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Mishio M, Sudo E, Ozaki H, Oguchi R, Fujimoto R, Fujii N, Hikosaka K. Heterotic growth of hybrids of Arabidopsis thaliana is enhanced by elevated atmospheric CO 2. AMERICAN JOURNAL OF BOTANY 2024; 111:e16317. [PMID: 38634444 DOI: 10.1002/ajb2.16317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 04/19/2024]
Abstract
PREMISE With the global atmospheric CO2 concentration on the rise, developing crops that can thrive in elevated CO2 has become paramount. We investigated the potential of hybridization as a strategy for creating crops with improved growth in predicted elevated atmospheric CO2. METHODS We grew parent accessions and their F1 hybrids of Arabidopsis thaliana in ambient and elevated atmospheric CO2 and analyzed numerous growth traits to assess their productivity and underlying mechanisms. RESULTS The heterotic increase in total dry mass, relative growth rate and leaf net assimilation rate was significantly greater in elevated CO2 than in ambient CO2. The CO2 response of net assimilation rate was positively correlated with the CO2 response of leaf nitrogen productivity and with that of leaf traits such as leaf size and thickness, suggesting that hybridization-induced changes in leaf traits greatly affected the improved performance in elevated CO2. CONCLUSIONS Vegetative growth of hybrids seems to be enhanced in elevated CO2 due to improved photosynthetic nitrogen-use efficiency compared with parents. The results suggest that hybrid crops should be well-suited for future conditions, but hybrid weeds may also be more competitive.
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Affiliation(s)
- Masako Mishio
- Graduate School of Life Sciences, Tohoku University, Aramaki, Aoba, Sendai, 980-8578, Miyagi, Japan
| | - Emi Sudo
- Graduate School of Life Sciences, Tohoku University, Aramaki, Aoba, Sendai, 980-8578, Miyagi, Japan
| | - Hiroshi Ozaki
- Graduate School of Life Sciences, Tohoku University, Aramaki, Aoba, Sendai, 980-8578, Miyagi, Japan
- Translational Research Support Section, National Cancer Center Hospital East, Kashiwa, 277-8577, Chiba, Japan
| | - Riichi Oguchi
- Graduate School of Life Sciences, Tohoku University, Aramaki, Aoba, Sendai, 980-8578, Miyagi, Japan
- Graduate School of Science, Osaka Metropolitan University, 2000, Kisaichi, Katano, 576-0004, Osaka, Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Nobuharu Fujii
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba, Sendai, 980-8577, Miyagi, Japan
| | - Kouki Hikosaka
- Graduate School of Life Sciences, Tohoku University, Aramaki, Aoba, Sendai, 980-8578, Miyagi, Japan
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Kakoulidou I, Piecyk RS, Meyer RC, Kuhlmann M, Gutjahr C, Altmann T, Johannes F. Mapping parental DMRs predictive of local and distal methylome remodeling in epigenetic F1 hybrids. Life Sci Alliance 2024; 7:e202402599. [PMID: 38290756 PMCID: PMC10828516 DOI: 10.26508/lsa.202402599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/01/2024] Open
Abstract
F1 hybrids derived from a cross between two inbred parental lines often display widespread changes in DNA methylation and gene expression patterns relative to their parents. An emerging challenge is to understand how parental epigenomic differences contribute to these events. Here, we generated a large mapping panel of F1 epigenetic hybrids, whose parents are isogenic but variable in their DNA methylation patterns. Using a combination of multi-omic profiling and epigenetic mapping strategies we show that differentially methylated regions in parental pericentromeres act as major reorganizers of hybrid methylomes and transcriptomes, even in the absence of genetic variation. These parental differentially methylated regions are associated with hybrid methylation remodeling events at thousands of target regions throughout the genome, both locally (in cis) and distally (in trans). Many of these distally-induced methylation changes lead to nonadditive expression of nearby genes and associate with phenotypic heterosis. Our study highlights the pleiotropic potential of parental pericentromeres in the functional remodeling of hybrid genomes and phenotypes.
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Affiliation(s)
- Ioanna Kakoulidou
- https://ror.org/02kkvpp62 Plant Epigenomics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Robert S Piecyk
- https://ror.org/02kkvpp62 Plant Epigenomics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Rhonda C Meyer
- https://ror.org/02skbsp27 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Markus Kuhlmann
- https://ror.org/02skbsp27 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Caroline Gutjahr
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Thomas Altmann
- https://ror.org/02skbsp27 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Frank Johannes
- https://ror.org/02kkvpp62 Plant Epigenomics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
- https://ror.org/02kkvpp62 Institute of Advanced Studies, Technical University of Munich, Munich, Germany
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Meyer RC, Weigelt-Fischer K, Tschiersch H, Topali G, Altschmied L, Heuermann MC, Knoch D, Kuhlmann M, Zhao Y, Altmann T. Dynamic growth QTL action in diverse light environments: characterization of light regime-specific and stable QTL in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5341-5362. [PMID: 37306093 DOI: 10.1093/jxb/erad222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 06/10/2023] [Indexed: 06/13/2023]
Abstract
Plant growth is a complex process affected by a multitude of genetic and environmental factors and their interactions. To identify genetic factors influencing plant performance under different environmental conditions, vegetative growth was assessed in Arabidopsis thaliana cultivated under constant or fluctuating light intensities, using high-throughput phenotyping and genome-wide association studies. Daily automated non-invasive phenotyping of a collection of 382 Arabidopsis accessions provided growth data during developmental progression under different light regimes at high temporal resolution. Quantitative trait loci (QTL) for projected leaf area, relative growth rate, and PSII operating efficiency detected under the two light regimes were predominantly condition-specific and displayed distinct temporal activity patterns, with active phases ranging from 2 d to 9 d. Eighteen protein-coding genes and one miRNA gene were identified as potential candidate genes at 10 QTL regions consistently found under both light regimes. Expression patterns of three candidate genes affecting projected leaf area were analysed in time-series experiments in accessions with contrasting vegetative leaf growth. These observations highlight the importance of considering both environmental and temporal patterns of QTL/allele actions and emphasize the need for detailed time-resolved analyses under diverse well-defined environmental conditions to effectively unravel the complex and stage-specific contributions of genes affecting plant growth processes.
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Affiliation(s)
- Rhonda C Meyer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Kathleen Weigelt-Fischer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Henning Tschiersch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Georgia Topali
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Marc C Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Dominic Knoch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Markus Kuhlmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Breeding Research, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Thomas Altmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
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Duruflé H, Balliau T, Blanchet N, Chaubet A, Duhnen A, Pouilly N, Blein-Nicolas M, Mangin B, Maury P, Langlade NB, Zivy M. Sunflower Hybrids and Inbred Lines Adopt Different Physiological Strategies and Proteome Responses to Cope with Water Deficit. Biomolecules 2023; 13:1110. [PMID: 37509146 PMCID: PMC10377273 DOI: 10.3390/biom13071110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Sunflower is a hybrid crop that is considered moderately drought-tolerant and adapted to new cropping systems required for the agro-ecological transition. Here, we studied the impact of hybridity status (hybrids vs. inbred lines) on the responses to drought at the molecular and eco-physiological level exploiting publicly available datasets. Eco-physiological traits and leaf proteomes were measured in eight inbred lines and their sixteen hybrids grown in the high-throughput phenotyping platform Phenotoul-Heliaphen. Hybrids and parental lines showed different growth strategies: hybrids grew faster in the absence of water constraint and arrested their growth more abruptly than inbred lines when subjected to water deficit. We identified 471 differentially accumulated proteins, of which 256 were regulated by drought. The amplitude of up- and downregulations was greater in hybrids than in inbred lines. Our results show that hybrids respond more strongly to water deficit at the molecular and eco-physiological levels. Because of presence/absence polymorphism, hybrids potentially contain more genes than their parental inbred lines. We propose that detrimental homozygous mutations and the lower number of genes in inbred lines lead to a constitutive defense mechanism that may explain the lower growth of inbred lines under well-watered conditions and their lower reactivity to water deficit.
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Affiliation(s)
- Harold Duruflé
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
- INRAE, ONF, BioForA, 45075 Orleans, France
| | - Thierry Balliau
- AgroParisTech, GQE-Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, 91190 Gif-sur-Yvette, France
| | - Nicolas Blanchet
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Adeline Chaubet
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Alexandra Duhnen
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Nicolas Pouilly
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Mélisande Blein-Nicolas
- AgroParisTech, GQE-Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, 91190 Gif-sur-Yvette, France
| | - Brigitte Mangin
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Pierre Maury
- INRAE, INP-ENSAT Toulouse, UMR AGIR, Université de Toulouse, 31000 Toulouse, France
| | | | - Michel Zivy
- AgroParisTech, GQE-Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, 91190 Gif-sur-Yvette, France
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5
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Le QTN, Sugi N, Yamaguchi M, Hirayama T, Kobayashi M, Suzuki Y, Kusano M, Shiba H. Morphological and metabolomics profiling of intraspecific Arabidopsis hybrids in relation to biomass heterosis. Sci Rep 2023; 13:9529. [PMID: 37308530 DOI: 10.1038/s41598-023-36618-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/07/2023] [Indexed: 06/14/2023] Open
Abstract
Heterosis contributes greatly to the worldwide agricultural yield. However, the molecular mechanism underlying heterosis remains unclear. This study took advantage of Arabidopsis intraspecific hybrids to identify heterosis-related metabolites. Forty-six intraspecific hybrids were used to examine parental effects on seed area and germination time. The degree of heterosis was evaluated based on biomass: combinations showing high heterosis of F1 hybrids exhibited a biomass increase from 6.1 to 44% over the better parent value (BPV), whereas that of the low- and no-heterosis hybrids ranged from - 19.8 to 9.8% over the BPV. Metabolomics analyses of F1 hybrids with high heterosis and those with low one suggested that changes in TCA cycle intermediates are key factors that control growth. Notably, higher fumarate/malate ratios were observed in the high heterosis F1 hybrids, suggesting they provide metabolic support associated with the increased biomass. These hybrids may produce more energy-intensive biomass by speeding up the efficiency of TCA fluxes. However, the expression levels of TCA-process-related genes in F1 hybrids were not associated with the intensity of heterosis, suggesting that the post-transcriptional or post-translational regulation of these genes may affect the productivity of the intermediates in the TCA cycle.
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Affiliation(s)
- Quynh Thi Ngoc Le
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan
- Thuyloi University, 175 Tay Son, Dong Da, Hanoi, Viet Nam
| | - Naoya Sugi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Masaaki Yamaguchi
- Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan
| | - Touko Hirayama
- Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan
| | - Makoto Kobayashi
- RIKEN Center for Sustainable Resource Science, Suehiro 1-7-22, Tsurumi, Yokohama, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Japan
| | - Miyako Kusano
- Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan
- RIKEN Center for Sustainable Resource Science, Suehiro 1-7-22, Tsurumi, Yokohama, Japan
| | - Hiroshi Shiba
- Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Ten-Nodai, Tsukuba, Ibaraki, Japan.
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Ten-Nodai 1-1-1, Tsukuba, Ibaraki, Japan.
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6
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Pi K, Huang Y, Luo W, Zeng S, Mo Z, Duan L, Liu R. Overdominant expression of genes plays a key role in root growth of tobacco hybrids. FRONTIERS IN PLANT SCIENCE 2023; 14:1107550. [PMID: 36798711 PMCID: PMC9927235 DOI: 10.3389/fpls.2023.1107550] [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: 11/25/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Heterosis has greatly improved the yield and quality of crops. However, previous studies often focused on improving the yield and quality of the shoot system, while research on the root system was neglected. We determined the root numbers of 12 F1 hybrids, all of which showed strong heterosis, indicating that tobacco F1 hybrids have general heterosis. To understand its molecular mechanism, we selected two hybrids with strong heterosis, GJ (G70 × Jiucaiping No.2) and KJ (K326 × Jiucaiping No.2), and their parents for transcriptome analysis. There were 84.22% and 90.25% of the differentially expressed genes were overdominantly expressed. The enrichment analysis of these overdominantly expressed genes showed that "Plant hormone signal transduction", "Phenylpropanoid biosynthesis", "MAPK signaling pathway - plant", and "Starch and sucrose metabolism" pathways were associated with root development. We focused on the analysis of the biosynthetic pathways of auxin(AUX), cytokinins(CTK), abscisic acid(ABA), ethylene(ET), and salicylic acid(SA), suggesting that overdominant expression of these hormone signaling pathway genes may enhance root development in hybrids. In addition, Nitab4.5_0011528g0020、Nitab4.5_0003282g0020、Nitab4.5_0004384g0070 may be the genes involved in root growth. Genome-wide comparative transcriptome analysis enhanced our understanding of the regulatory network of tobacco root development and provided new ideas for studying the molecular mechanisms of tobacco root development.
