangyu Chen
- Key Laboratory of Ministry of Education for Genetic Improvement and Comprehensive Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liangrong Jiang
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jingsheng Zheng
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Tiansheng Wang
- Quanzhou Agricultural Science Institute, Quanzhou 362212, China
| | - Huiqing Chen
- Quanzhou Agricultural Science Institute, Quanzhou 362212, China
| | - Wangyou Xie
- Quanzhou Agricultural Science Institute, Quanzhou 362212, China
| | - Senhao Huang
- Key Laboratory of Ministry of Education for Genetic Improvement and Comprehensive Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Houcong Wang
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yumin Huang
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Rongyu Huang
- School of Life Sciences, Xiamen University, Xiamen 361102, China.
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Sano N, Malabarba J, Chen Z, Gaillard S, Windels D, Verdier J. Chromatin dynamics associated with seed desiccation tolerance/sensitivity at early germination in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2022; 13:1059493. [PMID: 36507374 PMCID: PMC9729785 DOI: 10.3389/fpls.2022.1059493] [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: 10/01/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
Desiccation tolerance (DT) has contributed greatly to the adaptation of land plants to severe water-deficient conditions. DT is mostly observed in reproductive parts in flowering plants such as seeds. The seed DT is lost at early post germination stage but is temporally re-inducible in 1 mm radicles during the so-called DT window following a PEG treatment before being permanently silenced in 5 mm radicles of germinating seeds. The molecular mechanisms that activate/reactivate/silence DT in developing and germinating seeds have not yet been elucidated. Here, we analyzed chromatin dynamics related to re-inducibility of DT before and after the DT window at early germination in Medicago truncatula radicles to determine if DT-associated genes were transcriptionally regulated at the chromatin levels. Comparative transcriptome analysis of these radicles identified 948 genes as DT re-induction-related genes, positively correlated with DT re-induction. ATAC-Seq analyses revealed that the chromatin state of genomic regions containing these genes was clearly modulated by PEG treatment and affected by growth stages with opened chromatin in 1 mm radicles with PEG (R1P); intermediate openness in 1 mm radicles without PEG (R1); and condensed chromatin in 5 mm radicles without PEG (R5). In contrast, we also showed that the 103 genes negatively correlated with the re-induction of DT did not show any transcriptional regulation at the chromatin level. Additionally, ChIP-Seq analyses for repressive marks H2AK119ub and H3K27me3 detected a prominent signal of H3K27me3 on the DT re-induction-related gene sequences at R5 but not in R1 and R1P. Moreover, no clear H2AK119ub marks was observed on the DT re-induction-related gene sequences at both developmental radicle stages, suggesting that silencing of DT process after germination will be mainly due to H3K27me3 marks by the action of the PRC2 complex, without involvement of PRC1 complex. The dynamic of chromatin changes associated with H3K27me3 were also confirmed on seed-specific genes encoding potential DT-related proteins such as LEAs, oleosins and transcriptional factors. However, several transcriptional factors did not show a clear link between their decrease of chromatin openness and H3K27me3 levels, suggesting that their accessibility may also be regulated by additional factors, such as other histone modifications. Finally, in order to make these comprehensive genome-wide analyses of transcript and chromatin dynamics useful to the scientific community working on early germination and DT, we generated a dedicated genome browser containing all these data and publicly available at https://iris.angers.inrae.fr/mtseedepiatlas/jbrowse/?data=Mtruncatula.
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