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Zhao Y, Lu J, Hu B, Jiao P, Gao B, Jiang Z, Liu S, Guan S, Ma Y. Cloning and functional analysis of ZmMADS42 gene in maize. GM CROPS & FOOD 2024; 15:105-117. [PMID: 38466176 PMCID: PMC10936638 DOI: 10.1080/21645698.2024.2328384] [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: 01/14/2024] [Accepted: 03/05/2024] [Indexed: 03/12/2024]
Abstract
Maize (Zea mays L.) is the most important cereal crop in the world. Flowering period and photoperiod play important roles in the reproductive development of maize. This study, investigated ZmMADS42, a gene that is highly expressed in the shoot apical meristem. Agrobacterium infection was used to successfully obtain overexpressed ZmMADS42 plants. Fluorescence quantitative PCR revealed that the expression of the ZmMADS42 gene in the shoot apical meristem of transgenic plants was 2.8 times higher than that of the wild-type(WT). In addition, the expression of the ZmMADS42 gene in the endosperm was 2.4 times higher than that in the wild-type. The seed width of the T2 generation increased by 5.35%, whereas the seed length decreased by 7.78% compared with that of the wild-type. Dissection of the shoot tips of transgenic and wild-type plants from the 7-leaf stage to the 9-leaf stage revealed that the transgenic plants entered the differentiation stage earlier and exhibited more tassel meristems during their vegetative growth period. The mature transgenic plants were approximately 20 cm shorter in height and had a lower panicle position than the wild-type plants. Comparing the flowering period, the tasseling, powdering, and silking stages of the transgenic plants occurred 10 days earlier than those of the wild-type plants. The results showed that the ZmMADS42 gene played a significant role in regulating the flowering period and plant height of maize.
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Affiliation(s)
- Yang Zhao
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Jianyu Lu
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Bo Hu
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Peng Jiao
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Bai Gao
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Zhenzhong Jiang
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Siyan Liu
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Shuyan Guan
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Yiyong Ma
- College of Agronomy, Jilin Agricultural University, Changchun, China
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2
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Adhikari PB, Kasahara RD. An Overview on MADS Box Members in Plants: A Meta-Review. Int J Mol Sci 2024; 25:8233. [PMID: 39125803 PMCID: PMC11311456 DOI: 10.3390/ijms25158233] [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: 05/25/2024] [Revised: 07/21/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
Most of the studied MADS box members are linked to flowering and fruit traits. However, higher volumes of studies on type II of the two types so far suggest that the florigenic effect of the gene members could just be the tip of the iceberg. In the current study, we used a systematic approach to obtain a general overview of the MADS box members' cross-trait and multifactor associations, and their pleiotropic potentials, based on a manually curated local reference database. While doing so, we screened for the co-occurrence of terms of interest within the title or abstract of each reference, with a threshold of three hits. The analysis results showed that our approach can retrieve multi-faceted information on the subject of study (MADS box gene members in the current case), which could otherwise have been skewed depending on the authors' expertise and/or volume of the literature reference base. Overall, our study discusses the roles of MADS box members in association with plant organs and trait-linked factors among plant species. Our assessment showed that plants with most of the MADS box member studies included tomato, apple, and rice after Arabidopsis. Furthermore, based on the degree of their multi-trait associations, FLC, SVP, and SOC1 are suggested to have relatively higher pleiotropic potential among others in plant growth, development, and flowering processes. The approach devised in this study is expected to be applicable for a basic understanding of any study subject of interest, regardless of the depth of prior knowledge.
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Affiliation(s)
- Prakash Babu Adhikari
- Biotechnology and Bioscience Research Center, Nagoya University, Nagoya 464-8601, Japan
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3
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Bazakos C, Michailidis M, Tourvas N, Alexiou KG, Mellidou I, Polychroniadou C, Boutsika A, Xanthopoulou A, Moysiadis T, Skodra C, Kollaros MG, Glavakis E, Stournaras V, Karagiannis E, Aravanopoulos F, Molassiotis A, Tanou G, Ganopoulos I. Genetic mosaic of the Mediterranean fig: comprehensive genomic insights from a gene bank collection. PHYSIOLOGIA PLANTARUM 2024; 176:e14482. [PMID: 39149812 DOI: 10.1111/ppl.14482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/10/2024] [Indexed: 08/17/2024]
Abstract
High-depth whole-genome resequencing of 53 diverse fig tree genotypes yielded a rich dataset of genetic variants. We successfully identified 5,501,460 single-nucleotide polymorphisms (SNPs) and 1,228,537 insertions and deletions (InDels), providing a high-density and excellent-quality genetic map of the fig tree. We also performed a detailed population structure analysis, dividing the 53 genotypes into three geographical groups and assessing their genetic diversity and divergence. Analysis of structural variants (SVs) and copy number variations (CNVs) revealed their potential functional impact, particularly in plant-pathogen interaction and secondary metabolism. Metabolomic fingerprinting of fig genotypes uncovered extensive variation in primary metabolites and polyphenolic compounds, highlighting the influence of genotype on fruit quality traits such as nutritional content and bioactive compound composition. The genome-wide association study (GWAS) identified critical SNPs associated with fruit quality and morphological features. The discovery of significant candidate genes, such as AGL62, GDSL, and COBRA-like protein 4 genes, offers promising targets for marker-assisted selection and genome editing approaches to improve fig fruit morphological and quality traits. This extensive genomic analysis of fig trees enhances our understanding of the genetic basis of important agronomic traits and provides a rich resource for future research in this economically and nutritionally significant fruit.
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Affiliation(s)
- Christos Bazakos
- Institute of Plant Breeding and Genetic Resources, ELGO DIMITRA, Thermi, Greece
- Joint Laboratory of Horticulture, ELGO DIMITRA, Thermi, Greece
- Max Planck Institute for Plant Breeding Research, Department of Comparative Development and Genetics, Cologne, Germany
| | - Michail Michailidis
- Joint Laboratory of Horticulture, ELGO DIMITRA, Thermi, Greece
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thermi, Greece
| | - Nikolaos Tourvas
- Laboratory of Forest Genetics, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Konstantinos G Alexiou
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries, Barcelona, Spain
| | - Ifigeneia Mellidou
- Institute of Plant Breeding and Genetic Resources, ELGO DIMITRA, Thermi, Greece
- Joint Laboratory of Horticulture, ELGO DIMITRA, Thermi, Greece
| | - Chrysanthi Polychroniadou
- Joint Laboratory of Horticulture, ELGO DIMITRA, Thermi, Greece
- Institute of Soil and Water Resources, ELGO-DIMITRA, Thermi, Greece
| | - Anastasia Boutsika
- Institute of Plant Breeding and Genetic Resources, ELGO DIMITRA, Thermi, Greece
| | - Aliki Xanthopoulou
- Institute of Plant Breeding and Genetic Resources, ELGO DIMITRA, Thermi, Greece
- Joint Laboratory of Horticulture, ELGO DIMITRA, Thermi, Greece
| | - Theodoros Moysiadis
- Institute of Plant Breeding and Genetic Resources, ELGO DIMITRA, Thermi, Greece
- Institute of Soil and Water Resources, ELGO-DIMITRA, Thermi, Greece
- Department of Computer Science, School of Sciences and Engineering, University of Nicosia, Nicosia, Cyprus
| | - Christina Skodra
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thermi, Greece
| | - Marios-Georgios Kollaros
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thermi, Greece
| | | | - Vasileios Stournaras
- Institute of Olive Tree, Subtropical Crops and Viticulture, ELGO-DIMITRA, Department of Olive and Horticultural Crops, Kalamata, Greece
- Department of Agriculture, University of Ioannina, Arta, Greece
| | | | - Filippos Aravanopoulos
- Laboratory of Forest Genetics, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Athanassios Molassiotis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thermi, Greece
| | - Georgia Tanou
- Joint Laboratory of Horticulture, ELGO DIMITRA, Thermi, Greece
- Institute of Soil and Water Resources, ELGO-DIMITRA, Thermi, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, ELGO DIMITRA, Thermi, Greece
- Joint Laboratory of Horticulture, ELGO DIMITRA, Thermi, Greece
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4
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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.
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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.
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5
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Sharma I, Malathi P, Srinivasan R, Bhat SR, Sreenivasulu Y. Embryo sac cellularization defects lead to supernumerary egg cells and twin embryos in Arabidopsis thaliana. iScience 2024; 27:109890. [PMID: 38827396 PMCID: PMC11141147 DOI: 10.1016/j.isci.2024.109890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/26/2024] [Accepted: 04/30/2024] [Indexed: 06/04/2024] Open
Abstract
Arabidopsis lines with loss-of-function mutation in Embryo sac-specific Pectin MethylEsterase Inhibitor (Atepmei) gene showed seed sterility with embryo sac cellularization defects. Examination of tissue-cleared mature ovules revealed irregularly positioned nuclei/embryos within the embryo sacs. Egg cell-specific marker (DD45) expression analysis confirmed the presence of multiple egg cells in the mutant embryo sacs. These supernumerary egg cells were functional as evident from the production of twin embryos when supernumerary sperm cells were provided. The results of ruthenium red and tannic acid-ferric chloride staining of developing Atepmei mutant ovules showed that cell wall formation and maintenance were altered around embryo sac nuclei, which also coincided with change in the gamete specification. This report implicates the role of cell walls in gamete cell fate determination by altering cell-cell communication. Our analysis of the twin-embryo phenotype of epmei mutants also sheds light on the boundary conditions for double fertilization in plant reproduction.
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Affiliation(s)
- Isha Sharma
- CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Pinninti Malathi
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | | | | | - Yelam Sreenivasulu
- CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
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6
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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.
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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
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7
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He J, Wang J, Zhang Z. Toward unveiling transcriptome dynamics and regulatory modules at the maternal/filial interface of developing maize kernel. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2124-2140. [PMID: 38551088 DOI: 10.1111/tpj.16733] [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: 11/07/2023] [Revised: 02/21/2024] [Accepted: 03/12/2024] [Indexed: 06/14/2024]
Abstract
The basal region of maize (Zea mays) kernels, which includes the pedicel, placenta-chalazal, and basal endosperm transfer layers, serves as the maternal/filial interface for nutrient transfer from the mother plant to the developing seed. However, transcriptome dynamics of this maternal/filial interface remain largely unexplored. To address this gap, we conducted high-temporal-resolution RNA sequencing of the basal and upper kernel regions between 4 and 32 days after pollination and deeply analyzed transcriptome dynamics of the maternal/filial interface. Utilizing 790 specifically and highly expressed genes in the basal region, we performed the gene ontology (GO) term and weighted gene co-expression network analyses. In the early-stage basal region, we identified five MADS-box transcription factors (TFs) as hubs. Their homologs have been demonstrated as pivotal regulators at the maternal/filial interface of rice or Arabidopsis, suggesting their potential roles in maize kernel development. In the filling-stage basal region, numerous GO terms associated with transcriptional regulation and transporters are significantly enriched. Furthermore, we investigated the molecular function of three hub TFs. Through genome-wide DNA affinity purification sequencing combined with promoter transactivation assays, we suggested that these three TFs act as regulators of 10 basal-specific transporter genes involved in the transfer of sugars, amino acids, and ions. This study provides insights into transcriptomic dynamic and regulatory modules of the maternal/filial interface. In the future, genetic investigation of these hub regulators must advance our understanding of maternal/filial interface development and function.
