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Almeida-Silva F, Prost-Boxoen L, Van de Peer Y. hybridexpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors. THE NEW PHYTOLOGIST 2024; 243:811-819. [PMID: 38798271 PMCID: PMC7616114 DOI: 10.1111/nph.19862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024]
Abstract
Hybridization, the process of crossing individuals from diverse genetic backgrounds, plays a pivotal role in evolution, biological invasiveness, and crop breeding. At the transcriptional level, hybridization often leads to complex nonadditive effects, presenting challenges for understanding its consequences. Although standard transcriptomic analyses exist to compare hybrids to their progenitors, such analyses have not been implemented in a software package, hindering reproducibility. We introduce hybridexpress, an R/Bioconductor package designed to facilitate the analysis, visualization, and comparison of gene expression patterns in hybrid triplets (hybrids and their progenitors). hybridexpress provides users with a user-friendly and comprehensive workflow that includes all standard comparative analyses steps, including data normalization, calculation of midparent expression values, sample clustering, expression-based gene classification into categories and classes, and overrepresentation analysis for functional terms. We illustrate the utility of hybridexpress through comparative transcriptomic analyses of cotton allopolyploidization and rice root trait heterosis. hybridexpress is designed to streamline comparative transcriptomic studies of hybrid triplets, advancing our understanding of evolutionary dynamics in allopolyploids, and enhancing plant breeding strategies. hybridexpress is freely accessible from Bioconductor (https://bioconductor.org/packages/HybridExpress) and its source code is available on GitHub (https://github.com/almeidasilvaf/HybridExpress).
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Affiliation(s)
- Fabricio Almeida-Silva
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Lucas Prost-Boxoen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Biology, Ghent University, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
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2
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Wang F, Han T, Jeffrey Chen Z. Circadian and photoperiodic regulation of the vegetative to reproductive transition in plants. Commun Biol 2024; 7:579. [PMID: 38755402 PMCID: PMC11098820 DOI: 10.1038/s42003-024-06275-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 05/01/2024] [Indexed: 05/18/2024] Open
Abstract
As sessile organisms, plants must respond constantly to ever-changing environments to complete their life cycle; this includes the transition from vegetative growth to reproductive development. This process is mediated by photoperiodic response to sensing the length of night or day through circadian regulation of light-signaling molecules, such as phytochromes, to measure the length of night to initiate flowering. Flowering time is the most important trait to optimize crop performance in adaptive regions. In this review, we focus on interplays between circadian and light signaling pathways that allow plants to optimize timing for flowering and seed production in Arabidopsis, rice, soybean, and cotton. Many crops are polyploids and domesticated under natural selection and breeding. In response to adaptation and polyploidization, circadian and flowering pathway genes are epigenetically reprogrammed. Understanding the genetic and epigenetic bases for photoperiodic flowering will help improve crop yield and resilience in response to climate change.
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Affiliation(s)
- Fang Wang
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Tongwen Han
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
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3
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Dwivedi SL, Quiroz LF, Spillane C, Wu R, Mattoo AK, Ortiz R. Unlocking allelic variation in circadian clock genes to develop environmentally robust and productive crops. PLANTA 2024; 259:72. [PMID: 38386103 PMCID: PMC10884192 DOI: 10.1007/s00425-023-04324-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/24/2023] [Indexed: 02/23/2024]
Abstract
MAIN CONCLUSION Molecular mechanisms of biological rhythms provide opportunities to harness functional allelic diversity in core (and trait- or stress-responsive) oscillator networks to develop more climate-resilient and productive germplasm. The circadian clock senses light and temperature in day-night cycles to drive biological rhythms. The clock integrates endogenous signals and exogenous stimuli to coordinate diverse physiological processes. Advances in high-throughput non-invasive assays, use of forward- and inverse-genetic approaches, and powerful algorithms are allowing quantitation of variation and detection of genes associated with circadian dynamics. Circadian rhythms and phytohormone pathways in response to endogenous and exogenous cues have been well documented the model plant Arabidopsis. Novel allelic variation associated with circadian rhythms facilitates adaptation and range expansion, and may provide additional opportunity to tailor climate-resilient crops. The circadian phase and period can determine adaptation to environments, while the robustness in the circadian amplitude can enhance resilience to environmental changes. Circadian rhythms in plants are tightly controlled by multiple and interlocked transcriptional-translational feedback loops involving morning (CCA1, LHY), mid-day (PRR9, PRR7, PRR5), and evening (TOC1, ELF3, ELF4, LUX) genes that maintain the plant circadian clock ticking. Significant progress has been made to unravel the functions of circadian rhythms and clock genes that regulate traits, via interaction with phytohormones and trait-responsive genes, in diverse crops. Altered circadian rhythms and clock genes may contribute to hybrid vigor as shown in Arabidopsis, maize, and rice. Modifying circadian rhythms via transgenesis or genome-editing may provide additional opportunities to develop crops with better buffering capacity to environmental stresses. Models that involve clock gene‒phytohormone‒trait interactions can provide novel insights to orchestrate circadian rhythms and modulate clock genes to facilitate breeding of all season crops.
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Affiliation(s)
| | - Luis Felipe Quiroz
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland.
| | - Rongling Wu
- Beijing Yanqi Lake Institute of Mathematical Sciences and Applications, Beijing, 101408, China
| | - Autar K Mattoo
- USDA-ARS, Sustainable Agricultural Systems Laboratory, Beltsville, MD, 20705-2350, USA
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundsvagen, 10, Box 190, SE 23422, Lomma, Sweden.