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Affiliation(s)
- Kai Pi
- College of Tobacco, Guizhou University, Guiyang, China
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Ying Huang
- College of Tobacco, Guizhou University, Guiyang, China
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Wen Luo
- College of Tobacco, Guizhou University, Guiyang, China
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Shuaibo Zeng
- College of Tobacco, Guizhou University, Guiyang, China
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
| | - Zejun Mo
- College of Agriculture, Guizhou University, Guiyang, China
| | - Lili Duan
- College of Agriculture, Guizhou University, Guiyang, China
| | - Renxiang Liu
- College of Tobacco, Guizhou University, Guiyang, China
- Key Laboratory of Tobacco Quality in Guizhou Province, Guiyang, China
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Overdominance at the Gene Expression Level Plays a Critical Role in the Hybrid Root Growth of Brassica napus. Int J Mol Sci 2021; 22:ijms22179246. [PMID: 34502153 PMCID: PMC8431428 DOI: 10.3390/ijms22179246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 01/12/2023] Open
Abstract
Despite heterosis contributing to genetic improvements in crops, root growth heterosis in rapeseed plants is poorly understood at the molecular level. The current study was performed to discover key differentially expressed genes (DEGs) related to heterosis in two hybrids with contrasting root growth performance (FO; high hybrid and FV; low hybrid) based on analysis of the root heterosis effect. Based on comparative transcriptomic analysis, we believe that the overdominance at the gene expression level plays a critical role in hybrid roots’ early biomass heterosis. Our findings imply that a considerable increase in up-regulation of gene expression underpins heterosis. In the FO hybrid, high expression of DEGs overdominant in the starch/sucrose and galactose metabolic pathways revealed a link between hybrid vigor and root growth. DEGs linked to auxin, cytokinin, brassinosteroids, ethylene, and abscisic acid were also specified, showing that these hormones may enhance mechanisms of root growth and the development in the FO hybrid. Moreover, transcription factors such as MYB, ERF, bHLH, NAC, bZIP, and WRKY are thought to control downstream genes involved in root growth. Overall, this is the first study to provide a better understanding related to the regulation of the molecular mechanism of heterosis, which assists in rapeseed growth and yield improvement.
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Abstract
Hybrids account for nearly all commercially planted varieties of maize and many other crop plants because crosses between inbred lines of these species produce first-generation [F1] offspring that greatly outperform their parents. The mechanisms underlying this phenomenon, called heterosis or hybrid vigor, are not well understood despite over a century of intensive research. The leading hypotheses-which focus on quantitative genetic mechanisms (dominance, overdominance, and epistasis) and molecular mechanisms (gene dosage and transcriptional regulation)-have been able to explain some but not all of the observed patterns of heterosis. Abiotic stressors are known to impact the expression of heterosis; however, the potential role of microbes in heterosis has largely been ignored. Here, we show that heterosis of root biomass and other traits in maize is strongly dependent on the belowground microbial environment. We found that, in some cases, inbred lines perform as well by these criteria as their F1 offspring under sterile conditions but that heterosis can be restored by inoculation with a simple community of seven bacterial strains. We observed the same pattern for seedlings inoculated with autoclaved versus live soil slurries in a growth chamber and for plants grown in steamed or fumigated versus untreated soil in the field. In a different field site, however, soil steaming increased rather than decreased heterosis, indicating that the direction of the effect depends on community composition, environment, or both. Together, our results demonstrate an ecological phenomenon whereby soil microbes differentially impact the early growth of inbred and hybrid maize.
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Biological pathway expression complementation contributes to biomass heterosis in Arabidopsis. Proc Natl Acad Sci U S A 2021; 118:2023278118. [PMID: 33846256 DOI: 10.1073/pnas.2023278118] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The mechanisms underlying heterosis have long remained a matter of debate, despite its agricultural importance. How changes in transcriptional networks during plant development are relevant to the continuous manifestation of growth vigor in hybrids is intriguing and unexplored. Here, we present an integrated high-resolution analysis of the daily dynamic growth phenotypes and transcriptome atlases of young Arabidopsis seedlings (parental ecotypes [Col-0 and Per-1] and their F1 hybrid). Weighted gene coexpression network analysis uncovered divergent expression patterns between parents of the network hub genes, in which genes related to the cell cycle were more highly expressed in one parent (Col-0), whereas those involved in photosynthesis were more highly expressed in the other parent (Per-1). Notably, the hybrid exhibited spatiotemporal high-parent-dominant expression complementation of network hub genes in the two pathways during seedling growth. This suggests that the integrated capacities of cell division and photosynthesis contribute to hybrid growth vigor, which could be enhanced by temporal advances in the progression of leaf development in the hybrid relative to its parents. Altogether, this study provides evidence of expression complementation between fundamental biological pathways in hybrids and highlights the contribution of expression dominance in heterosis.
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Sugi N, Le QTN, Kobayashi M, Kusano M, Shiba H. Integrated transcript and metabolite profiling reveals coordination between biomass size and nitrogen metabolism in Arabidopsis F 1 hybrids. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:67-75. [PMID: 34177326 PMCID: PMC8215461 DOI: 10.5511/plantbiotechnology.20.1126a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 11/26/2020] [Indexed: 05/24/2023]
Abstract
Heterosis refers to the improved agronomic performance of F1 hybrids relative to their parents. Although this phenomenon is widely employed to increase biomass, yield, and stress tolerance of plants, the underlying molecular mechanisms remain unclear. To dissect the metabolic fluctuations derived from genomic and/or environmental differences contributing to the improved biomass of F1 hybrids relative to their parents, we optimized the growth condition for Arabidopsis thaliana F1 hybrids and their parents. Modest but statistically significant increase in the biomass of F1 hybrids was observed. Plant samples grown under the optimized condition were also utilized for integrated omics analysis to capture specific changes in the F1 hybrids. Metabolite profiling of F1 hybrids and parent plants was performed using gas chromatography-mass spectrometry. Among the detected 237 metabolites, 2-oxoglutarate (2-OG) and malate levels were lower and the level of aspartate was higher in the F1 hybrids than in each parent. In addition, microarray analysis revealed that there were 44 up-regulated and 12 down-regulated genes with more than 1.5-fold changes in expression levels in the F1 hybrid compared to each parent. Gene ontology (GO) analyses indicated that genes up-regulated in the F1 hybrids were largely related to organic nitrogen (N) process. Quantitative PCR verified that glutamine synthetase 2 (AtGLN2) was upregulated in the F1 hybrids, while other genes encoding enzymes in the GS-GOGAT cycle showed no significant differences between the hybrid and parent lines. These results suggested the existence of metabolic regulation that coordinates biomass and N metabolism involving AtGLN2 in F1 hybrids.
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Affiliation(s)
- Naoya Sugi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Quynh Thi Ngoc Le
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Makoto Kobayashi
- Metabolomics Research Group, RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Miyako Kusano
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572, Japan
- Metabolomics Research Group, RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroshi Shiba
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572, Japan
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Meyer RC, Weigelt-Fischer K, Knoch D, Heuermann M, Zhao Y, Altmann T. Temporal dynamics of QTL effects on vegetative growth in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:476-490. [PMID: 33080013 DOI: 10.1093/jxb/eraa490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
We assessed early vegetative growth in a population of 382 accessions of Arabidopsis thaliana using automated non-invasive high-throughput phenotyping. All accessions were imaged daily from 7 d to 18 d after sowing in three independent experiments and genotyped using the Affymetrix 250k SNP array. Projected leaf area (PLA) was derived from image analysis and used to calculate relative growth rates (RGRs). In addition, initial seed size was determined. The generated datasets were used jointly for a genome-wide association study that identified 238 marker-trait associations (MTAs) individually explaining up to 8% of the total phenotypic variation. Co-localization of MTAs occurred at 33 genomic positions. At 21 of these positions, sequential co-localization of MTAs for 2-9 consecutive days was observed. The detected MTAs for PLA and RGR could be grouped according to their temporal expression patterns, emphasizing that temporal variation of MTA action can be observed even during the vegetative growth phase, a period of continuous formation and enlargement of seemingly similar rosette leaves. This indicates that causal genes may be differentially expressed in successive periods. Analyses of the temporal dynamics of biological processes are needed to gain important insight into the molecular mechanisms of growth-controlling processes in plants.
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Affiliation(s)
- Rhonda C Meyer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Research Group Heterosis, OT Gatersleben, Corrensstraße, Seeland, Germany
| | - Kathleen Weigelt-Fischer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Research Group Heterosis, OT Gatersleben, Corrensstraße, Seeland, Germany
| | - Dominic Knoch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Research Group Heterosis, OT Gatersleben, Corrensstraße, Seeland, Germany
| | - Marc Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Research Group Heterosis, OT Gatersleben, Corrensstraße, Seeland, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Breeding Research, Research Group Quantitative Genetics, OT Gatersleben, Corrensstraße, Seeland, Germany
| | - Thomas Altmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, Research Group Heterosis, OT Gatersleben, Corrensstraße, Seeland, Germany
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12
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Phenotypic Variability and Genetic Diversity in a Pinus koraiensis Clonal Trial in Northeastern China. Genes (Basel) 2020; 11:genes11060673. [PMID: 32575537 PMCID: PMC7348814 DOI: 10.3390/genes11060673] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/10/2020] [Accepted: 06/15/2020] [Indexed: 11/16/2022] Open
Abstract
Combining phenotypic and genetic characteristics in a genetic variation study is of paramount importance to effectively orient the selection of producers’ elite trees in a seed orchard. In total, 28 phenotypic characteristics and 16 microsatellite loci were used to analyze the clonal genetic variation, to characterize the genetic diversity, and to refine the genetic classifications of 110 Pinus koraiensis clones grown in the Naozhi orchard in northeastern China. All clones were significantly different in most traits. Most of the phenotypic characteristics showed great genetic variation among clones, while the genotypic differentiation was weak between the selection sites of clones. The SSR markers showed a relatively high level of genetic diversity (Na = 4.67 ± 0.43, Ne = 2.916 ± 0.18, I = 1.15 ± 0.07, Ho = 0.69 ± 0.04, He = 0.62 ± 0.02, and mean polymorphic information content (PIC) of 0.574), with higher heterozygosity as an indication of a lower probability of inbreeding events in the orchard. Despite weak correlation coefficients between dissimilarity matrices (r(A/B), range equal to 0.022, p-value < 0.001), the genetic and phenotypic classifications congruently subdivided all the clones into three major groups. The patterns of phenotypic trait variations and genetic diversity are valuable to effectively select materials in breeding programs of P. koraiensis.