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Affiliation(s)
- Juan He
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Jincang Wang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Zhiyong Zhang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
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8
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Zhong S, Zhao P, Peng X, Li HJ, Duan Q, Cheung AY. From gametes to zygote: Mechanistic advances and emerging possibilities in plant reproduction. PLANT PHYSIOLOGY 2024; 195:4-35. [PMID: 38431529 PMCID: PMC11060694 DOI: 10.1093/plphys/kiae125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/13/2024] [Accepted: 02/13/2024] [Indexed: 03/05/2024]
Affiliation(s)
- Sheng Zhong
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, New Cornerstone Science Laboratory, College of Life Sciences, Peking University, Beijing 100871, China
| | - Peng Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiongbo Peng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Hong-Ju Li
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Center for Molecular Agrobiology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiaohong Duan
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Alice Y Cheung
- Department of Biochemistry and Molecular Biology, Molecular and Cellular Biology Program, Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
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Bennici S, Poles L, Di Guardo M, Percival-Alwyn L, Caccamo M, Licciardello C, Gentile A, Distefano G, La Malfa S. The origin and the genetic regulation of the self-compatibility mechanism in clementine ( Citrus clementina Hort. ex Tan.). FRONTIERS IN PLANT SCIENCE 2024; 15:1360087. [PMID: 38501136 PMCID: PMC10944956 DOI: 10.3389/fpls.2024.1360087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/19/2024] [Indexed: 03/20/2024]
Abstract
Self-incompatibility (SI) is a genetic mechanism common in flowering plants to prevent self-fertilization. Among citrus species, several pummelo, mandarin, and mandarin-like accessions show SI behavior. In these species, SI is coupled with a variable degree of parthenocarpy ensuring the production of seedless fruits, a trait that is highly appreciated by consumers. In Citrus, recent evidences have shown the presence of a gametophytic SI system based on S-ribonucleases (S-RNases) ability to impair self-pollen tube growth in the upper/middle part of the style. In the present study, we combined PCR analysis and next-generation sequencing technologies, to define the presence of S7- and S11-Rnases in the S-genotype of the Citrus clementina (Hort. ex Tan.), the self-incompatible 'Comune' clementine and its self-compatible natural mutant 'Monreal'. The reference genome of 'Monreal' clementine is presented for the first time, providing more robust results on the genetic sequence of the newly discovered S7-RNase. SNP discovery analysis coupled with the annotation of the variants detected enabled the identification of 7,781 SNPs effecting 5,661 genes in 'Monreal' compared to the reference genome of C. clementina. Transcriptome analysis of unpollinated pistils at the mature stage from both clementine genotypes revealed the lack of expression of S7-RNase in 'Monreal' suggesting its involvement in the loss of the SI response. RNA-seq analysis followed by gene ontology studies enabled the identification of 2,680 differentially expressed genes (DEGs), a significant number of those is involved in oxidoreductase and transmembrane transport activity. Merging of DNA sequencing and RNA data led to the identification of 164 DEGs characterized by the presence of at least one SNP predicted to induce mutations with a high effect on their amino acid sequence. Among them, four candidate genes referring to two Agamous-like MADS-box proteins, to MYB111 and to MLO-like protein 12 were validated. Moreover, the transcription factor MYB111 appeared to contain a binding site for the 2.0-kb upstream sequences of the S7- and S11-RNase genes. These results provide useful information about the genetic bases of SI indicating that SNPs present in their sequence could be responsible for the differential expression and the regulation of S7-RNase and consequently of the SI mechanism.
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Affiliation(s)
- Stefania Bennici
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Lara Poles
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Mario Di Guardo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | | | - Mario Caccamo
- National Institute of Agricultural Botany (NIAB), Cambridge, United Kingdom
| | - Concetta Licciardello
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
| | - Alessandra Gentile
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Gaetano Distefano
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Stefano La Malfa
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
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Qiao Z, Deng F, Zeng H, Li X, Lu L, Lei Y, Li L, Chen Y, Chen J. MADS-Box Family Genes in Lagerstroemia indica and Their Involvement in Flower Development. PLANTS (BASEL, SWITZERLAND) 2024; 13:709. [PMID: 38475555 DOI: 10.3390/plants13050709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/25/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
MADS-box is a key transcription factor regulating the transition to flowering and flower development. Lagerstroemia indica 'Xiang Yun' is a new cultivar of crape myrtle characterized by its non-fruiting nature. To study the molecular mechanism underlying the non-fruiting characteristics of 'Xiang Yun', 82 MADS-box genes were identified from the genome of L. indica. The physicochemical properties of these genes were examined using bioinformatics methods, and their expression as well as endogenous hormone levels at various stages of flower development were analyzed. The results showed that LiMADS genes were primarily classified into two types: type I and type II, with the majority being type II that contained an abundance of cis-acting elements in their promoters. By screening nine core proteins by predicted protein interactions and performing qRT-PCR analysis as well as in combination with transcriptome data, we found that the expression levels of most MADS genes involved in flower development were significantly lower in 'Xiang Yun' than in the wild type 'Hong Ye'. Hormonal analysis indicated that 'Xiang Yun' had higher levels of iP, IPR, TZR, and zeatin during its early stages of flower development than 'Hong Ye', whereas the MeJA content was substantially lower at the late stage of flower development of 'Hong Ye'. Finally, correlation analysis showed that JA, IAA, SA, and TZR were positively correlated with the expression levels of most type II genes. Based on these analyses, a working model for the non-fruiting 'Xiang Yun' was proposed. During the course of flower development, plant hormone response pathways may affect the expression of MADS genes, resulting in their low expression in flower development, which led to the abnormal development of the stamen and embryo sac and ultimately affected the fruiting process of 'Xiang Yun'.
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Affiliation(s)
- Zhongquan Qiao
- Hunan Provincial Key Laboratory of Forest Clonal Breeding, Hunan Academy of Forestry, Changsha 410004, China
| | - Fuyuan Deng
- Hunan Provincial Key Laboratory of Forest Clonal Breeding, Hunan Academy of Forestry, Changsha 410004, China
| | - Huijie Zeng
- Hunan Provincial Key Laboratory of Forest Clonal Breeding, Hunan Academy of Forestry, Changsha 410004, China
| | - Xuelu Li
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Liushu Lu
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Yuxing Lei
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Lu Li
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Yi Chen
- Hunan Provincial Key Laboratory of Forest Clonal Breeding, Hunan Academy of Forestry, Changsha 410004, China
| | - Jianjun Chen
- Mid-Florida Research and Education Center, Environmental Horticulture Department, University of Florida, 2725 S. Binion Road, Apopka, FL 32703, USA
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11
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Liang M, Du Z, Yang Z, Luo T, Ji C, Cui H, Li R. Genome-wide characterization and expression analysis of MADS-box transcription factor gene family in Perilla frutescens. FRONTIERS IN PLANT SCIENCE 2024; 14:1299902. [PMID: 38259943 PMCID: PMC10801092 DOI: 10.3389/fpls.2023.1299902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024]
Abstract
MADS-box transcription factors are widely involved in the regulation of plant growth, developmental processes, and response to abiotic stresses. Perilla frutescens, a versatile plant, is not only used for food and medicine but also serves as an economical oil crop. However, the MADS-box transcription factor family in P. frutescens is still largely unexplored. In this study, a total of 93 PfMADS genes were identified in P. frutescens genome. These genes, including 37 Type I and 56 Type II members, were randomly distributed across 20 chromosomes and 2 scaffold regions. Type II PfMADS proteins were found to contain a greater number of motifs, indicating more complex structures and diverse functions. Expression analysis revealed that most PfMADS genes (more than 76 members) exhibited widely expression model in almost all tissues. The further analysis indicated that there was strong correlation between some MIKCC-type PfMADS genes and key genes involved in lipid synthesis and flavonoid metabolism, which implied that these PfMADS genes might play important regulatory role in the above two pathways. It was further verified that PfMADS47 can effectively mediate the regulation of lipid synthesis in Chlamydomonas reinhardtii transformants. Using cis-acting element analysis and qRT-PCR technology, the potential functions of six MIKCC-type PfMADS genes in response to abiotic stresses, especially cold and drought, were studied. Altogether, this study is the first genome-wide analysis of PfMADS. This result further supports functional and evolutionary studies of PfMADS gene family and serves as a benchmark for related P. frutescens breeding studies.
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Affiliation(s)
- Mengjing Liang
- Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Zhongyang Du
- Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Ze Yang
- Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Tao Luo
- Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Chunli Ji
- Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Hongli Cui
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, China
| | - Runzhi Li
- Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Jinzhong, Shanxi, China
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12
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Zhang J, Zhang Z, Zhang R, Yang C, Zhang X, Chang S, Chen Q, Rossi V, Zhao L, Xiao J, Xin M, Du J, Guo W, Hu Z, Liu J, Peng H, Ni Z, Sun Q, Yao Y. Type I MADS-box transcription factor TaMADS-GS regulates grain size by stabilizing cytokinin signalling during endosperm cellularization in wheat. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:200-215. [PMID: 37752705 PMCID: PMC10754016 DOI: 10.1111/pbi.14180] [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: 05/03/2023] [Revised: 09/01/2023] [Accepted: 09/09/2023] [Indexed: 09/28/2023]
Abstract
Grain size is one of the important traits in wheat breeding programs aimed at improving yield, and cytokinins, mainly involved in cell division, have a positive impact on grain size. Here, we identified a novel wheat gene TaMADS-GS encoding type I MADS-box transcription factor, which regulates the cytokinins signalling pathway during early stages of grain development to modulate grain size and weight in wheat. TaMADS-GS is exclusively expressed in grains at early stage of seed development and its knockout leads to delayed endosperm cellularization, smaller grain size and lower grain weight. TaMADS-GS protein interacts with the Polycomb Repressive Complex 2 (PRC2) and leads to repression of genes encoding cytokinin oxidase/dehydrogenases (CKXs) stimulating cytokinins inactivation by mediating accumulation of the histone H3 trimethylation at lysine 27 (H3K27me3). Through the screening of a large wheat germplasm collection, an elite allele of the TaMADS-GS exhibits higher ability to repress expression of genes inactivating cytokinins and a positive correlation with grain size and weight, thus representing a novel marker for breeding programs in wheat. Overall, these findings support the relevance of TaMADS-GS as a key regulator of wheat grain size and weight.
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Affiliation(s)
- Jianing Zhang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Zhaoheng Zhang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Ruijie Zhang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Changfeng Yang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Xiaobang Zhang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Siyuan Chang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Qian Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Vincenzo Rossi
- Council for Agricultural Research and EconomicsResearch Centre for Cereal and Industrial CropsBergamoItaly
| | - Long Zhao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Jinkun Du
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Jie Liu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
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13
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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.