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Ren X, Chen L, Deng L, Zhao Q, Yao D, Li X, Cong W, Zang Z, Zhao D, Zhang M, Yang S, Zhang J. Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling heterosis and its relationship with hybrid contemporary seeds DNA methylation in soybean. FRONTIERS IN PLANT SCIENCE 2024; 15:1364284. [PMID: 38444535 PMCID: PMC10913200 DOI: 10.3389/fpls.2024.1364284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 01/31/2024] [Indexed: 03/07/2024]
Abstract
Heterosis is widely used in crop production, but phenotypic dominance and its underlying causes in soybeans, a significant grain and oil crop, remain a crucial yet unexplored issue. Here, the phenotypes and transcriptome profiles of three inbred lines and their resulting F1 seedlings were analyzed. The results suggest that F1 seedlings with superior heterosis in leaf size and biomass exhibited a more extensive recompilation in their transcriptional network and activated a greater number of genes compared to the parental lines. Furthermore, the transcriptional reprogramming observed in the four hybrid combinations was primarily non-additive, with dominant effects being more prevalent. Enrichment analysis of sets of differentially expressed genes, coupled with a weighted gene co-expression network analysis, has shown that the emergence of heterosis in seedlings can be attributed to genes related to circadian rhythms, photosynthesis, and starch synthesis. In addition, we combined DNA methylation data from previous immature seeds and observed similar recompilation patterns between DNA methylation and gene expression. We also found significant correlations between methylation levels of gene region and gene expression levels, as well as the discovery of 12 hub genes that shared or conflicted with their remodeling patterns. This suggests that DNA methylation in contemporary hybrid seeds have an impact on both the F1 seedling phenotype and gene expression to some extent. In conclusion, our study provides valuable insights into the molecular mechanisms of heterosis in soybean seedlings and its practical implications for selecting superior soybean varieties.
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Affiliation(s)
- Xiaobo Ren
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Liangyu Chen
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
- Zhanjiang City Key Laboratory for Tropical Crops Genetic Improvement, South Subtropical Crops Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Lin Deng
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Qiuzhu Zhao
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Dan Yao
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Xueying Li
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Weixuan Cong
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Zhenyuan Zang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Dingyi Zhao
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Miao Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Songnan Yang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Jun Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
- National Crop Variety Approval and Characteristic Identification Station, Jilin Agricultural University, Changchun, China
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5
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June V, Xu D, Papoulas O, Boutz D, Marcotte EM, Chen ZJ. Protein nonadditive expression and solubility contribute to heterosis in Arabidopsis hybrids and allotetraploids. FRONTIERS IN PLANT SCIENCE 2023; 14:1252564. [PMID: 37780492 PMCID: PMC10538547 DOI: 10.3389/fpls.2023.1252564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023]
Abstract
Hybrid vigor or heterosis has been widely applied in agriculture and extensively studied using genetic and gene expression approaches. However, the biochemical mechanism underlying heterosis remains elusive. One theory suggests that a decrease in protein aggregation may occur in hybrids due to the presence of protein variants between parental alleles, but it has not been experimentally tested. Here, we report comparative analysis of soluble and insoluble proteomes in Arabidopsis intraspecific and interspecific hybrids or allotetraploids formed between A. thaliana and A. arenosa. Both allotetraploids and intraspecific hybrids displayed nonadditive expression (unequal to the sum of the two parents) of the proteins, most of which were involved in biotic and abiotic stress responses. In the allotetraploids, homoeolog-expression bias was not observed among all proteins examined but accounted for 17-20% of the nonadditively expressed proteins, consistent with the transcriptome results. Among expression-biased homoeologs, there were more A. thaliana-biased than A. arenosa-biased homoeologs. Analysis of the insoluble and soluble proteomes revealed more soluble proteins in the hybrids than their parents but not in the allotetraploids. Most proteins in ribosomal biosynthesis and in the thylakoid lumen, membrane, and stroma were in the soluble fractions, indicating a role of protein stability in photosynthetic activities for promoting growth. Thus, nonadditive expression of stress-responsive proteins and increased solubility of photosynthetic proteins may contribute to heterosis in Arabidopsis hybrids and allotetraploids and possibly hybrid crops.
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Affiliation(s)
- Viviana June
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Dongqing Xu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Ophelia Papoulas
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Daniel Boutz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Edward M. Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Z. Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
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Muhammad S, Xu X, Zhou W, Wu L. Alternative splicing: An efficient regulatory approach towards plant developmental plasticity. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1758. [PMID: 35983878 DOI: 10.1002/wrna.1758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/28/2022] [Accepted: 07/19/2022] [Indexed: 05/13/2023]
Abstract
Alternative splicing (AS) is a gene regulatory mechanism that plants adapt to modulate gene expression (GE) in multiple ways. AS generates alternative isoforms of the same gene following various development and environmental stimuli, increasing transcriptome plasticity and proteome complexity. AS controls the expression levels of certain genes and regulates GE networks that shape plant adaptations through nonsense-mediated decay (NMD). This review intends to discuss AS modulation, from interaction with noncoding RNAs to the established roles of splicing factors (SFs) in response to endogenous and exogenous cues. We aim to gather such studies that highlight the magnitude and impact of AS, which are not always clear from individual articles, when AS is increasing in individual genes and at a global level. This work also anticipates making plant researchers know that AS is likely to occur in their investigations and that dynamic changes in AS and their effects must be frequently considered. We also review our understanding of AS-mediated posttranscriptional modulation of plant stress tolerance and discuss its potential application in crop improvement in the future. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Processing > Splicing Mechanisms RNA-Based Catalysis > RNA Catalysis in Splicing and Translation.