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13
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Liu PC, Peacock WJ, Wang L, Furbank R, Larkum A, Dennis ES. Leaf growth in early development is key to biomass heterosis in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2439-2450. [PMID: 31960925 PMCID: PMC7178430 DOI: 10.1093/jxb/eraa006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/14/2020] [Indexed: 05/12/2023]
Abstract
Arabidopsis thaliana hybrids have similar properties to hybrid crops, with greater biomass relative to the parents. We asked whether the greater biomass was due to increased photosynthetic efficiency per unit leaf area or to overall increased leaf area and increased total photosynthate per plant. We found that photosynthetic parameters (electron transport rate, CO2 assimilation rate, chlorophyll content, and chloroplast number) were unchanged on a leaf unit area and unit fresh weight basis between parents and hybrids, indicating that heterosis is not a result of increased photosynthetic efficiency. To investigate the possibility of increased leaf area producing more photosynthate per plant, we studied C24×Landsberg erecta (Ler) hybrids in detail. These hybrids have earlier germination and leaf growth than the parents, leading to a larger leaf area at any point in development of the plant. The developing leaves of the hybrids are significantly larger than those of the parents, with consequent greater production of photosynthate and an increased contribution to heterosis. The set of leaves contributing to heterosis changes as the plant develops; the four most recently emerged leaves make the greatest contribution. As a leaf matures, its contribution to heterosis attenuates. While photosynthesis per unit leaf area is unchanged at any stage of development in the hybrid, leaf area is greater and the amount of photosynthate per plant is increased.
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Affiliation(s)
- Pei-Chuan Liu
- Agriculture and Food, Commonwealth Scientific and Industry Research Organisation, Canberra, ACT, Australia
- Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - W James Peacock
- Agriculture and Food, Commonwealth Scientific and Industry Research Organisation, Canberra, ACT, Australia
- Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Li Wang
- Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Robert Furbank
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Anthony Larkum
- Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Elizabeth S Dennis
- Agriculture and Food, Commonwealth Scientific and Industry Research Organisation, Canberra, ACT, Australia
- Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
- Correspondence:
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14
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Botet R, Keurentjes JJB. The Role of Transcriptional Regulation in Hybrid Vigor. FRONTIERS IN PLANT SCIENCE 2020; 11:410. [PMID: 32351526 PMCID: PMC7174566 DOI: 10.3389/fpls.2020.00410] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/23/2020] [Indexed: 05/19/2023]
Abstract
The genetic basis of hybrid vigor in plants remains largely unsolved but strong evidence suggests that variation in transcriptional regulation can explain many aspects of this phenomenon. Natural variation in transcriptional regulation is highly abundant in virtually all species and thus a potential source of heterotic variability. Allele Specific Expression (ASE), which is tightly linked to parent of origin effects and modulated by complex interactions in cis and in trans, is generally considered to play a key role in explaining the differences between hybrids and parental lines. Here we discuss the recent developments in elucidating the role of transcriptional variation in a number of aspects of hybrid vigor, thereby bridging old paradigms and hypotheses with contemporary research in various species.
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Affiliation(s)
- Ramon Botet
- Laboratory of Genetics, Wageningen University & Research, Wageningen, Netherlands
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15
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Mehraj H, Kawanabe T, Shimizu M, Miyaji N, Akter A, Dennis ES, Fujimoto R. In Arabidopsis thaliana Heterosis Level Varies among Individuals in an F 1 Hybrid Population. PLANTS 2020; 9:plants9040414. [PMID: 32230994 PMCID: PMC7238264 DOI: 10.3390/plants9040414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/23/2020] [Accepted: 03/23/2020] [Indexed: 11/28/2022]
Abstract
Heterosis or hybrid vigour is a phenomenon in which hybrid progeny exhibit superior yield and biomass to parental lines and has been used to breed F1 hybrid cultivars in many crops. A similar level of heterosis in all F1 individuals is expected as they are genetically identical. However, we found variation in rosette size in individual F1 plants from a cross between C24 and Columbia-0 accessions of Arabidopsis thaliana. Big-sized F1 plants had 26.1% larger leaf area in the first and second leaves than medium-sized F1 plants at 14 days after sowing in spite of the identical genetic background. We identified differentially expressed genes between big- and medium-sized F1 plants by microarray; genes involved in the category of stress response were overrepresented. We made transgenic plants overexpressing 21 genes, which were differentially expressed between the two size classes, and some lines had increased plant size at 14 or 21 days after sowing but not at all time points during development. Change of expression levels in stress-responsive genes among individual F1 plants could generate the variation in plant size of individual F1 plants in A. thaliana.
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Affiliation(s)
- Hasan Mehraj
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan; (H.M.); (N.M.); (A.A.)
| | - Takahiro Kawanabe
- School of Agriculture, Tokai University, Toroku, Higashi-ku, Kumamoto 862-8652, Japan
- Correspondence: (T.K.); (R.F.)
| | - Motoki Shimizu
- Iwate Biotechnology Research Center, Narita, Kitakami, Iwate 024-0003, Japan;
| | - Naomi Miyaji
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan; (H.M.); (N.M.); (A.A.)
| | - Ayasha Akter
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan; (H.M.); (N.M.); (A.A.)
- Department of Horticulture, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Elizabeth S. Dennis
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia;
- University of Technology, Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan; (H.M.); (N.M.); (A.A.)
- Correspondence: (T.K.); (R.F.)
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16
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Blocked synthesis of sporopollenin and jasmonic acid leads to pollen wall defects and anther indehiscence in genic male sterile wheat line 4110S at high temperatures. Funct Integr Genomics 2019; 20:383-396. [PMID: 31729646 DOI: 10.1007/s10142-019-00722-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 10/10/2019] [Accepted: 10/16/2019] [Indexed: 12/13/2022]
Abstract
Environment-sensitive genic male sterility is a valid tool for hybrid production and hybrid breeding, but there are no previous reports of the molecular mechanism of fertility conversion. In this study, RNA-seq, phenotypic and cytological observations, and physiological indexes were applied to analyze thermo-sensitive genic male sterility line 4110S under different temperature conditions to explore the fertility transformation mechanism. In total, 3420 differentially expressed genes (DEGs) were identified comprising 2331 upregulated genes and 1089 downregulated genes. The DEGs were apparently distributed among 54 Gene Ontology functional groups. The phenylpropanoid, long-chain fatty acid, and jasmonic acid (JA) biosynthesis pathways were related to male sterility, where their downregulation blocked the synthesis of sporopollenin and JA. Phenotypic and cytological analyses showed that pollen wall defects and anther indehiscence at high temperatures induced sterility. Moreover, enzyme-linked immunosorbent assay results indicated that the abundance of JA was lower in 4110S under restrictive conditions (high temperature) than permissive conditions (low temperature). A possible regulated network of pathways associated with male sterility was suggested. These results provided insights into the molecular mechanism of fertility conversion in the thermosensitive male sterility system.
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17
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Wang L, Wu LM, Greaves IK, Dennis ES, Peacock WJ. In Arabidopsis hybrids and Hybrid Mimics, up-regulation of cell wall biogenesis is associated with the increased plant size. PLANT DIRECT 2019; 3:e00174. [PMID: 31709383 PMCID: PMC6834268 DOI: 10.1002/pld3.174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 09/10/2019] [Indexed: 05/12/2023]
Abstract
Hybrid breeding is of economic importance in agriculture for increasing yield, yet the basis of heterosis is not well understood. In Arabidopsis, crosses between different accessions produce hybrids with different levels of heterosis relative to parental phenotypes in biomass. In all hybrids, the advantage of the F1 hybrid in both phenotypic uniformity and yield gain is lost in the heterogeneous F2. F5/F6 Hybrid Mimics generated from a cross between C24 and Landsberg erecta (Ler) ecotypes demonstrated that the large plant phenotype of the F1 hybrids can be stabilized. Hybrid Mimic selection was applied to Wassilewskija (Ws)/Ler and Col/Ler hybrids. The two hybrids show different levels of heterosis. The Col/Ler hybrid generated F7 Hybrid Mimics with rosette diameter and fresh weight equivalent to the F1 hybrid at 30 DAS; F7 Ws/Ler Hybrid Mimics outperformed the F1 hybrid in both the rosette size and biomass. Transcriptome analysis revealed up-regulation of cell wall biosynthesis, and cell wall expansion genes could be a common pathway in increased size in the Arabidopsis hybrids and Hybrid Mimics. Intercross of two independent Hybrid Mimic lines can further increase the biomass gain. Our results encourage the use of Hybrid Mimics for breeding and for investigating the molecular basis of heterosis.
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Affiliation(s)
- Li Wang
- Faculty of ScienceUniversity of TechnologySydneyNSWAustralia
| | - Li Min Wu
- Agriculture and FoodCommonwealth Scientific Industrial Research OrganisationCanberraACTAustralia
| | - Ian K. Greaves
- Agriculture and FoodCommonwealth Scientific Industrial Research OrganisationCanberraACTAustralia
| | - Elizabeth S. Dennis
- Faculty of ScienceUniversity of TechnologySydneyNSWAustralia
- Agriculture and FoodCommonwealth Scientific Industrial Research OrganisationCanberraACTAustralia
| | - William James Peacock
- Faculty of ScienceUniversity of TechnologySydneyNSWAustralia
- Agriculture and FoodCommonwealth Scientific Industrial Research OrganisationCanberraACTAustralia
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18
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Le QTN, Sugi N, Furukawa J, Kobayashi M, Saito K, Kusano M, Shiba H. Association analysis of phenotypic and metabolomic changes in Arabidopsis accessions and their F 1 hybrids affected by different photoperiod and sucrose supply. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2019; 36:155-165. [PMID: 31768117 PMCID: PMC6854347 DOI: 10.5511/plantbiotechnology.19.0604a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Photoperiod and sucrose (Suc) assimilation play important roles in the regulation of plant growth and development. However, it remains unclear how natural variation of plants could contribute to metabolic changes under various growth conditions. Here, we investigated the developmental and metabolomic responses of two natural accessions of Arabidopsis thaliana, Columbia (Col) and C24, and their reciprocal F1 hybrids grown under four carbon source regimens, i.e., two different photoperiods and the presence or absence of exogenous Suc supply. The effect of exogenous Suc clearly appeared in the growth of Col and the F1 hybrid but not in C24, whereas long-day conditions had significant positive effects on the growth of all lines. Comparative metabolite profiling of Col, C24, and the F1 hybrid revealed that changes in metabolite levels, particularly sugars, were highly dependent on genotype-specific responses rather than growth conditions. The presence of Suc led to over-accumulation of seven metabolites, including four sugars, a polyamine, and two amino acids in C24, whereas no such accumulation was observed in the profiles of Col and the F1 hybrid. Thus, the comparative metabolite profiling revealed that the two parental lines of the hybrid show a distinct difference in sugar metabolism.
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Affiliation(s)
- Quynh Thi Ngoc Le
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Naoya Sugi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Jun Furukawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Makoto Kobayashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Miyako Kusano
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Hiroshi Shiba
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- E-mail: Tel & Fax: +81-29-853-6355
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19
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Singh S, Dey SS, Bhatia R, Kumar R, Sharma K, Behera TK. Heterosis and combining ability in cytoplasmic male sterile and doubled haploid based Brassica oleracea progenies and prediction of heterosis using microsatellites. PLoS One 2019; 14:e0210772. [PMID: 31425498 PMCID: PMC6699688 DOI: 10.1371/journal.pone.0210772] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 08/06/2019] [Indexed: 12/17/2022] Open
Abstract
In Brassica oleracea, heterosis is the most efficient tool providing impetus to hybrid vegetable industry. In this context, we presented the first report on identifying superior heterotic crosses for yield and commercial traits in cauliflower involving cytoplasmic male sterile (CMS) and doubled haploid (DH) lines as parents. We studied the suitability of genomic-SSRs and EST-SSRs based genetic distance (GD) and agronomic trait based phenotypic distance (PD) for predicting heterosis in F1 hybrids using CMS and DH based parents. 120 F1 hybrids derived from 20Ogura based CMS lines and 6 DH based testers were evaluated for 16 agronomic traits along with the 26 parental lines and 4 commercial standard checks. The genomic-SSRs and EST-SSRs based genetic structure analysis grouped the 26 parental lines into 4 distinct clusters. The CMS lines Ogu118-6A, Ogu33A, Ogu34-1A were good general combiner for developing early maturity hybrids. The SCA effects were significantly associated with heterosis suggesting non-additive gene effects for the heterotic response of hybrids. Less than unity value of σ2A/D coupled with σ2gca/σ2sca indicated the predominance of non-additive gene action in the expression of studied traits. The correlation analysis of genetic distance with heterosis for commercial traits suggested that microsatellites based genetic distance estimates can be helpful in heterosis prediction to some extent.