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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
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14
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Bramsiepe J, Krabberød AK, Bjerkan KN, Alling RM, Johannessen IM, Hornslien KS, Miller JR, Brysting AK, Grini PE. Structural evidence for MADS-box type I family expansion seen in new assemblies of Arabidopsis arenosa and A. lyrata. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:942-961. [PMID: 37517071 DOI: 10.1111/tpj.16401] [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: 01/22/2023] [Revised: 05/24/2023] [Accepted: 07/13/2023] [Indexed: 08/01/2023]
Abstract
Arabidopsis thaliana diverged from A. arenosa and A. lyrata at least 6 million years ago. The three species differ by genome-wide polymorphisms and morphological traits. The species are to a high degree reproductively isolated, but hybridization barriers are incomplete. A special type of hybridization barrier is based on the triploid endosperm of the seed, where embryo lethality is caused by endosperm failure to support the developing embryo. The MADS-box type I family of transcription factors is specifically expressed in the endosperm and has been proposed to play a role in endosperm-based hybridization barriers. The gene family is well known for its high evolutionary duplication rate, as well as being regulated by genomic imprinting. Here we address MADS-box type I gene family evolution and the role of type I genes in the context of hybridization. Using two de-novo assembled and annotated chromosome-level genomes of A. arenosa and A. lyrata ssp. petraea we analyzed the MADS-box type I gene family in Arabidopsis to predict orthologs, copy number, and structural genomic variation related to the type I loci. Our findings were compared to gene expression profiles sampled before and after the transition to endosperm cellularization in order to investigate the involvement of MADS-box type I loci in endosperm-based hybridization barriers. We observed substantial differences in type-I expression in the endosperm of A. arenosa and A. lyrata ssp. petraea, suggesting a genetic cause for the endosperm-based hybridization barrier between A. arenosa and A. lyrata ssp. petraea.
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Affiliation(s)
- Jonathan Bramsiepe
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
- CEES, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Anders K Krabberød
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Katrine N Bjerkan
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
- CEES, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Renate M Alling
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
- CEES, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Ida M Johannessen
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Karina S Hornslien
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Jason R Miller
- College of STEM, Shepherd University, Shepherdstown, West Virginia, 25443-5000, USA
| | - Anne K Brysting
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
- CEES, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Paul E Grini
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
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15
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Liu L, Trendel J, Jiang G, Liu Y, Bruckmann A, Küster B, Sprunck S, Dresselhaus T, Bleckmann A. RBPome identification in egg-cell like callus of Arabidopsis. Biol Chem 2023; 404:1137-1149. [PMID: 37768858 DOI: 10.1515/hsz-2023-0195] [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: 04/29/2023] [Accepted: 09/11/2023] [Indexed: 09/30/2023]
Abstract
RNA binding proteins (RBPs) have multiple and essential roles in transcriptional and posttranscriptional regulation of gene expression in all living organisms. Their biochemical identification in the proteome of a given cell or tissue requires significant protein amounts, which limits studies in rare and highly specialized cells. As a consequence, we know almost nothing about the role(s) of RBPs in reproductive processes such as egg cell development, fertilization and early embryogenesis in flowering plants. To systematically identify the RBPome of egg cells in the model plant Arabidopsis, we performed RNA interactome capture (RIC) experiments using the egg cell-like RKD2-callus and were able to identify 728 proteins associated with poly(A+)-RNA. Transcripts for 97 % of identified proteins could be verified in the egg cell transcriptome. 46 % of identified proteins can be associated with the RNA life cycle. Proteins involved in mRNA binding, RNA processing and metabolism are highly enriched. Compared with the few available RBPome datasets of vegetative plant tissues, we identified 475 egg cell-enriched RBPs, which will now serve as a resource to study RBP function(s) during egg cell development, fertilization and early embryogenesis. First candidates were already identified showing an egg cell-specific expression pattern in ovules.
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Affiliation(s)
- Liping Liu
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Jakob Trendel
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), D-85354 Freising, Germany
| | - Guojing Jiang
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Yanhui Liu
- College of Life Science, Longyan University, Longyan 364012, China
| | - Astrid Bruckmann
- Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
| | - Bernhard Küster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), D-85354 Freising, Germany
| | - Stefanie Sprunck
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Andrea Bleckmann
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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16
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Chettoor AM, Yang B, Evans MMS. Control of cellularization, nuclear localization, and antipodal cell cluster development in maize embryo sacs. Genetics 2023; 225:iyad101. [PMID: 37232380 DOI: 10.1093/genetics/iyad101] [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: 03/30/2023] [Revised: 03/30/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023] Open
Abstract
The maize female gametophyte contains four cell types: two synergids, an egg cell, a central cell, and a variable number of antipodal cells. In maize, these cells are produced after three rounds of free-nuclear divisions followed by cellularization, differentiation, and proliferation of the antipodal cells. Cellularization of the eight-nucleate syncytium produces seven cells with two polar nuclei in the central cell. Nuclear localization is tightly controlled in the embryo sac. This leads to precise allocation of the nuclei into the cells upon cellularization. Nuclear positioning within the syncytium is highly correlated with their identity after cellularization. Two mutants are described with extra polar nuclei, abnormal antipodal cell morphology, and reduced antipodal cell number, as well as frequent loss of antipodal cell marker expression. Mutations in one of these genes, indeterminate gametophyte2 encoding a MICROTUBULE ASSOCIATED PROTEIN65-3 homolog, shows a requirement for MAP65-3 in cellularization of the syncytial embryo sac as well as for normal seed development. The timing of the effects of ig2 suggests that the identity of the nuclei in the syncytial female gametophyte can be changed very late before cellularization.
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Affiliation(s)
- Antony M Chettoor
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Bing Yang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Matthew M S Evans
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
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17
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Zhou P, Wang Z, Li Y, Zhou Q. Identification and Expression of the MADS-box Gene Family in Different Versions of the Ginkgo biloba Genome. PLANTS (BASEL, SWITZERLAND) 2023; 12:3334. [PMID: 37765498 PMCID: PMC10535167 DOI: 10.3390/plants12183334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023]
Abstract
MADS-box transcription factors play important roles in many organisms. These transcription factors are involved in processes such as the formation of the flower organ structure and the seed development of plants. Ginkgo biloba has two genome versions (version 2019 and version 2021), and there is no analysis or comparison of the MADS-box gene family in these two genomes. In this study, 26 and 20 MADS-box genes were identified from the two genomes of Ginkgo, of which 12 pairs of genes reached more than 80% similarity. According to our phylogenetic analysis results, we divided these genes into type I (Mα and Mγ subfamilies) and type II (MIKC and Mδ subfamilies) members. We found that both sets of genomes lacked the Mβ gene, while the MIKC gene was the most numerous. Further analysis of the gene structure showed that the MIKC genes in the two genomes had extralong introns (≥20 kb); these introns had different splicing patterns, and their expression might be more abundant. The gene expression analysis proved that GbMADS genes were expressed to varying degrees in eight Ginkgo biological tissues. Type II GbMADS genes not only were found to be related to female flower bud differentiation and development but also are important in seed development. Therefore, MADS-box genes may play important roles in the development of Ginkgo reproductive organs, which may suggest a genetic role in sexual differentiation. This study further contributes to the research on MADS-box genes and provides new insights into sex determination in Ginkgo.
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Affiliation(s)
- Pengyan Zhou
- Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (P.Z.); (Y.L.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China;
| | - Zesen Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China;
| | - Yingang Li
- Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (P.Z.); (Y.L.)
| | - Qi Zhou
- Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (P.Z.); (Y.L.)
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18
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Ma L, Liu KW, Li Z, Hsiao YY, Qi Y, Fu T, Tang GD, Zhang D, Sun WH, Liu DK, Li Y, Chen GZ, Liu XD, Liao XY, Jiang YT, Yu X, Hao Y, Huang J, Zhao XW, Ke S, Chen YY, Wu WL, Hsu JL, Lin YF, Huang MD, Li CY, Huang L, Wang ZW, Zhao X, Zhong WY, Peng DH, Ahmad S, Lan S, Zhang JS, Tsai WC, Van de Peer Y, Liu ZJ. Diploid and tetraploid genomes of Acorus and the evolution of monocots. Nat Commun 2023; 14:3661. [PMID: 37339946 DOI: 10.1038/s41467-023-38829-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/17/2023] [Indexed: 06/22/2023] Open
Abstract
Monocots are a major taxon within flowering plants, have unique morphological traits, and show an extraordinary diversity in lifestyle. To improve our understanding of monocot origin and evolution, we generate chromosome-level reference genomes of the diploid Acorus gramineus and the tetraploid Ac. calamus, the only two accepted species from the family Acoraceae, which form a sister lineage to all other monocots. Comparing the genomes of Ac. gramineus and Ac. calamus, we suggest that Ac. gramineus is not a potential diploid progenitor of Ac. calamus, and Ac. calamus is an allotetraploid with two subgenomes A, and B, presenting asymmetric evolution and B subgenome dominance. Both the diploid genome of Ac. gramineus and the subgenomes A and B of Ac. calamus show clear evidence of whole-genome duplication (WGD), but Acoraceae does not seem to share an older WGD that is shared by most other monocots. We reconstruct an ancestral monocot karyotype and gene toolkit, and discuss scenarios that explain the complex history of the Acorus genome. Our analyses show that the ancestors of monocots exhibit mosaic genomic features, likely important for that appeared in early monocot evolution, providing fundamental insights into the origin, evolution, and diversification of monocots.
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Affiliation(s)
- Liang Ma
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ke-Wei Liu
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan City, 701, Taiwan
| | - Yiying Qi
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Tao Fu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Guang-Da Tang
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, China
| | - Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei-Hong Sun
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Gui-Zhen Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xue-Die Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xing-Yu Liao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yu-Ting Jiang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xia Yu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yang Hao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jie Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xue-Wei Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shijie Ke
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - You-Yi Chen
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Wan-Lin Wu
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Jui-Ling Hsu
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Yu-Fu Lin
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Ming-Der Huang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan
| | - Chia-Ying Li
- Department of Applied Chemistry, National Pingtung University, Pingtung City, Pingtung County, 900003, Taiwan
| | - Laiqiang Huang
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | | | | | | | - Dong-Hui Peng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Sagheer Ahmad
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Ji-Sen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China.
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China.
| | - Wen-Chieh Tsai
- Orchid Research and Development Center, National Cheng Kung University, Tainan City, 701, Taiwan.
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium.
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
- College of Horticulture, Nanjing Agricultural University, Academy for Advanced Interdisciplinary Studies, Nanjing, 210095, China.
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.
- Institute of Vegetable and Flowers, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005, China.
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19
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Li W, Wang D, Hong X, Shi J, Hong J, Su S, Loaiciga CR, Li J, Liang W, Shi J, Zhang D. Identification and validation of new MADS-box homologous genes in 3010 rice pan-genome. PLANT CELL REPORTS 2023; 42:975-988. [PMID: 37016094 DOI: 10.1007/s00299-023-03006-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/17/2023] [Indexed: 05/12/2023]
Abstract
KEY MESSAGE Identification and validation of ten new MADS-box homologous genes in 3010 rice pan-genome for rice breeding. The functional genome is significant for rice breeding. MADS-box genes encode transcription factors that are indispensable for rice growth and development. The reported 15,362 novel genes in the rice pan-genome (RPAN) of Asian cultivated rice accessions provided a useful gene reservoir for the identification of more MADS-box candidates to overcome the limitation for the usage of only 75 MADS-box genes identified in Nipponbare for rice breeding. Here, we report the identification and validation of ten MADS-box homologous genes in RPAN. Origin and identity analysis indicated that they are originated from different wild rice accessions and structure of motif analysis revealed high variations in their amino acid sequences. Phylogenetic results with 277 MADS-box genes in 41 species showed that all these ten MADS-box homologous genes belong to type I (SRF-like, M-type). Gene expression analysis confirmed the existence of these ten MADS-box genes in IRIS_313-10,394, all of them were expressed in flower tissues, and six of them were highly expressed during seed development. Altogether, we identified and validated experimentally, for the first time, ten novel MADS-box genes in RPAN, which provides new genetic sources for rice improvement.