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Affiliation(s)
- Sajid Muhammad
- Hainan Yazhou Bay Seed Laboratory, Hainan Institute of Zhejiang University, Sanya, Hainan, China
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoli Xu
- Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Weijun Zhou
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Liang Wu
- Hainan Yazhou Bay Seed Laboratory, Hainan Institute of Zhejiang University, Sanya, Hainan, China
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
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7
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Liu X, Gu S, Wen W, Lu X, Jin Y, Zhang Y, Guo X. Disentangling the Heterosis in Biomass Production and Radiation Use Efficiency in Maize: A Phytomer-Based 3D Modelling Approach. PLANTS (BASEL, SWITZERLAND) 2023; 12:1229. [PMID: 36986918 PMCID: PMC10052571 DOI: 10.3390/plants12061229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
Maize (Zea mays L.) benefits from heterosis in-yield formation and photosynthetic efficiency through optimizing canopy structure and improving leaf photosynthesis. However, the role of canopy structure and photosynthetic capacity in determining heterosis in biomass production and radiation use efficiency has not been separately clarified. We developed a quantitative framework based on a phytomer-based three-dimensional canopy photosynthesis model and simulated light capture and canopy photosynthetic production in scenarios with and without heterosis in either canopy structure or leaf photosynthetic capacity. The accumulated above-ground biomass of Jingnongke728 was 39% and 31% higher than its male parent, Jing2416, and female parent, JingMC01, while accumulated photosynthetically active radiation was 23% and 14% higher, correspondingly, leading to an increase of 13% and 17% in radiation use efficiency. The increasing post-silking radiation use efficiency was mainly attributed to leaf photosynthetic improvement, while the dominant contributing factor differs for male and female parents for heterosis in post-silking yield formation. This quantitative framework illustrates the potential to identify the key traits related to yield and radiation use efficiency and helps breeders to make selections for higher yield and photosynthetic efficiency.
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Affiliation(s)
- Xiang Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding 071000, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing 100097, China
| | - Shenghao Gu
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing 100097, China
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Weiliang Wen
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing 100097, China
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xianju Lu
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing 100097, China
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yu Jin
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing 100097, China
| | - Yongjiang Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding 071000, China
| | - Xinyu Guo
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing 100097, China
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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8
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Li R, Nie S, Zhang N, Tian M, Zhang L. Transcriptome Analysis Reveals a Major Gene Expression Pattern and Important Metabolic Pathways in the Control of Heterosis in Chinese Cabbage. PLANTS (BASEL, SWITZERLAND) 2023; 12:1195. [PMID: 36904055 PMCID: PMC10005390 DOI: 10.3390/plants12051195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Although heterosis is commonly used in Chinese cabbage, its molecular basis is poorly understood. In this study, 16Chinese cabbage hybrids were utilized as test subjects to explore the potential molecular mechanism of heterosis. RNA sequencing revealed 5815-10,252 differentially expressed genes (DEGs) (female parent vs. male parent), 1796-5990 DEGs (female parent-vs-hybrid), and 2244-7063 DEGs (male parent vs. hybrid) in 16 cross combinations at the middle stage of heading. Among of them, 72.83-84.20% DEGs conformed to the dominant expression pattern, which is the predominant expression pattern in hybrids. There were 13 pathways in which DEGs were significantly enriched in most cross combinations. Among them, the plant-pathogen interaction (ko04626) and circadian rhythm-plant (ko04712)were significantly enriched by DEGs in strong heterosis hybrids. WGCNA also proved that the two pathways were significantly related to heterosis in Chinese cabbage.
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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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Zhan W, Guo G, Cui L, Rashid MAR, Jiang L, Sun G, Yang J, Zhang Y. Combined transcriptome and metabolome analysis reveals the effects of light quality on maize hybrids. BMC PLANT BIOLOGY 2023; 23:41. [PMID: 36653749 PMCID: PMC9847186 DOI: 10.1186/s12870-023-04059-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Heterosis, or hybrid vigor, refers to the phenotypic superiority of an F1 hybrid relative to its parents in terms of growth rate, biomass production, grain yield, and stress tolerance. Light is an energy source and main environmental cue with marked impacts on heterosis in plants. Research into the production applications and mechanism of heterosis has been conducted for over a century and a half, but little is known about the effect of light on plant heterosis. RESULTS In this study, an integrated transcriptome and metabolome analysis was performed using maize (Zea mays L.) inbred parents, B73 and Mo17, and their hybrids, B73 × Mo17 (BM) and Mo17 × B73 (MB), grown in darkness or under far-red, red, or blue light. Most differentially expressed genes (73.72-92.50%) and differentially accumulated metabolites (84.74-94.32%) exhibited non-additive effects in BM and MB hybrids. Gene Ontology analysis revealed that differential genes and metabolites were involved in glutathione transfer, carbohydrate transport, terpenoid biosynthesis, and photosynthesis. The darkness, far-red, red, and blue light treatments were all associated with phenylpropanoid-flavonoid biosynthesis by Weighted Gene Co-expression Network Analysis and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. Five genes and seven metabolites related to phenylpropanoid-flavonoid biosynthesis pathway were identified as potential contributors to the interactions between maize heterosis and light conditions. Consistent with the strong mid-parent heterosis observed for metabolites, significant increases in both fresh and dry weights were found in the MB and BM hybrids compared with their inbred parents. Unexpectedly, increasing light intensity resulted in higher biomass heterosis in MB, but lower biomass heterosis in BM. CONCLUSIONS The transcriptomic and metabolomic results provide unique insights into the effects of light quality on gene expression patterns and genotype-environment interactions, and have implications for gene mining of heterotic loci to improve maize production.