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Affiliation(s)
- Saurabh Singh
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - S. S. Dey
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
- * E-mail:
| | - Reeta Bhatia
- Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Raj Kumar
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Kanika Sharma
- ICAR-Indian Agricultural Research Institute, Regional Station, Katrain, Kullu, Himachal Pradesh, India
| | - T. K. Behera
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
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20
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Vasseur F, Fouqueau L, de Vienne D, Nidelet T, Violle C, Weigel D. Nonlinear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana. PLoS Biol 2019; 17:e3000214. [PMID: 31017902 PMCID: PMC6481775 DOI: 10.1371/journal.pbio.3000214] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 03/21/2019] [Indexed: 12/22/2022] Open
Abstract
Heterosis describes the phenotypic superiority of hybrids over their parents in traits related to agronomic performance and fitness. Understanding and predicting nonadditive inheritance such as heterosis is crucial for evolutionary biology as well as for plant and animal breeding. However, the physiological bases of heterosis remain debated. Moreover, empirical data in various species have shown that diverse genetic and molecular mechanisms are likely to explain heterosis, making it difficult to predict its emergence and amplitude from parental genotypes alone. In this study, we examined a model of physiological dominance initially proposed by Sewall Wright to explain the nonadditive inheritance of traits like metabolic fluxes at the cellular level. We evaluated Wright's model for two fitness-related traits at the whole-plant level, growth rate and fruit number, using 450 hybrids derived from crosses among natural accessions of A. thaliana. We found that allometric relationships between traits constrain phenotypic variation in a nonlinear and similar manner in hybrids and accessions. These allometric relationships behave predictably, explaining up to 75% of heterosis amplitude, while genetic distance among parents at best explains 7%. Thus, our findings are consistent with Wright's model of physiological dominance and suggest that the emergence of heterosis on plant performance is an intrinsic property of nonlinear relationships between traits. Furthermore, our study highlights the potential of a geometric approach of phenotypic relationships for predicting heterosis of major components of crop productivity and yield.
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Affiliation(s)
- François Vasseur
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier, EPHE, IRD, Montpellier, France
- Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), INRA, Montpellier SupAgro, UMR759, Montpellier, France
| | - Louise Fouqueau
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier, EPHE, IRD, Montpellier, France
| | - Dominique de Vienne
- GQE–Le Moulon, INRA, Univ Paris-Sud, CNRS, AgroParisTech, Univ Paris-Saclay, Gif-sur-Yvette, France
| | - Thibault Nidelet
- SPO, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Cyrille Violle
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier, EPHE, IRD, Montpellier, France
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
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21
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Wang L, Liu PC, Wu LM, Tan J, Peacock WJ, Dennis ES. Cotyledons contribute to plant growth and hybrid vigor in Arabidopsis. PLANTA 2019; 249:1107-1118. [PMID: 30552582 DOI: 10.1007/s00425-018-3068-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 12/10/2018] [Indexed: 05/03/2023]
Abstract
In hybrids of Arabidopsis, cotyledons influence the amount and proportion of hybrid vigor in total plant growth. We found Arabidopsis cotyledons are essential for plant growth and in some hybrids for hybrid vigor. In hybrids between C24 and Landsberg erecta (Ler), biomass vigor (heterosis) occurs in the first few days after sowing (DAS), with hybrid cotyledons being larger than those of their parents. C24xLer hybrids are ahead of their parents in activating photosynthesis and auxin pathway genes in cotyledons at 3-4 DAS. "Earliness" is also present in newly emerged C24xLer hybrid leaves. We showed cotyledon removal at 4 DAS caused significant biomass reduction in later growth in hybrids and parental lines. The biomass decrease caused by cotyledon removal can be partially rescued by exogenous sucrose or auxin with different genotypes responding to sucrose and/or auxin differently. Cotyledon removal has different effects on heterosis in different hybrids. After cotyledon removal, in C24xLer hybrids, both growth and heterosis were reduced in similar proportions, but the level of hybrid vigor was reduced as a proportion of growth in C24xColumbia (Col) and ColxLer hybrids. The removal of cotyledons at 4 DAS markedly decreased the level of growth and eliminated the heterotic phenotype of Wassilewskija (Ws)/Ler hybrids. In mutant Ws/Ler hybrids which had a reduced level of photosynthesis in the cotyledons, there was a reduction in plant growth and loss of heterosis. The variation in contribution of cotyledons to heterosis in different hybrids indicates there are multiple pathways to achieve heterotic phenotypes.
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Affiliation(s)
- Li Wang
- Faculty of Science, University of Technology, Sydney, NSW, 2007, Australia
| | - Pei-Chuan Liu
- Faculty of Science, University of Technology, Sydney, NSW, 2007, Australia
| | - Li Min Wu
- Agriculture and Food, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT, 2601, Australia
| | - Jiafu Tan
- Faculty of Science, University of Technology, Sydney, NSW, 2007, Australia
| | - W James Peacock
- Faculty of Science, University of Technology, Sydney, NSW, 2007, Australia
- Agriculture and Food, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT, 2601, Australia
| | - Elizabeth S Dennis
- Faculty of Science, University of Technology, Sydney, NSW, 2007, Australia.
- Agriculture and Food, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT, 2601, Australia.
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22
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Pullen N, Zhang N, Dobon Alonso A, Penfield S. Growth rate regulation is associated with developmental modification of source efficiency. NATURE PLANTS 2019; 5:148-152. [PMID: 30718925 DOI: 10.1038/s41477-018-0357-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 12/21/2018] [Indexed: 05/19/2023]
Abstract
Plants modulate their growth rate according to seasonal and environmental cues using a suite of growth repressors known to interact directly with cellular machinery controlling cell division and growth. Mutants lacking growth repressors show increased growth rates1,2, but the mechanism by which these plants ensure source availability for faster growth is unclear. Here, we undertake a comprehensive analysis of the fast-growth phenotype of a quintuple growth-repressor mutant, using a combination of theoretical and experimental approaches to understand the physiological basis of source-sink coordination. Our results show that, in addition to the control of tissue growth rates, growth repressors also affect tissue composition and leaf thickness, modulating the efficiency of production of new photosynthetic capacity. Modelling suggests that increases in growth efficiency underlie growth-rate differences between the wild type and spatula della growth-repressor mutant, with spatula della requiring less carbon to synthesize a comparable photosynthetic capability to the wild type, and fixing more carbon per unit mass. We conclude that through control of leaf development, growth repressors regulate both source availability and sink strength to achieve growth-rate variation without risking a carbon deficit.
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Affiliation(s)
- Nick Pullen
- Crop Genetics, John Innes Centre, Norwich, UK
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23
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Hatzig SV, Nuppenau JN, Snowdon RJ, Schießl SV. Drought stress has transgenerational effects on seeds and seedlings in winter oilseed rape (Brassica napus L.). BMC PLANT BIOLOGY 2018; 18:297. [PMID: 30470194 PMCID: PMC6251133 DOI: 10.1186/s12870-018-1531-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/15/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND Drought stress has a negative effect on both seed yield and seed quality in Brassica napus (oilseed rape, canola). Here we show that while drought impairs the maternal plant performance, it also increases the vigour of progeny of stressed maternal plants. We investigated the transgenerational influence of abiotic stress by detailed analysis of yield, seed quality, and seedling performance on a growth-related and metabolic level. Seeds of eight diverse winter oilseed rape genotypes were generated under well-watered and drought stress conditions under controlled-environment conditions in large plant containers. RESULTS We found a decrease in seed quality in seeds derived from mother plants that were exposed to drought stress. At the same time, the seeds that developed under stress conditions showed higher seedling vigour compared to non-stressed controls.This effect on seed quality and seedling vigour was found to be independent of maternal plant yield performance. CONCLUSIONS Drought stress has a positive transgenerational effect on seedling vigour. Three potential causes for stress-induced improvement of seedling vigour are discussed: (1) Heterotic effects caused by a tendency towards a higher outcrossing rate in response to stress; (2) an altered reservoir of seed storage metabolites to which the seedling resorts during early growth, and (3) inter-generational stress memory, formed by stress-induced changes in the epigenome of the seedling.
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Affiliation(s)
- Sarah V. Hatzig
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Jan-Niklas Nuppenau
- Department of Ecology, Environment and Plant Sciences, 106 91 Stockholm, Sweden
| | - Rod J. Snowdon
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Sarah V. Schießl
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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van Hulten MHA, Paulo MJ, Kruijer W, Blankestijn-De Vries H, Kemperman B, Becker FFM, Yang J, Lauss K, Stam ME, van Eeuwijk FA, Keurentjes JJB. Assessment of heterosis in two Arabidopsis thaliana common-reference mapping populations. PLoS One 2018; 13:e0205564. [PMID: 30312352 PMCID: PMC6185836 DOI: 10.1371/journal.pone.0205564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 09/27/2018] [Indexed: 12/01/2022] Open
Abstract
Hybrid vigour, or heterosis, has been of tremendous importance in agriculture for the improvement of both crops and livestock. Notwithstanding large efforts to study the phenomenon of heterosis in the last decades, the identification of common molecular mechanisms underlying hybrid vigour remain rare. Here, we conducted a systematic survey of the degree of heterosis in Arabidopsis thaliana hybrids. For this purpose, two overlapping Arabidopsis hybrid populations were generated by crossing a large collection of naturally occurring accessions to two common reference lines. In these Arabidopsis hybrid populations the range of heterosis for several developmental and yield related traits was examined, and the relationship between them was studied. The traits under study were projected leaf area at 17 days after sowing, flowering time, height of the main inflorescence, number of side branches from the main stem or from the rosette base, total seed yield, seed weight, seed size and the estimated number of seeds per plant. Predominantly positive heterosis was observed for leaf area and height of the main inflorescence, whereas mainly negative heterosis was observed for rosette branching. For the other traits both positive and negative heterosis was observed in roughly equal amounts. For flowering time and seed size only low levels of heterosis were detected. In general the observed heterosis levels were highly trait specific. Furthermore, no correlation was observed between heterosis levels and the genetic distance between the parental lines. Since all selected lines were a part of the Arabidopsis genome wide association (GWA) mapping panel, a genetic mapping approach was applied to identify possible regions harbouring genetic factors causal for heterosis, with separate calculations for additive and dominance effects. Our study showed that the genetic mechanisms underlying heterosis were highly trait specific in our hybrid populations and greatly depended on the genetic background, confirming the elusive character of heterosis.