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Affiliation(s)
- Weihua Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Duoxiang Wang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaokun Hong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Hong
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Su Su
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572024, China
| | - Cristopher Reyes Loaiciga
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jing Li
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572024, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572024, China.
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572024, China
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, Adelaide, 5064, Australia
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20
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Gupta S, Harkess A, Soble A, Van Etten M, Leebens-Mack J, Baucom RS. Interchromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance. THE NEW PHYTOLOGIST 2023; 238:1263-1277. [PMID: 36721257 DOI: 10.1111/nph.18782] [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: 11/15/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The adaptation of weeds to herbicide is both a significant problem in agriculture and a model of rapid adaptation. However, significant gaps remain in our knowledge of resistance controlled by many loci and the evolutionary factors that influence the maintenance of resistance. Here, using herbicide-resistant populations of the common morning glory (Ipomoea purpurea), we perform a multilevel analysis of the genome and transcriptome to uncover putative loci involved in nontarget-site herbicide resistance (NTSR) and to examine evolutionary forces underlying the maintenance of resistance in natural populations. We found loci involved in herbicide detoxification and stress sensing to be under selection and confirmed that detoxification is responsible for glyphosate (RoundUp) resistance using a functional assay. We identified interchromosomal linkage disequilibrium (ILD) among loci under selection reflecting either historical processes or additive effects leading to the resistance phenotype. We further identified potential fitness cost loci that were strongly linked to resistance alleles, indicating the role of genetic hitchhiking in maintaining the cost. Overall, our work suggests that NTSR glyphosate resistance in I. purpurea is conferred by multiple genes which are potentially maintained through generations via ILD, and that the fitness cost associated with resistance in this species is likely a by-product of genetic hitchhiking.
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Affiliation(s)
- Sonal Gupta
- Ecology and Evolutionary Biology Department, University of Michigan, 4034 Biological Sciences Building, Ann Arbor, MI, 48109, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Alex Harkess
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Anah Soble
- Ecology and Evolutionary Biology Department, University of Michigan, 4034 Biological Sciences Building, Ann Arbor, MI, 48109, USA
| | - Megan Van Etten
- Biology Department, Pennsylvania State University, Dunmore, PA, 18512, USA
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Regina S Baucom
- Ecology and Evolutionary Biology Department, University of Michigan, 4034 Biological Sciences Building, Ann Arbor, MI, 48109, USA
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21
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Li Y, Luo J, Chen R, Zhou Y, Yu H, Chu Z, Lu Y, Gu X, Wu S, Wang P, Kuang H, Ouyang B. Folate shapes plant root architecture by affecting auxin distribution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:969-985. [PMID: 36587293 DOI: 10.1111/tpj.16093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/26/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
Folate (vitamin B9) is important for plant root development, but the mechanism is largely unknown. Here we characterized a root defective mutant, folb2, in Arabidopsis, which has severe developmental defects in the primary root. The root apical meristem of the folb2 mutant is impaired, and adventitious roots are frequently found at the root-hypocotyl junction. Positional cloning revealed that a 61-bp deletion is present in the predicted junction region of the promoter and the 5' untranslated region of AtFolB2, a gene encoding a dihydroneopterin aldolase that functions in folate biosynthesis. This mutation leads to a significant reduction in the transcript level of AtFolB2. Liquid chromatography-mass spectrometry analysis showed that the contents of the selected folate compounds were decreased in folb2. Arabidopsis AtFolB2 knockdown lines phenocopy the folb2 mutant. On the other hand, the application of exogenous 5-formyltetrahydrofolic acid could rescue the root phenotype of folb2, indicating that the root phenotype is indeed related to the folate level. Further analysis revealed that folate could promote rootward auxin transport through auxin transporters and that folate may affect particular auxin/indole-3-acetic acid proteins and auxin response factors. Our findings provide new insights into the important role of folic acid in shaping root structure.
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Affiliation(s)
- Ying Li
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- College of Horticulture, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Jinying Luo
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Rong Chen
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yuhong Zhou
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Huiyang Yu
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhuannan Chu
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yongen Lu
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shuang Wu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Pengwei Wang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Hanhui Kuang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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22
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Zhu M, Tao L, Zhang J, Liu R, Tian H, Hu C, Zhu Y, Li M, Wei Z, Yi J, Li J, Gou X. The type-B response regulators ARR10, ARR12, and ARR18 specify the central cell in Arabidopsis. THE PLANT CELL 2022; 34:4714-4737. [PMID: 36130292 PMCID: PMC9709988 DOI: 10.1093/plcell/koac285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/15/2022] [Indexed: 06/15/2023]
Abstract
In Arabidopsis thaliana, the female gametophyte consists of two synergid cells, an egg cell, a diploid central cell, and three antipodal cells. CYTOKININ INDEPENDENT 1 (CKI1), a histidine kinase constitutively activating the cytokinin signaling pathway, specifies the central cell and restricts the egg cell. However, the mechanism regulating CKI1-dependent central cell specification is largely unknown. Here, we showed that the type-B ARABIDOPSIS RESPONSE REGULATORS10, 12, and 18 (ARR10/12/18) localize at the chalazal pole of the female gametophyte. Phenotypic analysis showed that the arr10 12 18 triple mutant is female sterile. We examined the expression patterns of embryo sac marker genes and found that the embryo sac of arr10 12 18 plants had lost central cell identity, a phenotype similar to that of the Arabidopsis cki1 mutant. Genetic analyses demonstrated that ARR10/12/18, CKI1, and ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN2, 3, and 5 (AHP2/3/5) function in a common pathway to regulate female gametophyte development. In addition, constitutively activated ARR10/12/18 in the cki1 embryo sac partially restored the fertility of cki1. Results of transcriptomic analysis supported the conclusion that ARR10/12/18 and CKI1 function together to regulate the identity of the central cell. Our results demonstrated that ARR10/12/18 function downstream of CKI1-AHP2/3/5 as core factors to determine cell fate of the female gametophyte.
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Affiliation(s)
- Mingsong Zhu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Liang Tao
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jinghua Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Ruini Liu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Hongai Tian
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Chong Hu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yafen Zhu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Meizhen Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Zhuoyun Wei
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jing Yi
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaoping Gou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
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23
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Li C, Hu F, Chen H, Zhao J. Transcriptome characteristics during cell wall formation of endosperm cellularization and embryo differentiation in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:998664. [PMID: 36262665 PMCID: PMC9575994 DOI: 10.3389/fpls.2022.998664] [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: 07/20/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Embryonic and endosperm development are important biological events during Arabidopsis seed development, and are controlled by dynamic changes in a range of gene expression. Nevertheless, the regulatory mechanisms of endosperm cellularization and embryo differentiation remain unclear. Here, we characterized the early embryo and endosperm development of the naa15 mutant that had abnormal embryo differentiation and incomplete endosperm cellularization compared to WT of Arabidopsis, and comparatively investigated the changes of gene expressions in WT seeds at 3, 4, and 5 days after pollination (3W, 4W, and 5W) and the white homozygous aborted naa15 seeds at 5, 6, and 7 DAP (5M, 6M, and 7M) from naa15-1/+ siliques using RNA sequencing and qPCR assays. The transcriptome analyses showed that there were 2040 and 3630 differentially expressed genes (DEGs) in 4W (at endosperm cellularization initiation stage and heart embryo stage) vs 3W (at syncytium stage and globular embryo stage), and 5W (at end of endosperm cellularization stage and torpedo embryo stage) vs 4W, respectively. The KEGG and GO analyses showed that lipid metabolic processes and transmembrane transport related to cell wall biogenesis, cell division and differentiation, the plant hormone signaling pathway, photosynthesis, and transcription regulator activity were evidently enriched in WT and naa15. The heatmap and qPCR analyses showed that auxin response genes (ARFs), auxin transport genes (PINs) cytokinin synthesis genes (LOGs), cytokinin dehydrogenase genes (CKXs), cytokinin receptor, transcription factors (MYB, bHLH, MADS-box, and ERF) were significantly downregulated in naa15 compared to WT. A series of cell wall genes annotated to xyloglucan endotransglycosylase/hydrolase, pectin methyl esterase, and pectin methyl esterase inhibitor were also identified in these DEGs. Moreover, using an immunofluorescent assay, the features of cell walls displayed that cellulose fluorescence signals in the embryo and endosperm of naa15 were significantly decreased, and the signals of low- and high- methyl esterification of pectin were also obviously decreased in the endosperm of naa15. In summary, we identified a large number of DEGs and investigated the features of cell walls during endosperm cellularization and embryonic differentiation, which provided important information on transcription and gene expression to reveal their regulatory mechanisms.
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24
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Abstract
In angiosperms, double fertilization triggers the concomitant development of two closely juxtaposed tissues, the embryo and the endosperm. Successful seed development and germination require constant interactions between these tissues, which occur across their common interface. The embryo-endosperm interface is a complex and poorly understood compound apoplast comprising components derived from both tissues, across which nutrients transit to fuel embryo development. Interface properties, which affect molecular diffusion and thus communication, are themselves dynamically regulated by molecular and physical dialogues between the embryo and endosperm. We review the current understanding of embryo-endosperm interactions, with a focus on the structure, properties, and function of their shared interface. Concentrating on Arabidopsis, but with reference to other species, we aim to situate recent findings within the broader context of seed physiology, developmental biology, and genetic factors such as parental conflicts over resource allocation.
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Affiliation(s)
- Nicolas M Doll
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium;
- VIB Center of Plant Systems Biology, Ghent, Belgium
| | - Gwyneth C Ingram
- Laboratoire Reproduction et Développement des Plantes, ENS de Lyon, CNRS, INRAE, Université de Lyon 1, Lyon, France;
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25
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Williams BP, Bechen LL, Pohlmann DA, Gehring M. Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time. THE PLANT CELL 2022; 34:1189-1206. [PMID: 34954804 PMCID: PMC8972289 DOI: 10.1093/plcell/koab319] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/21/2021] [Indexed: 05/29/2023]
Abstract
Cytosine methylation is a reversible epigenetic modification of DNA. In plants, removal of cytosine methylation is accomplished by the four members of the DEMETER (DME) family of 5-methylcytosine DNA glycosylases, named DME, DEMETER-LIKE2 (DML2), DML3, and REPRESSOR OF SILENCING1 (ROS1) in Arabidopsis thaliana. Demethylation by DME is critical for seed development, preventing experiments to determine the function of the entire gene family in somatic tissues by mutant analysis. Here, we bypassed the reproductive defects of dme mutants to create somatic quadruple homozygous mutants of the entire DME family. dme; ros1; dml2; and dml3 (drdd) leaves exhibit hypermethylated regions compared with wild-type leaves and rdd triple mutants, indicating functional redundancy among all four demethylases. Targets of demethylation include regions co-targeted by RNA-directed DNA methylation and, surprisingly, CG gene body methylation, indicating dynamic methylation at these less-understood sites. Additionally, many tissue-specific methylation differences are absent in drdd, suggesting a role for active demethylation in generating divergent epigenetic states across wild-type tissues. Furthermore, drdd plants display an early flowering phenotype, which involves 5'-hypermethylation and transcriptional down-regulation of FLOWERING LOCUS C. Active DNA demethylation is therefore required for proper methylation across somatic tissues and defines the epigenetic landscape of intergenic and coding regions.