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Affiliation(s)
- Weimin Zhan
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guanghui Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, China
| | - Lianhua Cui
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Muhammad Abdul Rehman Rashid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Liangliang Jiang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guanghua Sun
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Jianping Yang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Yanpei Zhang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
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11
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Hackauf B, Siekmann D, Fromme FJ. Improving Yield and Yield Stability in Winter Rye by Hybrid Breeding. PLANTS (BASEL, SWITZERLAND) 2022; 11:2666. [PMID: 36235531 PMCID: PMC9571156 DOI: 10.3390/plants11192666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/27/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Rye is the only cross-pollinating small-grain cereal. The unique reproduction biology results in an exceptional complexity concerning genetic improvement of rye by breeding. Rye is a close relative of wheat and has a strong adaptation potential that refers to its mating system, making this overlooked cereal readily adjustable to a changing environment. Rye breeding addresses the emerging challenges of food security associated with climate change. The systematic identification, management, and use of its valuable natural diversity became a feasible option in outbreeding rye only following the establishment of hybrid breeding late in the 20th century. In this article, we review the most recent technological advances to improve yield and yield stability in winter rye. Based on recently released reference genome sequences, SMART breeding approaches are described to counterbalance undesired linkage drag effects of major restorer genes on grain yield. We present the development of gibberellin-sensitive semidwarf hybrids as a novel plant breeding innovation based on an approach that is different from current methods of increasing productivity in rye and wheat. Breeding of new rye cultivars with improved performance and resilience is indispensable for a renaissance of this healthy minor cereal as a homogeneous commodity with cultural relevance in Europe that allows for comparatively smooth but substantial complementation of wheat with rye-based diets, supporting the necessary restoration of the balance between human action and nature.
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Affiliation(s)
- Bernd Hackauf
- Julius Kühn Institute, Institute for Breeding Research on Agricultural Crops, Rudolf-Schick-Platz 3a, 18190 Sanitz, Germany
| | - Dörthe Siekmann
- Hybro Saatzucht GmbH & Co. KG, Langlinger Straße 3, 29565 Wriedel, Germany
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Michael TP. Core circadian clock and light signaling genes brought into genetic linkage across the green lineage. PLANT PHYSIOLOGY 2022; 190:1037-1056. [PMID: 35674369 PMCID: PMC9516744 DOI: 10.1093/plphys/kiac276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The circadian clock is conserved at both the level of transcriptional networks as well as core genes in plants, ensuring that biological processes are phased to the correct time of day. In the model plant Arabidopsis (Arabidopsis thaliana), the core circadian SHAQKYF-type-MYB (sMYB) genes CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and REVEILLE (RVE4) show genetic linkage with PSEUDO-RESPONSE REGULATOR 9 (PRR9) and PRR7, respectively. Leveraging chromosome-resolved plant genomes and syntenic ortholog analysis enabled tracing this genetic linkage back to Amborella trichopoda, a sister lineage to the angiosperm, and identifying an additional evolutionarily conserved genetic linkage in light signaling genes. The LHY/CCA1-PRR5/9, RVE4/8-PRR3/7, and PIF3-PHYA genetic linkages emerged in the bryophyte lineage and progressively moved within several genes of each other across an array of angiosperm families representing distinct whole-genome duplication and fractionation events. Soybean (Glycine max) maintained all but two genetic linkages, and expression analysis revealed the PIF3-PHYA linkage overlapping with the E4 maturity group locus was the only pair to robustly cycle with an evening phase, in contrast to the sMYB-PRR morning and midday phase. While most monocots maintain the genetic linkages, they have been lost in the economically important grasses (Poaceae), such as maize (Zea mays), where the genes have been fractionated to separate chromosomes and presence/absence variation results in the segregation of PRR7 paralogs across heterotic groups. The environmental robustness model is put forward, suggesting that evolutionarily conserved genetic linkages ensure superior microhabitat pollinator synchrony, while wide-hybrids or unlinking the genes, as seen in the grasses, result in heterosis, adaptation, and colonization of new ecological niches.
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Zhou J, Liu C, Chen Q, Liu L, Niu S, Chen R, Li K, Sun Y, Shi Y, Yang C, Shen S, Li Y, Xing J, Yuan H, Liu X, Fang C, Fernie AR, Luo J. Integration of rhythmic metabolome and transcriptome provides insights into the transmission of rhythmic fluctuations and temporal diversity of metabolism in rice. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1794-1810. [PMID: 35287184 DOI: 10.1007/s11427-021-2064-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Various aspects of the organisms adapt to cyclically changing environmental conditions via transcriptional regulation. However, the role of rhythmicity in altering the global aspects of metabolism is poorly characterized. Here, we subjected four rice (Oryza sativa) varieties to a range of metabolic profiles and RNA-seq to investigate the temporal relationships of rhythm between transcription and metabolism. More than 40% of the rhythmic genes and a quarter of metabolites conservatively oscillated across four rice accessions. Compared with the metabolome, the transcriptome was more strongly regulated by rhythm; however, the rhythm of metabolites had an obvious opposite trend between day and night. Through association analysis, the time delay of rhythmic transmission from the transcript to the metabolite level was ∼4 h under long-day conditions, although the transmission was nearly synchronous for carbohydrate and nucleotide metabolism. The rhythmic accumulation of metabolites maintained highly coordinated temporal relationships in the metabolic network, whereas the correlation of some rhythmic metabolites, such as branched-chain amino acids (BCAAs), was significantly different intervariety. We further demonstrated that the cumulative diversity of BCAAs was due to the differential expression of branched-chain aminotransferase 2 at dawn. Our research reveals the flexible pattern of rice metabolic rhythm existing with conservation and diversity.
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Affiliation(s)
- Junjie Zhou
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Chengyuan Liu
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Qiyu Chen
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Ling Liu
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Shuying Niu
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Ridong Chen
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Kang Li
- College of Tropical Crops, Hainan University, Haikou, 570288, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, China
| | - Yangyang Sun
- College of Tropical Crops, Hainan University, Haikou, 570288, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, China
| | - Yuheng Shi
- College of Tropical Crops, Hainan University, Haikou, 570288, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, China
| | - Chenkun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangqian Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yufei Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Junwei Xing
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Honglun Yuan
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Xianqing Liu
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Chuanying Fang
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, 144776, Germany
- Center of Plant System Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, 570288, China.