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Affiliation(s)
| | - Maria-Joāo Paulo
- Biometris, Wageningen University and Research, Wageningen, The Netherlands
| | - Willem Kruijer
- Biometris, Wageningen University and Research, Wageningen, The Netherlands
| | | | - Brend Kemperman
- Laboratory of Genetics, Wageningen University and Research, Wageningen, the Netherlands
| | - Frank F. M. Becker
- Laboratory of Genetics, Wageningen University and Research, Wageningen, the Netherlands
| | - Jiaming Yang
- Laboratory of Genetics, Wageningen University and Research, Wageningen, the Netherlands
| | - Kathrin Lauss
- Plant Development & (Epi)Genetics, Faculty of Science, Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Amsterdam, The Netherlands
| | - Maike E. Stam
- Plant Development & (Epi)Genetics, Faculty of Science, Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Amsterdam, The Netherlands
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Hallahan BF, Fernandez-Tendero E, Fort A, Ryder P, Dupouy G, Deletre M, Curley E, Brychkova G, Schulz B, Spillane C. Hybridity has a greater effect than paternal genome dosage on heterosis in sugar beet (Beta vulgaris). BMC PLANT BIOLOGY 2018; 18:120. [PMID: 29907096 PMCID: PMC6003118 DOI: 10.1186/s12870-018-1338-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/31/2018] [Indexed: 05/30/2023]
Abstract
BACKGROUND The phenomenon of heterosis is critical to plant breeding and agricultural productivity. Heterosis occurs when F1 hybrid offspring display quantitative improvements in traits to levels that do not occur in the parents. Increasing the genome dosage (i.e. ploidy level) of F1 offspring can contribute to heterosis effects. Sugar beet (Beta vulgaris) provides a model for investigating the relative effects of genetic hybridity and genome dosage on heterosis. Sugar beet lines of different ploidy levels were crossed to generate diploid and triploid F1 offspring to investigate the effect of; (1) paternal genome dosage increase on F1 heterosis, and; (2) homozygous versus heterozygous tetraploid male parents on F1 triploid heterosis. A range of traits of agronomic and commercial importance were analyzed for the extent of heterosis effects observed in the F1 offspring. RESULTS Comparisons of parental lines to diploid (EA, EB) and triploid (EAA, EBB) F1 hybrids for total yield, root yield, and sugar yield indicated that there was no effect of paternal genome dosage increases on heterosis levels, indicating that hybridity is the main contributor to the heterosis levels observed. For all traits measured (apart from seed viability), F1 triploid hybrids derived from heterozygous tetraploid male parents displayed equivalent levels of heterosis as F1 triploid hybrids generated with homozygous tetraploid male parents, suggesting that heterosis gains in F1 triploids do not arise by simply increasing the extent of multi-locus heterozygosity in sugar beet F1 offspring. CONCLUSIONS Overall, our study indicates that; (1) increasing the paternal genome dosage does not enhance heterosis in F1 hybrids, and; (2) increasing multi-locus heterozygosity using highly heterozygous paternal genomes to generate F1 triploid hybrids does not enhance heterosis. Our findings have implications for the design of future F1 hybrid improvement programs for sugar beet.
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Affiliation(s)
- Brendan F. Hallahan
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Eva Fernandez-Tendero
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Antoine Fort
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Peter Ryder
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Gilles Dupouy
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Marc Deletre
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Edna Curley
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Galina Brychkova
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | | | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
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Liu C, Wang M, Wang L, Guo Q, Liang G. Extensive genetic and DNA methylation variation contribute to heterosis in triploid loquat hybrids. Genome 2018; 61:437-447. [PMID: 29687741 DOI: 10.1139/gen-2017-0232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We aim to overcome the unclear origin of the loquat and elucidate the heterosis mechanism of the triploid loquat. Here we investigated the genetic and epigenetic variations between the triploid plant and its parental lines using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified fragment length polymorphism (MSAP) analyses. We show that in addition to genetic variations, extensive DNA methylation variation occurred during the formation process of triploid loquat, with the triploid hybrid having increased DNA methylation compared to the parents. Furthermore, a correlation existed between genetic variation and DNA methylation remodeling, suggesting that genome instability may lead to DNA methylation variation or vice versa. Sequence analysis of the MSAP bands revealed that over 53% of them overlap with protein-coding genes, which may indicate a functional role of the differential DNA methylation in gene regulation and hence heterosis phenotypes. Consistent with this, the genetic and epigenetic alterations were associated closely to the heterosis phenotypes of triploid loquat, and this association varied for different traits. Our results suggested that the formation of triploid is accompanied by extensive genetic and DNA methylation variation, and these changes contribute to the heterosis phenotypes of the triploid loquats from the two cross lines.
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Affiliation(s)
- Chao Liu
- a Key Laboratory of Horticulture Science for Southern Mountainous Region, Ministry of Education/College of Horticulture and Landscape Architecture, Southwest University, Tiansheng Road 2, 400715, Chongqing, P.R. China
| | - Mingbo Wang
- b CSIRO Agriculture and Food, Clunies Ross Street, Canberra ACT 2061, Australia
| | - Lingli Wang
- c Technical Advice Station of Economic Crop, Yubei district, Chongqing, P.R. China
| | - Qigao Guo
- a Key Laboratory of Horticulture Science for Southern Mountainous Region, Ministry of Education/College of Horticulture and Landscape Architecture, Southwest University, Tiansheng Road 2, 400715, Chongqing, P.R. China
| | - Guolu Liang
- a Key Laboratory of Horticulture Science for Southern Mountainous Region, Ministry of Education/College of Horticulture and Landscape Architecture, Southwest University, Tiansheng Road 2, 400715, Chongqing, P.R. China
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Dissecting the Genetic Architecture of Shoot Growth in Carrot ( Daucus carota L.) Using a Diallel Mating Design. G3-GENES GENOMES GENETICS 2018; 8:411-426. [PMID: 29187419 PMCID: PMC5919754 DOI: 10.1534/g3.117.300235] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Crop establishment in carrot (Daucus carota L.) is limited by slow seedling growth and delayed canopy closure, resulting in high management costs for weed control. Varieties with improved growth habit (i.e., larger canopy and increased shoot biomass) may help mitigate weed control, but the underlying genetics of these traits in carrot is unknown. This project used a diallel mating design coupled with recent Bayesian analytical methods to determine the genetic basis of carrot shoot growth. Six diverse carrot inbred lines with variable shoot size were crossed in WI in 2014. F1 hybrids, reciprocal crosses, and parental selfs were grown in a randomized complete block design with two blocks in WI (2015) and CA (2015, 2016). Measurements included canopy height, canopy width, shoot biomass, and root biomass. General and specific combining abilities were estimated using Griffing’s Model I, which is a common analysis for plant breeding experiments. In parallel, additive, inbred, cross-specific, and maternal effects were estimated from a Bayesian mixed model, which is robust to dealing with data imbalance and outliers. Both additive and nonadditive effects significantly influenced shoot traits, with nonadditive effects playing a larger role early in the growing season, when weed control is most critical. Results suggest the presence of heritable variation and thus potential for improvement of these phenotypes in carrot. In addition, results present evidence of heterosis for root biomass, which is a major component of carrot yield.
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Lauss K, Wardenaar R, Oka R, van Hulten MHA, Guryev V, Keurentjes JJB, Stam M, Johannes F. Parental DNA Methylation States Are Associated with Heterosis in Epigenetic Hybrids. PLANT PHYSIOLOGY 2018; 176:1627-1645. [PMID: 29196538 PMCID: PMC5813580 DOI: 10.1104/pp.17.01054] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/14/2017] [Indexed: 05/18/2023]
Abstract
Despite the importance and wide exploitation of heterosis in commercial crop breeding, the molecular mechanisms behind this phenomenon are not completely understood. Recent studies have implicated changes in DNA methylation and small RNAs in hybrid performance; however, it remains unclear whether epigenetic changes are a cause or a consequence of heterosis. Here, we analyze a large panel of over 500 Arabidopsis (Arabidopsis thaliana) epigenetic hybrid plants (epiHybrids), which we derived from near-isogenic but epigenetically divergent parents. This proof-of-principle experimental system allowed us to quantify the contribution of parental methylation differences to heterosis. We measured traits such as leaf area, growth rate, flowering time, main stem branching, rosette branching, and final plant height and observed several strong positive and negative heterotic phenotypes among the epiHybrids. Using an epigenetic quantitative trait locus mapping approach, we were able to identify specific differentially methylated regions in the parental genomes that are associated with hybrid performance. Sequencing of methylomes, transcriptomes, and genomes of selected parent-epiHybrid combinations further showed that these parental differentially methylated regions most likely mediate the remodeling of methylation and transcriptional states at specific loci in the hybrids. Taken together, our data suggest that locus-specific epigenetic divergence between the parental lines can directly or indirectly trigger heterosis in Arabidopsis hybrids independent of genetic changes. These results add to a growing body of evidence that points to epigenetic factors as one of the key determinants of hybrid performance.
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Affiliation(s)
- Kathrin Lauss
- University of Amsterdam, Swammerdam Institute for Life Sciences, 1098XH Amsterdam, The Netherlands
| | - René Wardenaar
- University of Groningen, Groningen Bioinformatics Centre, Faculty of Mathematics and Natural Sciences, 9747 AG Groningen, The Netherlands
| | - Rurika Oka
- University of Amsterdam, Swammerdam Institute for Life Sciences, 1098XH Amsterdam, The Netherlands
| | - Marieke H A van Hulten
- Wageningen University and Research, Laboratory of Genetics, 6708PB Wageningen, The Netherlands
| | - Victor Guryev
- Genome Structure Aging, European Research Institute for the Biology of Aging, University Medical Centre Groningen and University of Groningen, 9713 AV Groningen, The Netherlands
| | - Joost J B Keurentjes
- Wageningen University and Research, Laboratory of Genetics, 6708PB Wageningen, The Netherlands
| | - Maike Stam
- University of Amsterdam, Swammerdam Institute for Life Sciences, 1098XH Amsterdam, The Netherlands
| | - Frank Johannes
- Population Epigenetics and Epigenomics, Department of Plant Sciences, Technical University of Munich, 85354 Freising, Germany
- Institute for Advanced Study, Technical University of Munich, 85748 Garching, Germany
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29
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Li Z, Coffey L, Garfin J, Miller ND, White MR, Spalding EP, de Leon N, Kaeppler SM, Schnable PS, Springer NM, Hirsch CN. Genotype-by-environment interactions affecting heterosis in maize. PLoS One 2018; 13:e0191321. [PMID: 29342221 PMCID: PMC5771596 DOI: 10.1371/journal.pone.0191321] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 01/03/2018] [Indexed: 12/17/2022] Open
Abstract
The environment can influence heterosis, the phenomena in which the offspring of two inbred parents exhibits phenotypic performance beyond the inbred parents for specific traits. In this study we measured 25 traits in a set of 47 maize hybrids and their inbred parents grown in 16 different environments with varying levels of average productivity. By quantifying 25 vegetative and reproductive traits across the life cycle we were able to analyze interactions between the environment and multiple distinct instances of heterosis. The magnitude and rank among hybrids for better-parent heterosis (BPH) varied for the different traits and environments. Across the traits, a higher within plot variance was observed for inbred lines compared to hybrids. However, for most traits, variance across environments was not significantly different for inbred lines compared to hybrids. Further, for many traits the correlations of BPH to hybrid performance and BPH to better parent performance were of comparable magnitude. These results indicate that inbred lines and hybrids show similar trends in environmental response and both are contributing to observed genotype-by-environment interactions for heterosis. This study highlights the degree of heterosis is not an inherent trait of a specific hybrid, but varies depending on the trait measured and the environment where that trait is measured. Studies that attempt to correlate molecular processes with heterosis are hindered by the fact that heterosis is not a consistent attribute of a specific hybrid.
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Affiliation(s)
- Zhi Li
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Lisa Coffey
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | - Jacob Garfin
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Nathan D. Miller
- Department of Botany, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Michael R. White
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Edgar P. Spalding
- Department of Botany, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Shawn M. Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Patrick S. Schnable
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | - Nathan M. Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Candice N. Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota, United States of America
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30
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Itabashi E, Osabe K, Fujimoto R, Kakizaki T. Epigenetic regulation of agronomical traits in Brassicaceae. PLANT CELL REPORTS 2018; 37:87-101. [PMID: 29058037 DOI: 10.1007/s00299-017-2223-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/05/2017] [Indexed: 05/08/2023]
Abstract
Epigenetic regulation, covalent modification of DNA and changes in histone proteins are closely linked to plant development and stress response through flexibly altering the chromatin structure to regulate gene expression. In this review, we will illustrate the importance of epigenetic influences by discussing three agriculturally important traits of Brassicaceae. (1) Vernalization, an acceleration of flowering by prolonged cold exposure regulated through epigenetic silencing of a central floral repressor, FLOWERING LOCUS C. This is associated with cold-dependent repressive histone mark accumulation, which confers competency of consequence vegetative-to-reproductive phase transition. (2) Hybrid vigor, in which an F1 hybrid shows superior performance to the parental lines. Combination of distinct epigenomes with different DNA methylation states between parental lines is important for increase in growth rate in a hybrid progeny. This is independent of siRNA-directed DNA methylation but dependent on the chromatin remodeler DDM1. (3) Self-incompatibility, a reproductive mating system to prevent self-fertilization. This is controlled by the S-locus consisting of SP11 and SRK which are responsible for self/non-self recognition. Because self-incompatibility in Brassicaceae is sporophytically controlled, there are dominance relationships between S haplotypes in the stigma and pollen. The dominance relationships in the pollen rely on de novo DNA methylation at the promoter region of a recessive allele, which is triggered by siRNA production from a flanking region of a dominant allele.