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Affiliation(s)
- Ben P Williams
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Lindsey L Bechen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Deborah A Pohlmann
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mary Gehring
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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26
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Han B, Wu D, Zhang Y, Li DZ, Xu W, Liu A. Epigenetic regulation of seed-specific gene expression by DNA methylation valleys in castor bean. BMC Biol 2022; 20:57. [PMID: 35227267 PMCID: PMC8886767 DOI: 10.1186/s12915-022-01259-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/18/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Understanding the processes governing angiosperm seed growth and development is essential both for fundamental plant biology and for agronomic purposes. Master regulators of angiosperm seed development are expressed in a seed-specific manner. However, it is unclear how this seed specificity of transcription is established. In some vertebrates, DNA methylation valleys (DMVs) are highly conserved and strongly associated with key developmental genes, but comparable studies in plants are limited to Arabidopsis and soybean. Castor bean (Ricinus communis) is a valuable model system for the study of seed biology in dicots and source of economically important castor oil. Unlike other dicots such as Arabidopsis and soybean, castor bean seeds have a relatively large and persistent endosperm throughout seed development, representing substantial structural differences in mature seeds. Here, we performed an integrated analysis of RNA-seq, whole-genome bisulfite sequencing, and ChIP-seq for various histone marks in the castor bean. RESULTS We present a gene expression atlas covering 16 representative tissues and identified 1162 seed-specific genes in castor bean (Ricinus communis), a valuable model for the study of seed biology in dicots. Upon whole-genome DNA methylation analyses, we detected 32,567 DMVs across five tissues, covering ~33% of the castor bean genome. These DMVs are highly hypomethylated during development and conserved across plant species. We found that DMVs have the potential to activate transcription, especially that of tissue-specific genes. Focusing on seed development, we found that many key developmental regulators of seed/endosperm development, including AGL61, AGL62, LEC1, LEC2, ABI3, and WRI1, were located within DMVs. ChIP-seq for five histone modifications in leaves and seeds clearly showed that the vast majority of histone modification peaks were enriched within DMVs, and their remodeling within DMVs has a critical role in the regulation of seed-specific gene expression. Importantly, further experiment analysis revealed that distal DMVs may act as cis-regulatory elements, like enhancers, to activate downstream gene expression. CONCLUSIONS Our results point to the importance of DMVs and special distal DMVs behaving like enhancers, in the regulation of seed-specific genes, via the reprogramming of histone modifications within DMVs. Furthermore, these results provide a comprehensive understanding of the epigenetic regulator roles in seed development in castor bean and other important crops.
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Affiliation(s)
- Bing Han
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Di Wu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanyu Zhang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Wei Xu
- Germplasm Bank of Wild Species, 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.
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27
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Qiu Y, Köhler C. Endosperm Evolution by Duplicated and Neofunctionalized Type I MADS-Box Transcription Factors. Mol Biol Evol 2022; 39:msab355. [PMID: 34897514 PMCID: PMC8788222 DOI: 10.1093/molbev/msab355] [Citation(s) in RCA: 2] [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] [Indexed: 12/13/2022] Open
Abstract
MADS-box transcription factors (TFs) are present in nearly all major eukaryotic groups. They are divided into Type I and Type II that differ in domain structure, functional roles, and rates of evolution. In flowering plants, major evolutionary innovations like flowers, ovules, and fruits have been closely connected to Type II MADS-box TFs. The role of Type I MADS-box TFs in angiosperm evolution remains to be identified. Here, we show that the formation of angiosperm-specific Type I MADS-box clades of Mγ and Mγ-interacting Mα genes (Mα*) can be tracked back to the ancestor of all angiosperms. Angiosperm-specific Mγ and Mα* genes were preferentially expressed in the endosperm, consistent with their proposed function as heterodimers in the angiosperm-specific embryo nourishing endosperm tissue. We propose that duplication and diversification of Type I MADS genes underpin the evolution of the endosperm, a developmental innovation closely connected to the origin and success of angiosperms.
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Affiliation(s)
- Yichun Qiu
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala, Sweden
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala, Sweden
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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Shao Z, He M, Zeng Z, Chen Y, Hanna AD, Zhu H. Genome-Wide Identification and Expression Analysis of the MADS-Box Gene Family in Sweet Potato [ Ipomoea batatas (L.) Lam]. Front Genet 2021; 12:750137. [PMID: 34868221 PMCID: PMC8636027 DOI: 10.3389/fgene.2021.750137] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
MADS-box gene, one of the largest transcription factor families in plants, is a class of transcription factors widely present in eukaryotes. It plays an important role in plant growth and development and participates in the growth and development of flowers and fruits. Sweet potato is the seventh most important food crop in the world. Its tuberous roots, stems, and leaves contain a large number of proteins, lipids, carotenoids, anthocyanins, conjugated phenolic acids, and minerals, which have high edible, forage, and medicinal value, and is also an important energy crop. At present, MADS-box genes in sweet potato have rarely been reported, and there has been no study on the genome-wide identification and classification of MADS-box genes in Ipomoea batatas. This study provided the first comprehensive analysis of sweet potato MADS-box genes. We identified 95 MADS-box genes, analyzed the structure and protein of sweet potato MADS-box genes, and categorized them based on phylogenetic analysis with Arabidopsis MADS-box proteins. Chromosomal localization indicated an unequal number of MADS-box genes in all 14 chromosomes except LG3, with more than 10 MADS-box genes located on chromosomes LG7, LG11, and LG15. The MADS domain and core motifs of the sweet potato MADS-box genes were identified by motif analysis. We identified 19 MADS-box genes with collinear relationships and analyzed duplication events. Cis-acting elements, such as light-responsive, auxin-responsive, drought-inducible, and MeJA-responsive elements, were found in the promoter region of the MADS-box genes in sweet potato, which further indicates the basis of MADS-box gene regulation in response to environmental changes and hormones. RNA-seq suggested that sweet potato MADS-box genes exhibit tissue-specific expression patterns, with 34 genes highly expressed in sweet potato flowers and fruits, and 19 genes highly expressed in the tuberous root, pencil root, or fibrous root. qRT-PCR again validated the expression levels of the 10 genes and found that IbMADS1, IbMADS18, IbMADS19, IbMADS79, and IbMADS90 were highly expressed in the tuberous root or fibrous root, and IbMADS18, IbMADS31, and IbMADS83 were highly expressed in the fruit. In this study, the molecular basis of MADS-box genes of sweet potato was analyzed from various angles. The effects of MADS-box genes on the growth and development of sweet potato were investigated, which may provide a certain theoretical basis for molecular breeding of sweet potato.
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Affiliation(s)
- Zhengwei Shao
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Minhong He
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Zhipeng Zeng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Yanzhu Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Amoanimaa-Dede Hanna
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Hongbo Zhu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
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Liang Y, Wei K, Wei F, Qin S, Deng C, Lin Y, Li M, Gu L, Wei G, Miao J, Zhang Z. Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis. BMC PLANT BIOLOGY 2021; 21:566. [PMID: 34856930 PMCID: PMC8641164 DOI: 10.1186/s12870-021-03334-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Sophora tonkinensis Gagnep is a traditional Chinese medical plant that is mainly cultivated in southern China. Drought stress is one of the major abiotic stresses that negatively impacts S. tonkinensis growth. However, the molecular mechanisms governing the responses to drought stress in S. tonkinensis at the transcriptional and posttranscriptional levels are not well understood. RESULTS To identify genes and miRNAs involved in drought stress responses in S. tonkinensis, both mRNA and small RNA sequencing was performed in root samples under control, mild drought, and severe drought conditions. mRNA sequencing revealed 66,476 unigenes, and the differentially expressed unigenes (DEGs) were associated with several key pathways, including phenylpropanoid biosynthesis, sugar metabolism, and quinolizidine alkaloid biosynthesis pathways. A total of 10 and 30 transcription factors (TFs) were identified among the DEGs under mild and severe drought stress, respectively. Moreover, small RNA sequencing revealed a total of 368 miRNAs, including 255 known miRNAs and 113 novel miRNAs. The differentially expressed miRNAs and their target genes were involved in the regulation of plant hormone signal transduction, the spliceosome, and ribosomes. Analysis of the regulatory network involved in the response to drought stress revealed 37 differentially expressed miRNA-mRNA pairs. CONCLUSION This is the first study to simultaneously profile the expression patterns of mRNAs and miRNAs on a genome-wide scale to elucidate the molecular mechanisms of the drought stress responses of S. tonkinensis. Our results suggest that S. tonkinensis implements diverse mechanisms to modulate its responses to drought stress.
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Affiliation(s)
- Ying Liang
- College of Agriculture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002, People's Republic of China
- Guangxi key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, No. 189 Changgang Road, Xingning District, Nanning, 530023, People's Republic of China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Kunhua Wei
- Guangxi key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, No. 189 Changgang Road, Xingning District, Nanning, 530023, People's Republic of China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Fan Wei
- Guangxi key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, No. 189 Changgang Road, Xingning District, Nanning, 530023, People's Republic of China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Shuangshuang Qin
- Guangxi key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, No. 189 Changgang Road, Xingning District, Nanning, 530023, People's Republic of China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Chuanhua Deng
- Guangxi Forest Inventory and Planning Institute, Nanning, 530011, China
| | - Yang Lin
- Guangxi key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, No. 189 Changgang Road, Xingning District, Nanning, 530023, People's Republic of China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Mingjie Li
- College of Agriculture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002, People's Republic of China
| | - Li Gu
- College of Agriculture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002, People's Republic of China
| | - Guili Wei
- Guangxi key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, No. 189 Changgang Road, Xingning District, Nanning, 530023, People's Republic of China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Jianhua Miao
- Guangxi key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, No. 189 Changgang Road, Xingning District, Nanning, 530023, People's Republic of China.
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China.
| | - Zhongyi Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou, 350002, People's Republic of China.