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, China.
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Mbebi AJ, Breitler JC, Bordeaux M, Sulpice R, McHale M, Tong H, Toniutti L, Castillo JA, Bertrand B, Nikoloski Z. A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids. G3 GENES|GENOMES|GENETICS 2022; 12:6632664. [PMID: 35792875 PMCID: PMC9434219 DOI: 10.1093/g3journal/jkac170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/14/2022] [Indexed: 11/14/2022]
Abstract
Abstract
Genomic prediction has revolutionized crop breeding despite remaining issues of transferability of models to unseen environmental conditions and environments. Usage of endophenotypes rather than genomic markers leads to the possibility of building phenomic prediction models that can account, in part, for this challenge. Here, we compare and contrast genomic prediction and phenomic prediction models for 3 growth-related traits, namely, leaf count, tree height, and trunk diameter, from 2 coffee 3-way hybrid populations exposed to a series of treatment-inducing environmental conditions. The models are based on 7 different statistical methods built with genomic markers and ChlF data used as predictors. This comparative analysis demonstrates that the best-performing phenomic prediction models show higher predictability than the best genomic prediction models for the considered traits and environments in the vast majority of comparisons within 3-way hybrid populations. In addition, we show that phenomic prediction models are transferrable between conditions but to a lower extent between populations and we conclude that chlorophyll a fluorescence data can serve as alternative predictors in statistical models of coffee hybrid performance. Future directions will explore their combination with other endophenotypes to further improve the prediction of growth-related traits for crops.
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Affiliation(s)
- Alain J Mbebi
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam , Potsdam-Golm 14476, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology , Potsdam-Golm 14476, Germany
| | - Jean-Christophe Breitler
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier 34398, France
| | - Mélanie Bordeaux
- Fundación Nicafrance , Finca La Cumplida Km. 147 Carretera Matagalpa - La Dalia, 3 Km al Noreste, Matagalpa, Nicaragua
| | - Ronan Sulpice
- National University Ireland Galway, Plant Systems Biology Laboratory, Ryan Institute, School of Natural Sciences , Galway H91 TK33, Ireland
| | - Marcus McHale
- National University Ireland Galway, Plant Systems Biology Laboratory, Ryan Institute, School of Natural Sciences , Galway H91 TK33, Ireland
| | - Hao Tong
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam , Potsdam-Golm 14476, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology , Potsdam-Golm 14476, Germany
- Center for Plant Systems Biology and Biotechnology , Plovdiv 4000, Bulgaria
| | - Lucile Toniutti
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier 34398, France
| | - Jonny Alonso Castillo
- Fundación Nicafrance , Finca La Cumplida Km. 147 Carretera Matagalpa - La Dalia, 3 Km al Noreste, Matagalpa, Nicaragua
| | - Benoît Bertrand
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier 34398, France
| | - Zoran Nikoloski
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam , Potsdam-Golm 14476, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology , Potsdam-Golm 14476, Germany
- Center for Plant Systems Biology and Biotechnology , Plovdiv 4000, Bulgaria
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15
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Description of an Arabica Coffee Ideotype for Agroforestry Cropping Systems: A Guideline for Breeding More Resilient New Varieties. PLANTS 2022; 11:plants11162133. [PMID: 36015436 PMCID: PMC9414076 DOI: 10.3390/plants11162133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022]
Abstract
Climate change (CC) is already impacting Arabica coffee cultivation in the intertropical zone. To deal with this situation, it is no longer possible to manage this crop using industrial agriculture techniques, which has been the main strategy implemented since the Green Revolution. Developing a more sustainable agriculture system that respects people and the environment is essential to guarantee future generations’ access to natural resources. In the case of Arabica coffee, the solution has been found. Agroforestry is proposed as an ecosystem-based strategy to mitigate and adapt to CC. At least 60% of Arabica coffee is produced in agroforestry systems (AFSs), which are the most sustainable way to produce coffee. Nevertheless, AFS coffee cultivation is currently uncompetitive partly because all modern varieties, selected for full-sun intensive cropping systems, have low yields in shaded environments. Here we review the reasons why agroforestry is part of the solution to CC, and why no breeding work has been undertaken for this cropping system. Based on the literature data, for breeding purposes we also define for the first time one possible coffee ideotype required for AFS coffee cultivation. The four main traits are: (1) productivity based on F1 hybrid vigor, tree volume and flowering intensity under shade; (2) beverage quality by using wild Ethiopian accessions as female progenitors and selecting for this criterion using specific biochemical and molecular predictors; (3) plant health to ensure good tolerance to stress, especially biotic; and (4) low fertilization to promote sustainable production. For each of these traits, numerous criteria with threshold values to be achieved per trait were identified. Through this research, an ecosystem-based breeding strategy was defined to help create new F1 hybrid varieties within the next 10 years.