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Affiliation(s)
- Etsuko Itabashi
- Institute of Vegetable and Floriculture Science, NARO, Kusawa, Ano, Tsu, Mie, 514-2392, Japan.
| | - Kenji Osabe
- Okinawa Institute of Science and Technology Graduate University, Onna-son, Kunigami, Okinawa, 904-0495, Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501, Japan
| | - Tomohiro Kakizaki
- Institute of Vegetable and Floriculture Science, NARO, Kusawa, Ano, Tsu, Mie, 514-2392, Japan
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Abstract
While DNA sequence variation is known to be a major driver of phenotypic divergence, epigenetic variation has long been disregarded. One reason for that was the lack of suitable tools. The creation of epigenetically divergent but otherwise largely isogenic Arabidopsis populations has now alleviated some of these constraints. Epigenetic recombinant inbred line (epiRIL) populations allow for examining the effects of epigenetic variation on phenotypes. In addition, epiRILs enabled the development of epigenetic quantitative trait locus (QTLepi) mapping, an approach to identify causal epigenetic factors. Here, we describe the successive steps of QTLepi mapping in a broad sense, from the creation of epigenetically divergent populations to the identification of causal genes underlying particular phenotypes in Arabidopsis.
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Affiliation(s)
- Kathrin Lauss
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
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Inheritance patterns in metabolism and growth in diallel crosses of Arabidopsis thaliana from a single growth habitat. Heredity (Edinb) 2017; 120:463-473. [PMID: 29234160 DOI: 10.1038/s41437-017-0030-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/09/2017] [Accepted: 10/30/2017] [Indexed: 12/25/2022] Open
Abstract
Metabolism is a key determinant of plant growth and modulates plant adaptive responses. Increased metabolic variation due to heterozygosity may be beneficial for highly homozygous plants if their progeny is to respond to sudden changes in the habitat. Here, we investigate the extent to which heterozygosity contributes to the variation in metabolism and size of hybrids of Arabidopsis thaliana whose parents are from a single growth habitat. We created full diallel crosses among seven parents, originating from Southern Germany, and analysed the inheritance patterns in primary and secondary metabolism as well as in rosette size in situ. In comparison to primary metabolites, compounds from secondary metabolism were more variable and showed more pronounced non-additive inheritance patterns which could be attributed to epistasis. In addition, we showed that glucosinolates, among other secondary metabolites, were positively correlated with a proxy for plant size. Therefore, our study demonstrates that heterozygosity in local A. thaliana population generates metabolic variation and may impact several tasks directly linked to metabolism.
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Zhu W, Hu B, Becker C, Doğan ES, Berendzen KW, Weigel D, Liu C. Altered chromatin compaction and histone methylation drive non-additive gene expression in an interspecific Arabidopsis hybrid. Genome Biol 2017; 18:157. [PMID: 28830561 PMCID: PMC5568265 DOI: 10.1186/s13059-017-1281-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 07/18/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The merging of two diverged genomes can result in hybrid offspring that phenotypically differ greatly from both parents. In plants, interspecific hybridization plays important roles in evolution and speciation. In addition, many agricultural and horticultural species are derived from interspecific hybridization. However, the detailed mechanisms responsible for non-additive phenotypic novelty in hybrids remain elusive. RESULTS In an interspecific hybrid between Arabidopsis thaliana and A. lyrata, the vast majority of genes that become upregulated or downregulated relative to the parents originate from A. thaliana. Among all differentially expressed A. thaliana genes, the majority is downregulated in the hybrid. To understand why parental origin affects gene expression in this system, we compare chromatin packing patterns and epigenomic landscapes in the hybrid and parents. We find that the chromatin of A. thaliana, but not that of A. lyrata, becomes more compact in the hybrid. Parental patterns of DNA methylation and H3K27me3 deposition are mostly unaltered in the hybrid, with the exception of higher CHH DNA methylation in transposon-rich regions. However, A. thaliana genes enriched for the H3K27me3 mark are particularly likely to differ in expression between the hybrid and parent. CONCLUSIONS It has long been suspected that genome-scale properties cause the differential responses of genes from one or the other parent to hybridization. Our work links global chromatin compactness and H3K27me3 histone modification to global differences in gene expression in an interspecific Arabidopsis hybrid.
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Affiliation(s)
- Wangsheng Zhu
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Bo Hu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, 72076, Germany
| | - Claude Becker
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany.,Present Address: Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, A-1030, Vienna, Austria
| | - Ezgi Süheyla Doğan
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, 72076, Germany
| | - Kenneth Wayne Berendzen
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, 72076, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany.
| | - Chang Liu
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany. .,Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, 72076, Germany.
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Zhang C, Lin C, Fu F, Zhong X, Peng B, Yan H, Zhang J, Zhang W, Wang P, Ding X, Zhang W, Zhao L. Comparative transcriptome analysis of flower heterosis in two soybean F1 hybrids by RNA-seq. PLoS One 2017; 12:e0181061. [PMID: 28708857 PMCID: PMC5510844 DOI: 10.1371/journal.pone.0181061] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 06/26/2017] [Indexed: 01/05/2023] Open
Abstract
Heterosis has been widely exploited as an approach to enhance crop traits during breeding. However, its underlying molecular genetic mechanisms remain unclear. Recent advances in RNA sequencing technology (RNA-seq) have provided an opportunity to conduct transcriptome profiling for heterosis studies. We used RNA-seq to analyze the flower transcriptomes of two F1 hybrid soybeans (HYBSOY-1 and HYBSOY-5) and their parents. More than 385 million high-quality reads were generated and aligned against the soybean reference genome. A total of 681 and 899 genes were identified as being differentially expressed between HYBSOY-1 and HYBSOY-5 and their parents, respectively. These differentially expressed genes (DEGs) were categorized into four major expression categories with 12 expression patterns. Furthermore, gene ontology (GO) term analysis showed that the DEGs were enriched in the categories metabolic process and catalytic activity, while Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis found that metabolic pathway and biosynthesis of secondary metabolites were enriched in the two F1 hybrids. Comparing the DEGs of the two F1 hybrids by GO term and KEGG pathway analyses identified 26 common DEGs that showed transgressive up-regulation, and which could be considered potential candidate genes for heterosis in soybean F1 hybrids. This identification of an extensive transcriptome dataset gives a comprehensive overview of the flower transcriptomes in two F1 hybrids, and provides useful information for soybean hybrid breeding. These findings lay the foundation for future studies on molecular mechanisms underlying soybean heterosis.
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Affiliation(s)
- Chunbao Zhang
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Chunjing Lin
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Fuyou Fu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, United States of America
| | - Xiaofang Zhong
- Agro-Biotechnology Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Bao Peng
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Hao Yan
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Jingyong Zhang
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Weilong Zhang
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Pengnian Wang
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Xiaoyang Ding
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Wei Zhang
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Limei Zhao
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
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van Tol N, Rolloos M, Pinas JE, Henkel CV, Augustijn D, Hooykaas PJJ, van der Zaal BJ. Enhancement of Arabidopsis growth characteristics using genome interrogation with artificial transcription factors. PLoS One 2017; 12:e0174236. [PMID: 28358915 PMCID: PMC5373528 DOI: 10.1371/journal.pone.0174236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/06/2017] [Indexed: 11/18/2022] Open
Abstract
The rapidly growing world population has a greatly increasing demand for plant biomass, thus creating a great interest in the development of methods to enhance the growth and biomass accumulation of crop species. In this study, we used zinc finger artificial transcription factor (ZF-ATF)-mediated genome interrogation to manipulate the growth characteristics and biomass of Arabidopsis plants. We describe the construction of two collections of Arabidopsis lines expressing fusions of three zinc fingers (3F) to the transcriptional repressor motif EAR (3F-EAR) or the transcriptional activator VP16 (3F-VP16), and the characterization of their growth characteristics. In total, six different 3F-ATF lines with a consistent increase in rosette surface area (RSA) of up to 55% were isolated. For two lines we demonstrated that 3F-ATF constructs function as dominant in trans acting causative agents for an increase in RSA and biomass, and for five larger plant lines we have investigated 3F-ATF induced transcriptomic changes. Our results indicate that genome interrogation can be used as a powerful tool for the manipulation of plant growth and biomass and that it might supply novel cues for the discovery of genes and pathways involved in these properties.
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Affiliation(s)
- Niels van Tol
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
- BioSolar Cells, Wageningen, The Netherlands
| | - Martijn Rolloos
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Johan E. Pinas
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Christiaan V. Henkel
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Dieuwertje Augustijn
- Leiden Institute of Chemistry, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Paul J. J. Hooykaas
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Bert J. van der Zaal
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
- * E-mail:
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Makabe S, Yamori W, Kong K, Niimi H, Nakamura I. Expression of rice 45S rRNA promotes cell proliferation, leading to enhancement of growth in transgenic tobacco. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2017; 34:29-38. [PMID: 31275005 PMCID: PMC6543702 DOI: 10.5511/plantbiotechnology.17.0216a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 02/16/2017] [Indexed: 06/09/2023]
Abstract
An increase in plant biomass production is desired to reduce emission of carbon dioxide emissions and arrest global climate change because it will provide a more source of energy production than fossil fuels. Recently, we found that forced expression of the rice 45S rRNA gene increased aboveground growth by ca. 2-fold in the transgenic Arabidopsis plants. Here, we created transgenic tobacco plants harboring the rice 45S rRNA driven by the maize ubiquitin promoter (UbiP::Os45SrRNA) or cauliflower mosaic virus 35S promoter (35SP::Os45SrRNA). In 35SP::Os45SrRNA and UbiP::Os45SrRNA transgenic tobacco plants, the leaf length and size were increased compared with control plants, leading to an increase of aboveground growth (dry weight) up to 2-fold at the early stage of seedling development. Conversely, leaf physiological traits, such as photosynthetic capacity, stomatal characteristics, and chlorophylls and RuBisCO protein contents, were similar between the transgenic and control plants. Flow cytometry analysis indicated that the transgenic plants had enhanced cell-proliferation especially in seedling root and leaf primordia. Microarray analysis revealed that genes encoding transcription factors, such as GIGANTEA-like, were more than 2-fold up-regulated in the transgenic plants. Although the mechanism underlying the increased growth has yet to be elucidated, this strategy could be used to increase biomass production in cereals, vegetables, and bio-energy plants.
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Affiliation(s)
- So Makabe
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba 271-8510, Japan
| | - Wataru Yamori
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kynet Kong
- Cambodian Agricultural Research and Development Institute, Phnom Penh, Cambodia
| | - Hiroyuki Niimi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba 271-8510, Japan
| | - Ikuo Nakamura
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba 271-8510, Japan
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Zhu A, Greaves IK, Dennis ES, Peacock WJ. Genome-wide analyses of four major histone modifications in Arabidopsis hybrids at the germinating seed stage. BMC Genomics 2017; 18:137. [PMID: 28173754 PMCID: PMC5297046 DOI: 10.1186/s12864-017-3542-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/02/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hybrid vigour (heterosis) has been used for decades in cropping agriculture, especially in the production of maize and rice, because hybrid varieties exceed their parents in plant biomass and seed yield. The molecular basis of hybrid vigour is not fully understood. Previous studies have suggested that epigenetic systems could play a role in heterosis. RESULTS In this project, we investigated genome-wide patterns of four histone modifications in Arabidopsis hybrids in germinating seeds. We found that although hybrids have similar histone modification patterns to the parents in most regions of the genome, they have altered patterns at specific loci. A small subset of genes show changes in histone modifications in the hybrids that correlate with changes in gene expression. Our results also show that genome-wide patterns of histone modifications in geminating seeds parallel those at later developmental stages of seedlings. CONCLUSION Ler/C24 hybrids showed similar genome-wide patterns of histone modifications as the parents at an early germination stage. However, a small subset of genes, such as FLC, showed correlated changes in histone modification and in gene expression in the hybrids. The altered patterns of histone modifications for those genes in hybrids could be related to some heterotic traits in Arabidopsis, such as flowering time, and could play a role in hybrid vigour establishment.