- Key Laboratory of Genetics, Breeding and Comprehensive Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Wang L, Ruan C, Bao A, Li H. Small RNA profiling for identification of microRNAs involved in regulation of seed development and lipid biosynthesis in yellowhorn. BMC PLANT BIOLOGY 2021; 21:464. [PMID: 34641783 PMCID: PMC8513341 DOI: 10.1186/s12870-021-03239-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 09/29/2021] [Indexed: 05/30/2023]
Abstract
BACKGROUND Yellowhorn (Xanthoceras sorbifolium), an endemic woody oil-bearing tree, has become economically important and is widely cultivated in northern China for bioactive oil production. However, the regulatory mechanisms of seed development and lipid biosynthesis affecting oil production in yellowhorn are still elusive. MicroRNAs (miRNAs) play crucial roles in diverse aspects of biological and metabolic processes in seeds, especially in seed development and lipid metabolism. It is still unknown how the miRNAs regulate the seed development and lipid biosynthesis in yellowhorn. RESULTS Here, based on investigations of differences in the seed growth tendency and embryo oil content between high-oil-content and low-oil-content lines, we constructed small RNA libraries from yellowhorn embryos at four seed development stages of the two lines and then profiled small RNA expression using high-throughput sequencing. A total of 249 known miRNAs from 46 families and 88 novel miRNAs were identified. Furthermore, by pairwise comparisons among the four seed development stages in each line, we found that 64 miRNAs (53 known and 11 novel miRNAs) were differentially expressed in the two lines. Across the two lines, 15, 11, 10, and 7 differentially expressed miRNAs were detected at 40, 54, 68, and 81 days after anthesis, respectively. Bioinformatic analysis was used to predict a total of 2654 target genes for 141 differentially expressed miRNAs (120 known and 21 novel miRNAs). Most of these genes were involved in the fatty acid biosynthetic process, regulation of transcription, nucleus, and response to auxin. Using quantitative real-time PCR and an integrated analysis of miRNA and mRNA expression, miRNA-target regulatory modules that may be involved in yellowhorn seed size, weight, and lipid biosynthesis were identified, such as miR172b-ARF2 (auxin response factor 2), miR7760-p3_1-AGL61 (AGAMOUS-LIKE 61), miR319p_1-FAD2-2 (omega-6 fatty acid desaturase 2-2), miR5647-p3_1-DGAT1 (diacylglycerol acyltransferase 1), and miR7760-p5_1-MED15A (Mediator subunit 15a). CONCLUSIONS This study provides new insights into the important regulatory roles of miRNAs in the seed development and lipid biosynthesis in yellowhorn. Our results will be valuable for dissecting the post-transcriptional and transcriptional regulation of seed development and lipid biosynthesis, as well as improving yellowhorn in northern China.
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Affiliation(s)
- Li Wang
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, College of Marine Life Science, Ocean University of China, Qingdao, 266100, China
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China.
| | - Aomin Bao
- Institute of Economic Forest, Tongliao Academy of Forestry Science and Technology, Tongliao, 028000, China
| | - He Li
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China
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Wu M, Liu H, Li B, Zhu T. Integrated analysis of mRNA-seq and miRNA-seq reveals the advantage of polyploid Solidago canadensis in sexual reproduction. BMC PLANT BIOLOGY 2021; 21:462. [PMID: 34635057 PMCID: PMC8504063 DOI: 10.1186/s12870-021-03240-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The invasion of Solidago canadensis probably related to polyploidy, which may promotes its potential of sexual reproductive. S. canadensis as an invasive species which rapidly widespread through yield huge numbers of seed, but the mechanism remains unknown. To better understand the advantages of sexual reproduction in hexaploid S. canadensis, transcriptome and small RNA sequencing of diploid and hexaploid cytotypes in flower bud and fruit development stages were performed in this study. RESULTS The transcriptome analysis showed that in the flower bud stage, 29 DEGs were MADS-box related genes with 14 up-regulated and 15 down-regulated in hexaploid S. canadensis; 12 SPL genes were detected differentially expressed with 5 up-regulated and 7 down-regulated. In the fruit development stage, 26 MADS-box related genes with 20 up-regulated and 6 down-regulated in hexaploid S. canadensis; 5 SPL genes were all up-regulated; 28 seed storage protein related genes with 18 were up-regulated and 10 down-regulated. The weighted gene co-expression network analysis (WGCNA) identified 19 modules which consisted of co-expressed DEGs with functions such as sexual reproduction, secondary metabolism and transcription factors. Furthermore, we discovered 326 miRNAs with 67 known miRNAs and 259 novel miRNAs. Some of miRNAs, such as miR156, miR156a and miR156f, which target the sexual reproduction related genes. CONCLUSION Our study provides a global view of the advantages of sexual reproduction in hexaploid S. canadensis based on the molecular mechanisms, which may promote hexaploid S. canadensis owing higher yield and fruit quality in the process of sexual reproduction and higher germination rate of seeds, and finally conductive to diffusion, faster propagation process and enhanced invasiveness.
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Affiliation(s)
- Miao Wu
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, 467041, Henan, China.
| | - Huiyuan Liu
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, 467041, Henan, China
| | - Bingbing Li
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, 467041, Henan, China
| | - Tao Zhu
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, 467041, Henan, China
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Stein RE, Nauerth BH, Binmöller L, Zühl L, Loreth A, Reinert M, Ibberson D, Schmidt A. RH17 restricts reproductive fate and represses autonomous seed coat development in sexual Arabidopsis. Development 2021; 148:272091. [PMID: 34495331 DOI: 10.1242/dev.198739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Plant sexual and asexual reproduction through seeds (apomixis) is tightly controlled by complex gene regulatory programs, which are not yet fully understood. Recent findings suggest that RNA helicases are required for plant germline development. This resembles their crucial roles in animals, where they are involved in controlling gene activity and the maintenance of genome integrity. Here, we identified previously unknown roles of Arabidopsis RH17 during reproductive development. Interestingly, RH17 is involved in repression of reproductive fate and of elements of seed development in the absence of fertilization. In lines carrying a mutant rh17 allele, development of supernumerary reproductive cell lineages in the female flower tissues (ovules) was observed, occasionally leading to formation of two embryos per seed. Furthermore, seed coat, and putatively also endosperm development, frequently initiated autonomously. Such induction of several features phenocopying distinct elements of apomixis by a single mutation is unusual and suggests that RH17 acts in regulatory control of plant reproductive development. Furthermore, an in-depth understanding of its action might be of use for agricultural applications.
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Affiliation(s)
- Ron Eric Stein
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Berit Helge Nauerth
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Laura Binmöller
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Luise Zühl
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Anna Loreth
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Maximilian Reinert
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - David Ibberson
- Deep Sequencing Core Facility, CellNetworks Excellence Cluster, Heidelberg University, Im Neuenheimer Feld 267, D-69120, Heidelberg, Germany
| | - Anja Schmidt
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
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The intervening domain is required for DNA-binding and functional identity of plant MADS transcription factors. Nat Commun 2021; 12:4760. [PMID: 34362909 PMCID: PMC8346517 DOI: 10.1038/s41467-021-24978-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/14/2021] [Indexed: 02/06/2023] Open
Abstract
The MADS transcription factors (TF) are an ancient eukaryotic protein family. In plants, the family is divided into two main lineages. Here, we demonstrate that DNA binding in both lineages absolutely requires a short amino acid sequence C-terminal to the MADS domain (M domain) called the Intervening domain (I domain) that was previously defined only in type II lineage MADS. Structural elucidation of the MI domains from the floral regulator, SEPALLATA3 (SEP3), shows a conserved fold with the I domain acting to stabilise the M domain. Using the floral organ identity MADS TFs, SEP3, APETALA1 (AP1) and AGAMOUS (AG), domain swapping demonstrate that the I domain alters genome-wide DNA-binding specificity and dimerisation specificity. Introducing AG carrying the I domain of AP1 in the Arabidopsis ap1 mutant resulted in strong complementation and restoration of first and second whorl organs. Taken together, these data demonstrate that the I domain acts as an integral part of the DNA-binding domain and significantly contributes to the functional identity of the MADS TF. MADS transcription factors regulate multiple aspects of plant development. Here the authors show that the intervening I domain is conserved in both type I and type II plant MADS lineages and contributes to the functional identity of the protein by influencing both DNA binding activity and dimerisation specificity.
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Susaki D, Suzuki T, Maruyama D, Ueda M, Higashiyama T, Kurihara D. Dynamics of the cell fate specifications during female gametophyte development in Arabidopsis. PLoS Biol 2021; 19:e3001123. [PMID: 33770073 DOI: 10.1101/2020.04.07.023028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/29/2021] [Indexed: 05/22/2023] Open
Abstract
The female gametophytes of angiosperms contain cells with distinct functions, such as those that enable reproduction via pollen tube attraction and fertilization. Although the female gametophyte undergoes unique developmental processes, such as several rounds of nuclear division without cell plate formation and final cellularization, it remains unknown when and how the cell fate is determined during development. Here, we visualized the living dynamics of female gametophyte development and performed transcriptome analysis of individual cell types to assess the cell fate specifications in Arabidopsis thaliana. We recorded time lapses of the nuclear dynamics and cell plate formation from the 1-nucleate stage to the 7-cell stage after cellularization using an in vitro ovule culture system. The movies showed that the nuclear division occurred along the micropylar-chalazal (distal-proximal) axis. During cellularization, the polar nuclei migrated while associating with the forming edge of the cell plate, and then, migrated toward each other to fuse linearly. We also tracked the gene expression dynamics and identified that the expression of MYB98pro::GFP-MYB98, a synergid-specific marker, was initiated just after cellularization in the synergid, egg, and central cells and was then restricted to the synergid cells. This indicated that cell fates are determined immediately after cellularization. Transcriptome analysis of the female gametophyte cells of the wild-type and myb98 mutant revealed that the myb98 synergid cells had egg cell-like gene expression profiles. Although in myb98, egg cell-specific gene expression was properly initiated in the egg cells only after cellularization, but subsequently expressed ectopically in one of the 2 synergid cells. These results, together with the various initiation timings of the egg cell-specific genes, suggest complex regulation of the individual gametophyte cells, such as cellularization-triggered fate initiation, MYB98-dependent fate maintenance, cell morphogenesis, and organelle positioning. Our system of live-cell imaging and cell type-specific gene expression analysis provides insights into the dynamics and mechanisms of cell fate specifications in the development of female gametophytes in plants.
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Affiliation(s)
- Daichi Susaki
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Daisuke Maruyama
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Minako Ueda
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Nagoya, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Nagoya, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Daisuke Kurihara
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Nagoya, Japan
- JST, PRESTO, Nagoya, Japan
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Li HJ, Yang WC. Central Cell in Flowering Plants: Specification, Signaling, and Evolution. FRONTIERS IN PLANT SCIENCE 2020; 11:590307. [PMID: 33193544 PMCID: PMC7609669 DOI: 10.3389/fpls.2020.590307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 09/28/2020] [Indexed: 05/05/2023]
Abstract
During the reproduction of animals and lower plants, one sperm cell usually outcompetes the rivals to fertilize a single egg cell. But in flowering plants, two sperm cells fertilize the two adjacent dimorphic female gametes, the egg and central cell, respectively, to initiate the embryo and endosperm within a seed. The endosperm nourishes the embryo development and is also the major source of nutrition in cereals for humankind. Central cell as one of the key innovations of flowering plants is the biggest cell in the multicellular haploid female gametophyte (embryo sac). The embryo sac differentiates from the meiotic products through successive events of nuclear divisions, cellularization, and cell specification. Nowadays, accumulating lines of evidence are raveling multiple roles of the central cell rather than only the endosperm precursor. In this review, we summarize the current understanding on its cell fate specification, intercellular communication, and evolution. We also highlight some key unsolved questions for the further studies in this field.