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Gong J, Tang Y, Liu Y, Sun R, Li Y, Ma J, Zhang S, Zhang F, Chen Z, Liao X, Sun H, Lu Z, Zhao C, Gao S. The Central Circadian Clock Protein TaCCA1 Regulates Seedling Growth and Spike Development in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:946213. [PMID: 35923880 PMCID: PMC9340162 DOI: 10.3389/fpls.2022.946213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/20/2022] [Indexed: 05/14/2023]
Abstract
The biological functions of the circadian clock on growth and development have been well elucidated in model plants, while its regulatory roles in crop species, especially the roles on yield-related traits, are poorly understood. In this study, we characterized the core clock gene CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) homoeologs in wheat and studied their biological functions in seedling growth and spike development. TaCCA1 homoeologs exhibit typical diurnal expression patterns, which are positively regulated by rhythmic histone modifications including histone H3 lysine 4 trimethylation (H3K4me3), histone H3 lysine 9 acetylation (H3K9Ac), and histone H3 lysine 36 trimethylation (H3K36me3). TaCCA1s are preferentially located in the nucleus and tend to form both homo- and heterodimers. TaCCA1 overexpression (TaCCA1-OE) transgenic wheat plants show disrupted circadian rhythmicity coupling with reduced chlorophyll and starch content, as well as biomass at seedling stage, also decreased spike length, grain number per spike, and grain size at the ripening stage. Further studies using DNA affinity purification followed by deep sequencing [DNA affinity purification and sequencing (DAP-seq)] indicated that TaCCA1 preferentially binds to sequences similarly to "evening elements" (EE) motif in the wheat genome, particularly genes associated with photosynthesis, carbon utilization, and auxin homeostasis, and decreased transcriptional levels of these target genes are observed in TaCCA1-OE transgenic wheat plants. Collectively, our study provides novel insights into a circadian-mediated mechanism of gene regulation to coordinate photosynthetic and metabolic activities in wheat, which is important for optimal plant growth and crop yield formation.
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Affiliation(s)
- Jie Gong
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yimiao Tang
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yongjie Liu
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Renwei Sun
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yanhong Li
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jinxiu Ma
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shengquan Zhang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Fengting Zhang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Zhaobo Chen
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiangzheng Liao
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Hui Sun
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Zefu Lu
- National Key Facility of Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Changping Zhao
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shiqing Gao
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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17
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Li T, Wang F, Yasir M, Li K, Qin Y, Zheng J, Luo K, Zhu S, Zhang H, Jiang Y, Zhang Y, Rong J. Expression Patterns Divergence of Reciprocal F 1 Hybrids Between Gossypium hirsutum and Gossypium barbadense Reveals Overdominance Mediating Interspecific Biomass Heterosis. FRONTIERS IN PLANT SCIENCE 2022; 13:892805. [PMID: 35845678 PMCID: PMC9284264 DOI: 10.3389/fpls.2022.892805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Hybrid breeding has provided an impetus to the process and achievement of a higher yield and quality of crops. Interspecific hybridization is critical for resolving parental genetic diversity bottleneck problems. The reciprocal interspecific hybrids and their parents (Gossypium hirsutum and Gossypium barbadense) have been applied in this study to elucidate the transcription regulatory mechanism of early biomass heterosis. Phenotypically, the seed biomass, plant height over parent heterosis, leaf area over parent heterosis, and fresh and dry biomass were found to be significantly higher in hybrids than in parents. Analysis of leaf areas revealed that the one-leaf stage exhibits the most significant performance in initial vegetative growth vigor and larger leaves in hybrids, increasing the synthesis of photosynthesis compounds and enhancing photosynthesis compound synthesis. Comparative transcriptome analysis showed that transgressive down-regulation (TDR) is the main gene expression pattern in the hybrids (G. hirsutum × G. barbadense, HB), and it was found that the genes of photosystem I and Adenosine triphosphate (ATP)-binding may promote early growth vigor. Transgressive up-regulation (TUR) is the major primary gene expression pattern in the hybrids (G. barbadense × G. hirsutum, BH), and photosystem II-related genes mediated the performance of early biomass heterosis. The above results demonstrated that overdominance mediates biomass heterosis in interspecific hybrid cotton and the supervisory mechanism divergence of hybrids with different females. Photosynthesis and other metabolic process are jointly involved in controlling early biomass heterosis in interspecific hybrid cotton. The expression pattern data of transcriptome sequencing were supported using the qRT-PCR analysis. Our findings could be useful in theoretical and practical studies of early interspecific biomass heterosis, and the results provide potential resources for the theoretical and applied research on early interspecific biomass heterosis.
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Affiliation(s)
- Tengyu Li
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Fuqiu Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Yasir
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Kui Li
- Institute of Food and Nutrition Development, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Qin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jing Zheng
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Kun Luo
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Shouhong Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hua Zhang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yurong Jiang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yongshan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Junkang Rong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
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18
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Wan J, Wang Q, Zhao J, Zhang X, Guo Z, Hu D, Meng S, Lin Y, Qiu X, Mu L, Ding D, Tang J. Gene expression variation explains maize seed germination heterosis. BMC PLANT BIOLOGY 2022; 22:301. [PMID: 35718761 PMCID: PMC9208091 DOI: 10.1186/s12870-022-03690-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Heterosis has been extensively utilized in plant breeding, however, the underlying molecular mechanism remains largely elusive. Maize (Zea mays), which exhibits strong heterosis, is an ideal material for studying heterosis. RESULTS In this study, there is faster imbibition and development in reciprocal crossing Zhengdan958 hybrids than in their parent lines during seed germination. To investigate the mechanism of heterosis of maize germination, comparative transcriptomic analyses were conducted. The gene expression patterns showed that 1324 (47.27%) and 1592 (66.44%) of the differential expression genes between hybrids and either parental line display parental dominance up or higher levels in the reciprocal cross of Zhengdan958, respectively. Notably, these genes were mainly enriched in metabolic pathways, including carbon metabolism, glycolysis/gluconeogenesis, protein processing in endoplasmic reticulum, etc. CONCLUSION: Our results provide evidence for the higher expression level genes in hybrid involved in metabolic pathways acting as main contributors to maize seed germinating heterosis. These findings provide new insights into the gene expression variation of maize embryos and improve the understanding of maize seed germination heterosis.
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Affiliation(s)
- Jiong Wan
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Qiyue Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jiawen Zhao
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhanyong Guo
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Desheng Hu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Shujun Meng
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yuan Lin
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaoqian Qiu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Liqin Mu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
- The Shennong Laboratory, Zhengzhou, 450002, China.