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Affiliation(s)
- Anyu Zhu
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, 2601, Australia.,Faculty of Science, University of Technology, Sydney, New South Wales, 2007, Australia
| | - Ian K Greaves
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, 2601, Australia
| | - Elizabeth S Dennis
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, 2601, Australia.,Faculty of Science, University of Technology, Sydney, New South Wales, 2007, Australia
| | - W James Peacock
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, 2601, Australia. .,Faculty of Science, University of Technology, Sydney, New South Wales, 2007, Australia.
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Makabe S, Motohashi R, Nakamura I. Growth increase of Arabidopsis by forced expression of rice 45S rRNA gene. PLANT CELL REPORTS 2017; 36:243-254. [PMID: 27864606 DOI: 10.1007/s00299-016-2075-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 11/08/2016] [Indexed: 06/06/2023]
Abstract
Forced expression of rice 45S rRNA gene conferred ca. 2-fold increase of above-ground growth in transgenic Arabidopsis . This growth increase was probably brought by cell proliferation, not by cell enlargement. Recent increase in carbon dioxide emissions is causing global climate change. The use of plant biomass as alternative energy source is one way to reduce these emissions. Therefore, reinforcement of plant biomass production is an urgent key issue to overcome both depletion of fossil energies and emission of carbon dioxide. Here, we created transgenic Arabidopsis with a 2-fold increase in above-ground growth by forced expression of the rice 45S rRNA gene using the maize ubiquitin promoter. Although the size of guard cells and ploidy of leaf-cells were similar between transgenic and control plants, numbers of stomata and pavement cells were much increased in the transgenic leaf. This data suggested that cell number, not cell expansion, was responsible for the growth increase, which might be brought by the forced expression of exogenous and full-length 45S rRNA gene. The expression level of rice 45S rRNA transcripts was very low, possibly triggering unknown machinery to enhance cell proliferation. Although microarray analysis showed enhanced expression of ethylene-responsive transcription factors, these factors might respond to ethylene induced by abiotic/biotic stresses or genomic incompatibility, which might be involved in the expression of species-specific internal transcribed spacer (ITS) sequences within rice 45S rRNA transcripts. Further analysis of the mechanism underlying the growth increase will contribute to understanding the regulation of the cell proliferation and the mechanism of hybrid vigor.
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Affiliation(s)
- So Makabe
- Plant Cell Technology Laboratory, Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Reiko Motohashi
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Shizuoka, Shizuoka, 422-8529, Japan
| | - Ikuo Nakamura
- Plant Cell Technology Laboratory, Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan.
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Zhu A, Greaves IK, Liu PC, Wu L, Dennis ES, Peacock WJ. Early changes of gene activity in developing seedlings of Arabidopsis hybrids relative to parents may contribute to hybrid vigour. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:597-607. [PMID: 27460790 DOI: 10.1111/tpj.13285] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/19/2016] [Accepted: 07/21/2016] [Indexed: 05/15/2023]
Abstract
Hybrid vigour (heterosis) has been used for decades in crop industries, especially in the production of maize and rice. Hybrid varieties usually exceed their parents in plant biomass and seed yield. But the molecular basis of hybrid vigour is not fully understood. In this project, we studied heterosis at early stages of seedling development in Arabidopsis hybrids derived from crossing Ler and C24 accessions. We found that early heterosis is associated with non-additive gene expression that resulted from earlier changes in gene expression in the hybrids relative to the parents. The non-additively expressed genes are involved in metabolic pathways, including photosynthesis, critical for plant growth. The early increased expression levels of genes involved in energy production in hybrids is associated with heterosis in the young seedlings that could be essential for biomass heterosis at later developmental stages of the plant.
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Affiliation(s)
- Anyu Zhu
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, 2600, Australia
- University of Technology, Sydney, NSW, 2007, Australia
| | - Ian K Greaves
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, 2600, Australia
| | - Pei-Chuan Liu
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, 2600, Australia
- University of Technology, Sydney, NSW, 2007, Australia
| | - Limin Wu
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, 2600, Australia
| | - Elizabeth S Dennis
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, 2600, Australia
- University of Technology, Sydney, NSW, 2007, Australia
| | - W James Peacock
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, 2600, Australia
- University of Technology, Sydney, NSW, 2007, Australia
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Genetic architecture of nonadditive inheritance in Arabidopsis thaliana hybrids. Proc Natl Acad Sci U S A 2016; 113:E7317-E7326. [PMID: 27803326 DOI: 10.1073/pnas.1615268113] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The ubiquity of nonparental hybrid phenotypes, such as hybrid vigor and hybrid inferiority, has interested biologists for over a century and is of considerable agricultural importance. Although examples of both phenomena have been subject to intense investigation, no general model for the molecular basis of nonadditive genetic variance has emerged, and prediction of hybrid phenotypes from parental information continues to be a challenge. Here we explore the genetics of hybrid phenotype in 435 Arabidopsis thaliana individuals derived from intercrosses of 30 parents in a half diallel mating scheme. We find that nonadditive genetic effects are a major component of genetic variation in this population and that the genetic basis of hybrid phenotype can be mapped using genome-wide association (GWA) techniques. Significant loci together can explain as much as 20% of phenotypic variation in the surveyed population and include examples that have both classical dominant and overdominant effects. One candidate region inherited dominantly in the half diallel contains the gene for the MADS-box transcription factor AGAMOUS-LIKE 50 (AGL50), which we show directly to alter flowering time in the predicted manner. Our study not only illustrates the promise of GWA approaches to dissect the genetic architecture underpinning hybrid performance but also demonstrates the contribution of classical dominance to genetic variance.
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Kawanabe T, Ishikura S, Miyaji N, Sasaki T, Wu LM, Itabashi E, Takada S, Shimizu M, Takasaki-Yasuda T, Osabe K, Peacock WJ, Dennis ES, Fujimoto R. Role of DNA methylation in hybrid vigor in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2016; 113:E6704-E6711. [PMID: 27791039 PMCID: PMC5087013 DOI: 10.1073/pnas.1613372113] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Hybrid vigor or heterosis refers to the superior performance of F1 hybrid plants over their parents. Heterosis is particularly important in the production systems of major crops. Recent studies have suggested that epigenetic regulation such as DNA methylation is involved in heterosis, but the molecular mechanism of heterosis is still unclear. To address the epigenetic contribution to heterosis in Arabidopsis thaliana, we used mutant genes that have roles in DNA methylation. Hybrids between C24 and Columbia-0 (Col) without RNA polymerase IV (Pol IV) or methyltransferase I (MET1) function did not reduce the level of biomass heterosis (as evaluated by rosette diameter). Hybrids with a mutation in decrease in dna methylation 1 (ddm1) showed a decreased heterosis level. Vegetative heterosis in the ddm1 mutant hybrid was reduced but not eliminated; a complete reduction could result if there was a change in methylation at all loci critical for generating the level of heterosis, whereas if only a proportion of the loci have methylation changes there may only be a partial reduction in heterosis.
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Affiliation(s)
- Takahiro Kawanabe
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Sonoko Ishikura
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Naomi Miyaji
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Taku Sasaki
- Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Li Min Wu
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT 2601, Australia
| | - Etsuko Itabashi
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Satoko Takada
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Motoki Shimizu
- Iwate Biotechnology Research Center, 22-174-4, Narita, Kitakami, Iwate, 024-0003, Japan
| | - Takeshi Takasaki-Yasuda
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Kenji Osabe
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
| | - W James Peacock
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT 2601, Australia; University of Technology, Sydney, Broadway, NSW 2007, Australia;
| | - Elizabeth S Dennis
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT 2601, Australia; University of Technology, Sydney, Broadway, NSW 2007, Australia
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan; Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, Saitama, 332-0012 Japan
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Methylation interactions in Arabidopsis hybrids require RNA-directed DNA methylation and are influenced by genetic variation. Proc Natl Acad Sci U S A 2016; 113:E4248-56. [PMID: 27382183 DOI: 10.1073/pnas.1607851113] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
DNA methylation is a conserved epigenetic mark in plants and many animals. How parental alleles interact in progeny to influence the epigenome is poorly understood. We analyzed the DNA methylomes of Arabidopsis Col and C24 ecotypes, and their hybrid progeny. Hybrids displayed nonadditive DNA methylation levels, termed methylation interactions, throughout the genome. Approximately 2,500 methylation interactions occurred at regions where parental DNA methylation levels are similar, whereas almost 1,000 were at differentially methylated regions in parents. Methylation interactions were characterized by an abundance of 24-nt small interfering RNAs. Furthermore, dysfunction of the RNA-directed DNA methylation pathway abolished methylation interactions but did not affect the increased biomass observed in hybrid progeny. Methylation interactions correlated with altered genetic variation within the genome, suggesting that they may play a role in genome evolution.
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Analysis of mating system and genetic structure in the endangered, amphicarpic plant, Lewton’s polygala (Polygala lewtonii). CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0860-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Tazoe Y, Sazuka T, Yamaguchi M, Saito C, Ikeuchi M, Kanno K, Kojima S, Hirano K, Kitano H, Kasuga S, Endo T, Fukuda H, Makino A. Growth Properties and Biomass Production in the Hybrid C4 Crop Sorghum bicolor. PLANT & CELL PHYSIOLOGY 2016; 57:944-952. [PMID: 26508521 DOI: 10.1093/pcp/pcv158] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 10/19/2015] [Indexed: 06/05/2023]
Abstract
Hybrid vigor (heterosis) has been used as a breeding technique for crop improvement to achieve enhanced biomass production, but the physiological mechanisms underlying heterosis remain poorly understood. In this study, to find a clue to the enhancement of biomass production by heterosis, we systemically evaluated the effect of heterosis on the growth rate and photosynthetic efficiency in sorghum hybrid [Sorghum bicolor (L.) Moench cv. Tentaka] and its parental lines (restorer line and maintainer line). The final biomass of Tentaka was 10-14 times greater than that of the parental lines grown in an experimental field, but the relative growth rate during the vegetative growth stage did not differ. Tentaka exhibited a relatively enlarged leaf area with lower leaf nitrogen content per leaf area (Narea). When the plants were grown hydroponically at different N levels, daily CO2 assimilation per leaf area (A) increased with Narea, and the ratio of A to Narea (N-use efficiency) was higher in the plants grown at low N levels but not different between Tentaka and the parental lines. The relationships between the CO2 assimilation rate, the amounts of photosynthetic enzymes, including ribulose-1,5-bisphosphate carboxylase/oxygenase, phosphoenolpyruvate carboxylase and pyruvate phosphate dikinase, Chl and Narea did not differ between Tentaka and the parental lines. Thus, Tentaka tended to exhibit enlargement of leaf area with lower N content, leading to a higher N-use efficiency for CO2 assimilation, but the photosynthetic properties did not differ. The greater biomass in Tentaka was mainly due to the prolonged vegetative growth period.