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Affiliation(s)
- Hong-Ju Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wei-Cai Yang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
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36
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Chen SP, Sun WH, Xiong YF, Jiang YT, Liu XD, Liao XY, Zhang DY, Jiang SZ, Li Y, Liu B, Ma L, Yu X, He L, Liu B, Feng JL, Feng LZ, Wang ZW, Zou SQ, Lan SR, Liu ZJ. The Phoebe genome sheds light on the evolution of magnoliids. HORTICULTURE RESEARCH 2020; 7:146. [PMID: 32922818 PMCID: PMC7459323 DOI: 10.1038/s41438-020-00368-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 06/04/2020] [Accepted: 06/19/2020] [Indexed: 05/09/2023]
Abstract
Lauraceae includes the genus Phoebe, and the family is linked to the evolution of magnoliids. We sequenced the genome of Phoebe bournei Nanmu. The assembled genome size was 989.19 Mb, with a contig N50 value of 2.05 Mb. A total of 28,198 protein-coding genes were annotated in P. bournei. Whole-genome duplication (WGD) analysis showed that Lauraceae has experienced two WGD events; the older WGD event occurred just before the divergence of Lauraceae and Magnoliales, and the more recent WGD was shared by all lineages of Lauraceae. The phylogenetic tree showed that magnoliids form a sister clade to monocots and eudicots. We also identified 63 MADS-box genes, including AGL12-like genes that may be related to the regulation of P. bournei roots and FIN219-like genes encoding GH3 proteins, which are involved in photomorphogenesis. SAUR50-like genes involved in light signal-mediated pedicel or stem development were also identified. Four ATMYB46- and three PtrEPSP-homologous genes related to lignin biosynthesis were identified. These genes may be associated with the formation of straight trunks in P. bournei. Overall, the P. bournei reference genome provides insight into the origin, evolution, and diversification of Phoebe and other magnoliids.
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Affiliation(s)
- Shi-Pin Chen
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Wei-Hong Sun
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Yuan-Fang Xiong
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Yu-Ting Jiang
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Xue-Die Liu
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Xing-Yu Liao
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Di-Yang Zhang
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Shu-Zhen Jiang
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Yu Li
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Bin Liu
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Liang Ma
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Xia Yu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Li He
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Bao Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Jin-Lin Feng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Li-Zhen Feng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | | | - Shuang-Quan Zou
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Si-Ren Lan
- College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, 325005 Wenzhou, China
- Institute of Vegetable and Flowers, Shandong Academy of Agricultural Sciences, 250100 Jinan, China
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37
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Hater F, Nakel T, Groß-Hardt R. Reproductive Multitasking: The Female Gametophyte. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:517-546. [PMID: 32442389 DOI: 10.1146/annurev-arplant-081519-035943] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Fertilization of flowering plants requires the organization of complex tasks, many of which become integrated by the female gametophyte (FG). The FG is a few-celled haploid structure that orchestrates division of labor to coordinate successful interaction with the sperm cells and their transport vehicle, the pollen tube. As reproductive outcome is directly coupled to evolutionary success, the underlying mechanisms are under robust molecular control, including integrity check and repair mechanisms. Here, we review progress on understanding the development and function of the FG, starting with the functional megaspore, which represents the haploid founder cell of the FG. We highlight recent achievements that have greatly advanced our understanding of pollen tube attraction strategies and the mechanisms that regulate plant hybridization and gamete fusion. In addition, we discuss novel insights into plant polyploidization strategies that expand current concepts on the evolution of flowering plants.
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Affiliation(s)
- Friederike Hater
- Centre for Biomolecular Interactions, University of Bremen, 28359 Bremen, Germany;
| | - Thomas Nakel
- Centre for Biomolecular Interactions, University of Bremen, 28359 Bremen, Germany;
| | - Rita Groß-Hardt
- Centre for Biomolecular Interactions, University of Bremen, 28359 Bremen, Germany;
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38
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Transcriptional repression specifies the central cell for double fertilization. Proc Natl Acad Sci U S A 2020; 117:6231-6236. [PMID: 32132210 DOI: 10.1073/pnas.1909465117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Double fertilization is a key innovation for the evolutionary success of angiosperms by which the two fertilized female gametes, the egg cell and central cell, generate the embryo and endosperm, respectively. The female gametophyte (embryo sac) enclosed in the sporophyte is derived from a one-celled haploid cell lineage. It undergoes successive events of mitotic divisions, cellularization, and cell specification to give rise to the mature embryo sac, which contains the two female gametes accompanied by two types of accessory cells, namely synergids and antipodals. How the cell fate of the central cell is specified has long been equivocal and is further complicated by the structural diversity of female gametophyte across plant taxa. Here, MADS-box protein AGL80 was verified as a transcriptional repressor that directly suppresses the expression of accessory cell-specific genes to specify the central cell. Further genetic rescue and phylogenetic assay of the AGL80 orthologs revealed a possible conserved mechanism in the Brassicaceae family. Results from this study provide insight into the molecular determination of the second female gamete cell in Brassicaceae.
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39
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Paul P, Dhatt BK, Miller M, Folsom JJ, Wang Z, Krassovskaya I, Liu K, Sandhu J, Yu H, Zhang C, Obata T, Staswick P, Walia H. MADS78 and MADS79 Are Essential Regulators of Early Seed Development in Rice. PLANT PHYSIOLOGY 2020; 182:933-948. [PMID: 31818903 PMCID: PMC6997703 DOI: 10.1104/pp.19.00917] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/27/2019] [Indexed: 05/20/2023]
Abstract
MADS box transcription factors (TFs) are subdivided into type I and II based on phylogenetic analysis. The type II TFs regulate floral organ identity and flowering time, but type I TFs are relatively less characterized. Here, we report the functional characterization of two type I MADS box TFs in rice (Oryza sativa), MADS78 and MADS79 Transcript abundance of both these genes in developing seed peaked at 48 h after fertilization and was suppressed by 96 h after fertilization, corresponding to syncytial and cellularized stages of endosperm development, respectively. Seeds overexpressing MADS78 and MADS 79 exhibited delayed endosperm cellularization, while CRISPR-Cas9-mediated single knockout mutants showed precocious endosperm cellularization. MADS78 and MADS 79 were indispensable for seed development, as a double knockout mutant failed to make viable seeds. Both MADS78 and 79 interacted with MADS89, another type I MADS box, which enhances nuclear localization. The expression analysis of Fie1, a rice FERTILIZATION-INDEPENDENT SEED-POLYCOMB REPRESSOR COMPLEX2 component, in MADS78 and 79 mutants and vice versa established an antithetical relation, suggesting that Fie1 could be involved in negative regulation of MADS78 and MADS 79 Misregulation of MADS78 and MADS 79 perturbed auxin homeostasis and carbon metabolism, as evident by misregulation of genes involved in auxin transport and signaling as well as starch biosynthesis genes causing structural abnormalities in starch granules at maturity. Collectively, we show that MADS78 and MADS 79 are essential regulators of early seed developmental transition and impact both seed size and quality in rice.
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Affiliation(s)
- Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583
| | - Balpreet K Dhatt
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583
| | - Michael Miller
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583
| | - Jing J Folsom
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583
| | - Zhen Wang
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583
| | - Inga Krassovskaya
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588
| | - Kan Liu
- School of Biological Science, University of Nebraska, Lincoln, Nebraska 68588
| | - Jaspreet Sandhu
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583
| | - Huihui Yu
- School of Biological Science, University of Nebraska, Lincoln, Nebraska 68588
| | - Chi Zhang
- School of Biological Science, University of Nebraska, Lincoln, Nebraska 68588
| | - Toshihiro Obata
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588
| | - Paul Staswick
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583
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40
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Huang L, Feng G, Yan H, Zhang Z, Bushman BS, Wang J, Bombarely A, Li M, Yang Z, Nie G, Xie W, Xu L, Chen P, Zhao X, Jiang W, Zhang X. Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:373-388. [PMID: 31276273 PMCID: PMC6953241 DOI: 10.1111/pbi.13205] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 05/27/2019] [Accepted: 06/29/2019] [Indexed: 05/18/2023]
Abstract
Orchardgrass (Dactylis glomerata L.) is an important forage grass for cultivating livestock worldwide. Here, we report an ~1.84-Gb chromosome-scale diploid genome assembly of orchardgrass, with a contig N50 of 0.93 Mb, a scaffold N50 of 6.08 Mb and a super-scaffold N50 of 252.52 Mb, which is the first chromosome-scale assembled genome of a cool-season forage grass. The genome includes 40 088 protein-coding genes, and 69% of the assembled sequences are transposable elements, with long terminal repeats (LTRs) being the most abundant. The LTRretrotransposons may have been activated and expanded in the grass genome in response to environmental changes during the Pleistocene between 0 and 1 million years ago. Phylogenetic analysis reveals that orchardgrass diverged after rice but before three Triticeae species, and evolutionarily conserved chromosomes were detected by analysing ancient chromosome rearrangements in these grass species. We also resequenced the whole genome of 76 orchardgrass accessions and found that germplasm from Northern Europe and East Asia clustered together, likely due to the exchange of plants along the 'Silk Road' or other ancient trade routes connecting the East and West. Last, a combined transcriptome, quantitative genetic and bulk segregant analysis provided insights into the genetic network regulating flowering time in orchardgrass and revealed four main candidate genes controlling this trait. This chromosome-scale genome and the online database of orchardgrass developed here will facilitate the discovery of genes controlling agronomically important traits, stimulate genetic improvement of and functional genetic research on orchardgrass and provide comparative genetic resources for other forage grasses.
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Affiliation(s)
- Linkai Huang
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Guangyan Feng
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Haidong Yan
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
- School of Plant and Environmental SciencesVirginia TechBlacksburgVAUSA
| | | | | | - Jianping Wang
- Agronomy DepartmentUniversity of FloridaGainesvilleFLUSA
| | | | - Mingzhou Li
- Animal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Zhongfu Yang
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Gang Nie
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Wengang Xie
- State Key Laboratory of Grassland Agro‐EcosystemsCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Lei Xu
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Peilin Chen
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Xinxin Zhao
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | | | - Xinquan Zhang
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
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41
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Paul P, Dhatt BK, Sandhu J, Hussain W, Irvin L, Morota G, Staswick P, Walia H. Divergent phenotypic response of rice accessions to transient heat stress during early seed development. PLANT DIRECT 2020; 4:e00196. [PMID: 31956854 PMCID: PMC6955394 DOI: 10.1002/pld3.196] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/05/2019] [Accepted: 12/19/2019] [Indexed: 05/03/2023]
Abstract
Increasing global surface temperatures is posing a major food security challenge. Part of the solution to address this problem is to improve crop heat resilience, especially during grain development, along with agronomic decisions such as shift in planting time and increasing crop diversification. Rice is a major food crop consumed by more than 3 billion people. For rice, thermal sensitivity of reproductive development and grain filling is well-documented, while knowledge concerning the impact of heat stress (HS) on early seed development is limited. Here, we aim to study the phenotypic variation in a set of diverse rice accessions for elucidating the HS response during early seed development. To explore the variation in HS sensitivity, we investigated aus (1), indica (2), temperate japonica (2), and tropical japonica (4) accessions for their HS (39/35°C) response during early seed development that accounts for transition of endosperm from syncytial to cellularization, which broadly corresponds to 24 and 96 hr after fertilization (HAF), respectively, in rice. The two indica and one of the tropical japonica accessions exhibited severe heat sensitivity with increased seed abortion; three tropical japonicas and an aus accession showed moderate heat tolerance, while temperate japonicas exhibited strong heat tolerance. The accessions exhibiting extreme heat sensitivity maintain seed size at the expense of number of fully developed mature seeds, while the accessions showing relative resilience to the transient HS maintained number of fully developed seeds but compromised on seed size, especially seed length. Further, histochemical analysis revealed that all the tested accessions have delayed endosperm cellularization upon exposure to the transient HS by 96 HAF; however, the rate of cellularization was different among the accessions. These findings were further corroborated by upregulation of cellularization-associated marker genes in the developing seeds from the heat-stressed samples.