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19
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Sun R, Gong J, Liu Y, Chen Z, Zhang F, Gao J, Cao J, Chen X, Zhang S, Zhao C, Gao S. Comprehensive molecular evaluation of the histone methyltransferase gene family and their important roles in two-line hybrid wheat. BMC PLANT BIOLOGY 2022; 22:290. [PMID: 35698040 PMCID: PMC9190116 DOI: 10.1186/s12870-022-03639-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Histone methylation usually plays important roles in plant development through post-translational regulation and may provide a new visual field for heterosis. The histone methyltransferase gene family has been identified in various plants, but its members and functions in hybrid wheat related in heterosis is poorly studied. RESULTS In this study, 175 histone methyltransferase (HMT) genes were identified in wheat, including 152 histone lysine methyltransferase (HKMT) genes and 23 protein arginine methyltransferase (PRMT) genes. Gene structure analysis, physicochemical properties and subcellular localization predictions of the proteins, exhibited the adequate complexity of this gene family. As an allohexaploid species, the number of the genes (seven HKMTs orthologous groups and four PRMTs orthologous groups) in wheat were about three times than those in diploids and showed certain degrees of conservation, while only a small number of subfamilies such as ASH-like and Su-(var) subfamilies have expanded their members. Transcriptome analysis showed that HMT genes were mainly expressed in the reproductive organs. Expression analysis showed that some TaHMT genes with different trends in various hybrid combinations may be regulated by lncRNAs with similar expression trends. Pearson correlation analysis of the expression of TaHMT genes and two yield traits indicated that four DEGs may participate in the yield heterosis of two-line hybrid wheat. ChIP-qPCR results showed that the histone modifications (H3K4me3, H3K36me3 and H3K9ac) enriched in promoter regions of three TaCCA1 genes which are homologous to Arabidopsis heterosis-related CCA1/LHY genes. The higher expression levels of TaCCA1 in F1 than its parents are positive with these histone modifications. These results showed that histone modifications may play important roles in wheat heterosis. CONCLUSIONS Our study identified characteristics of the histone methyltransferase gene family and enhances the understanding of the evolution and function of these members in allohexaploid wheat. The causes of heterosis of two-line hybrid wheat were partially explained from the perspective of histone modifications.
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Affiliation(s)
- Renwei Sun
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China
| | - Jie Gong
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China
| | - Yongjie Liu
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China
| | - Zhaobo Chen
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
| | - Fengting Zhang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
| | - Jiangang Gao
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
| | - Junmei Cao
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Xianchao Chen
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
| | - Shengquan Zhang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China.
| | - Changping Zhao
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China.
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China.
| | - Shiqing Gao
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China.
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China.
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Xiong J, Hu K, Shalby N, Zhuo C, Wen J, Yi B, Shen J, Ma C, Fu T, Tu J. Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling biomass heterosis in Brassica napus. BMC PLANT BIOLOGY 2022; 22:283. [PMID: 35676627 PMCID: PMC9178846 DOI: 10.1186/s12870-022-03671-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/16/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND Heterosis is an important biological phenomenon in which the hybrids exceed the parents in many traits. However, the molecular mechanism underlying seedling heterosis remains unclear. RESULTS In the present study, we analyzed the leaf transcriptomes of strong hybrids (AM, HM) and weak hybrids (CM, HW) and their parents (A, C, H, M, and W) at two periods. Phenotypically, hybrids had obvious biomass heterosis at the seedling stage, with statistically significant differences between the strong and weak hybrids. The transcriptomic analysis demonstrated that the number of differentially expressed genes (DEGs) between parents was the highest. Further analysis showed that most DEGs were biased toward parental expression. The biological processes of the two periods were significantly enriched in the plant hormone signal transduction and photosynthetic pathways. In the plant hormone signaling pathway, DEG expression was high in hybrids, with expression differences between strong and weak hybrids. In addition, DEGs related to cell size were identified. Similar changes were observed during photosynthesis. The enhanced leaf area of hybrids generated an increase in photosynthetic products, which was consistent with the phenotype of the biomass. Weighted gene co-expression network analysis of different hybrids and parents revealed that hub genes in vigorous hybrid were mainly enriched in the plant hormone signal transduction and regulation of plant hormones. CONCLUSION Plant hormone signaling and photosynthesis pathways, as well as differential expression of plant cell size-related genes, jointly regulate the dynamic changes between strong and weak hybrids and the generation of seedling-stage heterosis. This study may elucidate the molecular mechanism underlying early biomass heterosis and help enhance canola yield.
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Affiliation(s)
- Jie Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Nesma Shalby
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chenjian Zhuo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
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Wang Y, Nie L, Ma J, Zhou B, Han X, Cheng J, Lu X, Fan Z, Li Y, Cao Y. Transcriptomic Variations and Network Hubs Controlling Seed Size and Weight During Maize Seed Development. FRONTIERS IN PLANT SCIENCE 2022; 13:828923. [PMID: 35237291 PMCID: PMC8882617 DOI: 10.3389/fpls.2022.828923] [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: 12/04/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
To elucidate the mechanisms underlying seed development in maize, comprehensive RNA-seq analyses were conducted on Zhengdan1002 (ZD1002), Zhengdan958 (ZD958), and their parental lines during seven seed developmental stages. We found that gene expression levels were largely nonadditive in hybrids and that cis-only or trans × cis pattern played a large role in hybrid gene regulation during seed developmental stage. Weighted gene co-expression network (WGCNA) analysis showed that 36 modules were highly correlated (r = -0.90-0.92, p < 0.05) with kernel weight, length, and width during seed development. Forty-five transcription factors and 38 ribosomal protein genes were identified as major hub genes determining seed size/weight. We also described a network hub, Auxin Response Factor 12 of maize (ZmARF12), a member of a family of transcription factor that mediate gene expression in response to auxin, potentially links auxin signal pathways, cell division, and the size of the seeds. The ZmARF12 mutant exhibited larger seed size and higher grain weight. ZmARF12 transcription was negatively associated with cell division during seed development, which was confirmed by evaluating the yield of protoplasts that isolated from the kernels of the mutant and other inbred lines. Transient knock-down of ZmARF12 in maize plants facilitated cell expansion and division, whereas transient silencing of its potential interactor ZmIAA8 impaired cell division. ZmIAA8 expression was repressed in the ZmARF12 over-expressed protoplasts. The mutant phenotype and the genetics studies presented here illustrated evidence that ZmARF12 is a cell division repressor, and potentially determines the final seed size.