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Affiliation(s)
- Youshi Tazoe
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Sendai, 981-8555 Japan CREST, JST, Gobancho, Chiyoda-ku, Tokyo, 102-0076 Japan
| | - Takashi Sazuka
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601 Japan
| | - Miki Yamaguchi
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601 Japan
| | - Chieko Saito
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Masahiro Ikeuchi
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan
| | - Keiichi Kanno
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Sendai, 981-8555 Japan
| | - Soichi Kojima
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Sendai, 981-8555 Japan
| | - Ko Hirano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601 Japan
| | - Hideki Kitano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601 Japan
| | - Shigemitsu Kasuga
- Faculty of Agriculture, Education and Research Center of Alpine Field Science, Shinshu University, Nagano, 396-0111 Japan
| | - Tsuyoshi Endo
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501 Japan
| | - Hiroo Fukuda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Amane Makino
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Sendai, 981-8555 Japan CREST, JST, Gobancho, Chiyoda-ku, Tokyo, 102-0076 Japan
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Kawamura K, Kawanabe T, Shimizu M, Nagano AJ, Saeki N, Okazaki K, Kaji M, Dennis ES, Osabe K, Fujimoto R. Genetic distance of inbred lines of Chinese cabbage and its relationship to heterosis. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.plgene.2015.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Saeki N, Kawanabe T, Ying H, Shimizu M, Kojima M, Abe H, Okazaki K, Kaji M, Taylor JM, Sakakibara H, Peacock WJ, Dennis ES, Fujimoto R. Molecular and cellular characteristics of hybrid vigour in a commercial hybrid of Chinese cabbage. BMC PLANT BIOLOGY 2016; 16:45. [PMID: 26882898 PMCID: PMC4756405 DOI: 10.1186/s12870-016-0734-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 02/09/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Heterosis or hybrid vigour is a phenomenon in which hybrid progeny exhibit superior performance compared to their parental inbred lines. Most commercial Chinese cabbage cultivars are F1 hybrids and their level of hybrid vigour is of critical importance and is a key selection criterion in the breeding system. RESULTS We have characterized the heterotic phenotype of one F1 hybrid cultivar of Chinese cabbage and its parental lines from early- to late-developmental stages of the plants. Hybrid cotyledons are larger than those of the parents at 4 days after sowing and biomass in the hybrid, determined by the fresh weight of leaves, is greater than that of the larger parent line by approximately 20% at 14 days after sowing. The final yield of the hybrid harvested at 63 days after sowing is 25% greater than the yield of the better parent. The larger leaves of the hybrid are a consequence of increased cell size and number of the photosynthetic palisade mesophyll cells and other leaf cells. The accumulation of plant hormones in the F1 was within the range of the parental levels at both 2 and 10 days after sowing. Two days after sowing, the expression levels of chloroplast-targeted genes in the cotyledon cells were upregulated in the F1 hybrid relative to their mid parent values. Shutdown of chlorophyll biosynthesis in the cotyledon by norflurazon prevented the increased leaf area in the F1 hybrid. CONCLUSIONS In the cotyledons of F1 hybrids, chloroplast-targeted genes were upregulated at 2 days after sowing. The increased activity levels of this group of genes suggested that their differential transcription levels could be important for establishing early heterosis but the increased transcription levels were transient. Inhibition of the photosynthetic process in the cotyledon reduced heterosis in later seedling stages. These observations suggest early developmental events in the germinating seedling of the hybrid may be important for later developmental vigour and yield advantage.
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Affiliation(s)
- Natsumi Saeki
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan.
| | - Takahiro Kawanabe
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501, Japan.
| | - Hua Ying
- CSIRO Agriculture, Canberra, ACT 2601, Australia.
| | - Motoki Shimizu
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan.
| | - Mikiko Kojima
- Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, 230-0045, Japan.
| | - Hiroshi Abe
- Experimental Plant Division, RIKEN BioResource Center, Tsukuba, 305-0074, Japan.
| | - Keiichi Okazaki
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan.
| | - Makoto Kaji
- Watanabe Seed Co., Ltd, Machiyashiki, Misato-cho, Miyagi, 987-0003, Japan.
| | | | - Hitoshi Sakakibara
- Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, 230-0045, Japan.
| | - W James Peacock
- CSIRO Agriculture, Canberra, ACT 2601, Australia.
- University of Technology, Broadway, Sydney, PO Box 123, NSW, 2007, Australia.
| | - Elizabeth S Dennis
- CSIRO Agriculture, Canberra, ACT 2601, Australia.
- University of Technology, Broadway, Sydney, PO Box 123, NSW, 2007, Australia.
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501, Japan.
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), Saitama, 332-0012, Japan.
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Del Toro-De León G, Lepe-Soltero D, Gillmor CS. Zygotic genome activation in isogenic and hybrid plant embryos. CURRENT OPINION IN PLANT BIOLOGY 2016; 29:148-53. [PMID: 26802806 DOI: 10.1016/j.pbi.2015.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/11/2015] [Accepted: 12/18/2015] [Indexed: 05/24/2023]
Abstract
Zygotic genome activation (ZGA) is the onset of large-scale transcription that occurs after fertilization. In animal embryos, ZGA occurs after a period of transcriptional quiescence that varies between species. In plants, the timing of ZGA may also vary between species, and may or may not occur in a parent-of-origin dependent manner: some studies have shown a maternal bias in mRNA transcripts and gene activity in early embryogenesis, while other experiments have found the contribution of maternal and paternal genomes to be equal. In order to differentiate between maternal and paternal mRNAs, RNA sequencing studies of ZGA in plants have used embryos hybrid for polymorphic accessions. A recent genetic assay in Arabidopsis demonstrated significant variation in paternal allele activity between some hybrid combinations and isogenic embryos, as well as between different hybrid combinations, suggesting a possible source for conflicting results obtained by various experiments on paternal genome activation. We review recent literature on paternal genome activation studies in the zygote in both isogenic and hybrid embryos, and discuss possible explanations for the effects of hybridization on gene expression in early embryogenesis in plants.
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Affiliation(s)
- Gerardo Del Toro-De León
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
| | - Daniel Lepe-Soltero
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México
| | - C Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, México.
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48
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Zhu D, Zhou G, Xu C, Zhang Q. Genetic Components of Heterosis for Seedling Traits in an Elite Rice Hybrid Analyzed Using an Immortalized F2 Population. J Genet Genomics 2016; 43:87-97. [PMID: 26924691 DOI: 10.1016/j.jgg.2016.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 01/02/2016] [Accepted: 01/08/2016] [Indexed: 11/18/2022]
Abstract
Utilization of heterosis has greatly contributed to rice productivity in China and many Asian countries. Superior hybrids usually show heterosis at two stages: canopy development at vegetative stage and panicle development at reproductive stage resulting in heterosis in yield. Although the genetic basis of heterosis in rice has been extensively investigated, all the previous studies focused on yield traits at maturity stage. In this study, we analyzed the genetic basis of heterosis at seedling stage making use of an "immortalized F2" population composed of 105 hybrids produced by intercrossing recombinant inbred lines (RILs) from a cross between Zhenshan 97 and Minghui 63, the parents of Shanyou 63, which is an elite hybrid widely grown in China. Eight seedling traits, seedling height, tiller number, leaf number, root number, maximum root length, root dry weight, shoot dry weight and total dry weight, were investigated using hydroponic culture. We analyzed single-locus and digenic genetic effects at the whole genome level using an ultrahigh-density SNP bin map obtained by population re-sequencing. The analysis revealed large numbers of heterotic effects for seedling traits including dominance, overdominance and digenic dominance (epistasis) in both positive and negative directions. Overdominance effects were prevalent for all the traits, and digenic dominance effects also accounted for a large portion of the genetic effects. The results suggested that cumulative small advantages of the single-locus effects and two-locus interactions, most of which could not be detected statistically, could explain the genetic basis of seedling heterosis of the F1 hybrid.
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Affiliation(s)
- Dan Zhu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Gang Zhou
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Caiguo Xu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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49
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Fort A, Ryder P, McKeown PC, Wijnen C, Aarts MG, Sulpice R, Spillane C. Disaggregating polyploidy, parental genome dosage and hybridity contributions to heterosis in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2016; 209:590-9. [PMID: 26395035 DOI: 10.1111/nph.13650] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/05/2015] [Indexed: 05/10/2023]
Abstract
Heterosis is the phenomenon whereby hybrid offspring of genetically divergent parents display superior characteristics compared with their parents. Although hybridity and polyploidy can influence heterosis in hybrid plants, the differential contributions of hybridity vs polyploidy to heterosis effects remain unknown. To address this question, we investigated heterosis effects on rosette size and growth rate of 88 distinct F1 lines of Arabidopsis thaliana consisting of diploids, reciprocal triploids and tetraploids in isogenic and hybrid genetic contexts. 'Heterosis without hybridity' effects on plant size can be generated in genetically isogenic F1 triploid plants. Paternal genome excess F1 triploids display positive heterosis, whereas maternal genome excess F1 s display negative heterosis effects. Paternal genome dosage increases plant size in F1 hybrid triploid plants by, on average, 57% (in contrast with 35% increase displayed by F1 diploid hybrids). Such effects probably derive from differential seed size, as the growth rate of triploids was similar to diploids. Tetraploid plants display a lower growth rate compared with other ploidies, whereas hybrids display increased early stage growth rate. By disaggregating heterosis effects caused by hybridity vs genome dosage, we advance our understanding of heterosis in plants and facilitate novel paternal genome dosage-based strategies to enhance heterosis effects in crop plants.
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Affiliation(s)
- Antoine Fort
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, Áras de Brún, University Road, Galway, Ireland
| | - Peter Ryder
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, Áras de Brún, University Road, Galway, Ireland
| | - Peter C McKeown
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, Áras de Brún, University Road, Galway, Ireland
| | - Cris Wijnen
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, Building 107, 6708, PB Wageningen, the Netherlands
| | - Mark G Aarts
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, Building 107, 6708, PB Wageningen, the Netherlands
| | - Ronan Sulpice
- Systems Biology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, Áras de Brún, University Road, Galway, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, Áras de Brún, University Road, Galway, Ireland
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50
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Groszmann M, Gonzalez-Bayon R, Lyons RL, Greaves IK, Kazan K, Peacock WJ, Dennis ES. Hormone-regulated defense and stress response networks contribute to heterosis in Arabidopsis F1 hybrids. Proc Natl Acad Sci U S A 2015; 112:E6397-406. [PMID: 26527659 PMCID: PMC4655576 DOI: 10.1073/pnas.1519926112] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plant hybrids are extensively used in agriculture to deliver increases in yields, yet the molecular basis of their superior performance (heterosis) is not well understood. Our transcriptome analysis of a number of Arabidopsis F1 hybrids identified changes to defense and stress response gene expression consistent with a reduction in basal defense levels. Given the reported antagonism between plant immunity and growth, we suggest that these altered patterns of expression contribute to the greater growth of the hybrids. The altered patterns of expression in the hybrids indicate decreases to the salicylic acid (SA) biosynthesis pathway and increases in the auxin [indole-3-acetic acid (IAA)] biosynthesis pathway. SA and IAA are hormones known to control stress and defense responses as well as plant growth. We found that IAA-targeted gene activity is frequently increased in hybrids, correlating with a common heterotic phenotype of greater leaf cell numbers. Reduced SA concentration and target gene responses occur in the larger hybrids and promote increased leaf cell size. We demonstrated the importance of SA action to the hybrid phenotype by manipulating endogenous SA concentrations. Increasing SA diminished heterosis in SA-reduced hybrids, whereas decreasing SA promoted growth in some hybrids and phenocopied aspects of hybrid vigor in parental lines. Pseudomonas syringae infection of hybrids demonstrated that the reductions in basal defense gene activity in these hybrids does not necessarily compromise their ability to mount a defense response comparable to the parents.
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Affiliation(s)
| | | | - Rebecca L Lyons
- CSIRO Agriculture, Queensland Bioscience Precinct, Brisbane, QLD 4069, Australia
| | | | - Kemal Kazan
- CSIRO Agriculture, Queensland Bioscience Precinct, Brisbane, QLD 4069, Australia
| | - W James Peacock
- CSIRO Agriculture, Canberra, ACT 2601, Australia; University of Technology, Sydney, NSW 2007, Australia
| | - Elizabeth S Dennis
- CSIRO Agriculture, Canberra, ACT 2601, Australia; University of Technology, Sydney, NSW 2007, Australia
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