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Affiliation(s)
- Puneet Paul
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Balpreet K. Dhatt
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Jaspreet Sandhu
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Waseem Hussain
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
- International Rice Research InstituteLos BanosPhilippines
| | - Larissa Irvin
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Gota Morota
- Department of Animal and Poultry SciencesVirginia Polytechnic Institute and State UniversityBlacksburgVAUSA
| | - Paul Staswick
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Harkamal Walia
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
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42
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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.
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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
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43
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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.
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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
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44
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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).
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45
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Developmental and Molecular Changes Underlying the Vernalization-Induced Transition to Flowering in Aquilegia coerulea (James). Genes (Basel) 2019; 10:genes10100734. [PMID: 31546687 PMCID: PMC6826667 DOI: 10.3390/genes10100734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/05/2019] [Accepted: 09/18/2019] [Indexed: 01/20/2023] Open
Abstract
Reproductive success in plants is dependent on many factors but the precise timing of flowering is certainly among the most crucial. Perennial plants often have a vernalization or over-wintering requirement in order to successfully flower in the spring. The shoot apical meristem undergoes drastic developmental and molecular changes as it transitions into inflorescence meristem (IM) identity, which then gives rise to floral meristems (FMs). In this study, we have examined the developmental and gene expression changes underlying the transition from the vegetative to reproductive phases in the basal eudicot Aquilegia coerulea, which has evolved a vernalization response independently relative to other established model systems. Results from both our histology and scanning electron studies demonstrate that developmental changes in the meristem occur gradually during the third and fourth weeks of vernalization. Based on RNAseq data and cluster analysis, several known flowering time loci, including AqFT and AqFL1, exhibit dramatic changes in expression during the fourth week. Further consideration of candidate gene homologs as well as unexpected loci of interest creates a framework in which we can begin to explore the genetic basis of the flowering time transition in Aquilegia.
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46
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Zhao HB, Jia HM, Wang Y, Wang GY, Zhou CC, Jia HJ, Gao ZS. Genome-wide identification and analysis of the MADS-box gene family and its potential role in fruit development and ripening in red bayberry (Morella rubra). Gene 2019; 717:144045. [PMID: 31425741 DOI: 10.1016/j.gene.2019.144045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/10/2019] [Accepted: 08/12/2019] [Indexed: 02/08/2023]
Abstract
The MADS-box gene family encodes transcription factors and plays an important role in plant growth and the development of flower and fruit. A perennial dioecious plant, the red bayberry genome has been published recently, providing the opportunity to analyze the MADS-box gene family and its role in fruit development and ripening. Here, we identified 54 MADS-box genes in the red bayberry genome, and classified them into two types based on phylogenetic analysis. Thirteen Type I MADS-box genes were subdivided into three subfamilies and 41 Type II MADS-box genes into 13 subfamilies. A total of 46 MADS-box genes were distributed across eight red bayberry chromosomes, and the other eight genes were located on the unmapped scaffolds. Transcriptome analysis suggested that the expression of most Type II genes was higher than Type I in five female tissues. Moreover, 26 MADS-box genes were expressed during red bayberry fruit development and ten of them showed high expression. qRT-PCR showed that the expression of MrMADS01 (SEP, MIKCC), with differences between the pale pink and red varieties, increased significantly at the final ripening stage, suggesting it may participate in ripening as positive regulator and related to anthocyanin biosynthesis. These results provide some clues for future study of MADS-box genes in red bayberry, especially in ripening process.
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Affiliation(s)
- Hai-Bo Zhao
- Institute of Fruit Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hui-Min Jia
- Institute of Fruit Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; current address: Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, 201602, China.
| | - Yan Wang
- Institute of Fruit Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Guo-Yun Wang
- Agriculture Extensions and Services Station, Bureau of Agriculture and Rural Affairs, Yuyao, Ningbo 315400, China
| | - Chao-Chao Zhou
- Agriculture Extensions and Services Station, Bureau of Agriculture and Rural Affairs, Yuyao, Ningbo 315400, China
| | - Hui-Juan Jia
- Institute of Fruit Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhong-Shan Gao
- Institute of Fruit Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
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47
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Li N, Song D, Peng W, Zhan J, Shi J, Wang X, Liu G, Wang H. Maternal control of seed weight in rapeseed (Brassica napus L.): the causal link between the size of pod (mother, source) and seed (offspring, sink). PLANT BIOTECHNOLOGY JOURNAL 2019; 17:736-749. [PMID: 30191657 PMCID: PMC6419582 DOI: 10.1111/pbi.13011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 08/26/2018] [Accepted: 09/04/2018] [Indexed: 05/16/2023]
Abstract
Seed size/weight is one of the key traits related to plant domestication and crop improvement. In rapeseed (Brassica napus L.) germplasm, seed weight shows extensive variation, but its regulatory mechanism is poorly understood. To identify the key mechanism of seed weight regulation, a systematic comparative study was performed. Genetic, morphological and cytological evidence showed that seed weight was controlled by maternal genotype, through the regulation of seed size mainly via cell number. The physiological evidence indicated that differences in the pod length might result in differences in pod wall photosynthetic area, carbohydrates and the final seed weight. We also identified two pleiotropic major quantitative trait loci that acted indirectly on seed weight via their effects on pod length. RNA-seq results showed that genes related to pod development and hormones were significantly differentially expressed in the pod wall; genes related to development, cell division, nutrient reservoir and ribosomal proteins were all up-regulated in the seeds of the large-seed pool. Finally, we proposed a potential seed weight regulatory mechanism that is specific to rapeseed and novel in plants. The results demonstrate a causal link between the size of the pod (mother, source) and the seed (offspring, sink) in rapeseed, which provides novel insight into the maternal control of seed weight and will open a new research field in plants.
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Affiliation(s)
- Na Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
- Zhengzhou Fruit Research Institute of the Chinese Academy of Agricultural SciencesThe Laboratory of Melon CropsZhengzhouHenan ProvinceChina
| | - Dongji Song
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Wei Peng
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Jiepeng Zhan
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Jiaqin Shi
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Guihua Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
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48
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Meng D, Cao Y, Chen T, Abdullah M, Jin Q, Fan H, Lin Y, Cai Y. Evolution and functional divergence of MADS-box genes in Pyrus. Sci Rep 2019; 9:1266. [PMID: 30718750 PMCID: PMC6362034 DOI: 10.1038/s41598-018-37897-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 12/12/2018] [Indexed: 02/02/2023] Open
Abstract
MADS-box transcription factors widely regulate all aspects of plant growth including development and reproduction. Although the MADS-box gene family genes have been extensively characterized in many plants, they have not been studied in closely related species. In this study, 73 and 74 MADS-box genes were identified in European pear (Pyrus communis) and Chinese pear (Pyrus bretschneideri), respectively. Based on the phylogenetic relationship, these genes could be clustered into five groups (Mα, Mβ, Mr, MIKCC, MIKC*) and the MIKCC group was further categorized into 10 subfamilies. The distribution of MADS-box genes on each chromosome was significantly nonrandom. Thirty-seven orthologs, twenty-five PcpMADS (P. communis MADS-box) paralogs and nineteen PbrMADS (P. bretschneideri MADS-box) paralogs were predicted. Among these paralogous genes, two pairs arose from tandem duplications (TD), nineteen from segmental duplication (SD) events and twenty-three from whole genome duplication (WGD) events, indicating SD/WGD events led to the expansion of MADS-box gene family. The MADS-box genes expression profiles in pear fruits indicated functional divergence and neo-functionalization or sub-functionalization of some orthologous genes originated from a common ancestor. This study provided a useful reference for further analysis the mechanisms of species differentiation and biodiversity formation among closely related species.
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Affiliation(s)
- Dandan Meng
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yunpeng Cao
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Tianzhe Chen
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Muhammad Abdullah
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Qing Jin
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Honghong Fan
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yi Lin
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
| | - Yongping Cai
- College of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
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49
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Erbasol Serbes I, Palovaara J, Groß-Hardt R. Development and function of the flowering plant female gametophyte. Curr Top Dev Biol 2019; 131:401-434. [DOI: 10.1016/bs.ctdb.2018.11.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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50
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Shin HY, Nam KH. RAV1 Negatively Regulates Seed Development by Directly Repressing MINI3 and IKU2 in Arabidopsis. Mol Cells 2018; 41:1072-1080. [PMID: 30518173 PMCID: PMC6315318 DOI: 10.14348/molcells.2018.0259] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/16/2018] [Accepted: 10/01/2018] [Indexed: 11/27/2022] Open
Abstract
A plant-specific B3 domain and AP2 domain-containing transcription factor, RAV1 acts as a negative regulator of growth in many plant species and its transcription was downregulated by BR and ABA. In this study, we found that RAV1-overexpressing transgenic plants showed abnormally developed ovules, resulting in reduced seed size, weight, and number in a silique. Interestingly, the endogenous expression of RAV1 fluctuated during seed development; it remained low during the early stage of seed development and sharply increased in the seed maturation stage. In plants, seed development is a complex process that requires coordinated growth of the embryo, endosperm, and maternal integuments. Among many genes that are associated with endosperm proliferation and embryo development, three genes consisting of SHB1, MINI3, and IKU2 form a small unit positively regulating this process, and their expression was regulated by BR and ABA. Using the floral stage-specific RNAs, we found that the expression of MINI3 and IKU2, the two downstream genes of the SHB1-MINI3-IKU2 cascade in the seed development pathway, were particularly reduced in the RAV1-overexpressing transgenic plants. We further determined that RAV1 directly binds to the promoter of MINI3 and IKU2, resulting in their repression. Direct treatment with brassinolide (BL) improved seed development of RAV1-overexpressing plants, but treatment with ABA severely worsened it. Overall, these results suggest that RAV1 is an additional negative player in the early stages of seed development, during which ABA and BR signaling are coordinated.
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Affiliation(s)
- Hyun-young Shin
- Department of Biological Sciences, Sookmyung Women’s University, Seoul,
Korea
| | - Kyoung Hee Nam
- Department of Biological Sciences, Sookmyung Women’s University, Seoul,
Korea
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