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Affiliation(s)
- Yanzhao Wang
- Henan Provincial Key Laboratory of Maize Biology, Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Lihong Nie
- Institute of Industrial Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Juan Ma
- Henan Provincial Key Laboratory of Maize Biology, Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Bo Zhou
- Henan Provincial Key Laboratory of Maize Biology, Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaohua Han
- Henan Provincial Key Laboratory of Maize Biology, Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Junling Cheng
- Henan Provincial Key Laboratory of Maize Biology, Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaomin Lu
- Henan Provincial Key Laboratory of Maize Biology, Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Zaifeng Fan
- State Kay Laboratory of Agro-biotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing, China
| | - Yuling Li
- Henan Maize Engineering Technology Joint Center, Henan Agricultural University, Zhengzhou, China
| | - Yanyong Cao
- Henan Provincial Key Laboratory of Maize Biology, Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
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Wang M, Wang J. Transcriptome and DNA methylome analyses provide insight into the heterosis in flag leaf of inter-subspecific hybrid rice. PLANT MOLECULAR BIOLOGY 2022; 108:105-125. [PMID: 34855066 DOI: 10.1007/s11103-021-01228-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/22/2021] [Indexed: 05/26/2023]
Abstract
Flag leaf heterosis of inter-subspecific hybrid rice is suggested to be related to leaf area, gene expression pattern and allele-specific expression, putatively related to DNA methylation differences between the hybrid and its parents. Inter-subspecific hybrid rice combinations of indica × japonica have great potential to broaden genetic diversity and enhance the heterosis. The genetic and epigenetic molecular mechanism of its heterosis is not completely understood. Here, the dissection of gene expression and epigenetic regulation of an elite inter-subspecific hybrid rice were reported. In the hybrid, plant height, flag leaf area and Pn showed significant heterosis at the heading stage. Chloroplast-related differentially expressed genes (DEGs) and 530 allele-specific expression genes in hybrid were identified. Analysis of the genome-wide distribution of DNA methylation (5-methylcytosine, 5mC) and its association with transcription showed that there were variant DNA methylation maps and that the regulation of gene expression levels was negatively regulated by DNA methylation in the inter-subspecific hybrid rice. Differentially methylated DEGs were significantly enriched in photosynthetic functions. Moreover, distinct 5mC sequence contexts and distinct functional elements (promoter/gene body) may have different influences on heterosis related genes. The data identified heterosis related molecular mechanisms in inter-subspecific hybrid rice and suggested that epigenetic changes could extensively influence the flag leaf gene expression and heterosis.
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Affiliation(s)
- Mengyao Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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23
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Birdseye D, de Boer LA, Bai H, Zhou P, Shen Z, Schmelz EA, Springer NM, Briggs SP. Plant height heterosis is quantitatively associated with expression levels of plastid ribosomal proteins. Proc Natl Acad Sci U S A 2021; 118:e2109332118. [PMID: 34782463 PMCID: PMC8617506 DOI: 10.1073/pnas.2109332118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 11/25/2022] Open
Abstract
The use of hybrids is widespread in agriculture, yet the molecular basis for hybrid vigor (heterosis) remains obscure. To identify molecular components that may contribute to trait heterosis, we analyzed paired proteomic and transcriptomic data from seedling leaf and mature leaf blade tissues of maize hybrids and their inbred parents. Nuclear- and plastid-encoded subunits of complexes required for protein synthesis in the chloroplast and for the light reactions of photosynthesis were expressed above midparent and high-parent levels, respectively. Consistent with previous reports in Arabidopsis, ethylene biosynthetic enzymes were expressed below midparent levels in the hybrids, suggesting a conserved mechanism for heterosis between monocots and dicots. The ethylene biosynthesis mutant, acs2/acs6, largely phenocopied the hybrid proteome, indicating that a reduction in ethylene biosynthesis may mediate the differences between inbreds and their hybrids. To rank the relevance of expression differences to trait heterosis, we compared seedling leaf protein levels to the adult plant height of 15 hybrids. Hybrid/midparent expression ratios were most positively correlated with hybrid/midparent plant height ratios for the chloroplast ribosomal proteins. Our results show that increased expression of chloroplast ribosomal proteins in hybrid seedling leaves is mediated by reduced expression of ethylene biosynthetic enzymes and that the degree of their overexpression in seedlings can quantitatively predict adult trait heterosis.
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Affiliation(s)
- Devon Birdseye
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Laura A de Boer
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Hua Bai
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108
| | - Zhouxin Shen
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Eric A Schmelz
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108
| | - Steven P Briggs
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093;
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24
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Wu X, Liu Y, Zhang Y, Gu R. Advances in Research on the Mechanism of Heterosis in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:745726. [PMID: 34646291 PMCID: PMC8502865 DOI: 10.3389/fpls.2021.745726] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/06/2021] [Indexed: 05/13/2023]
Abstract
Heterosis is a common biological phenomenon in nature. It substantially contributes to the biomass yield and grain yield of plants. Moreover, this phenomenon results in high economic returns in agricultural production. However, the utilization of heterosis far exceeds the level of theoretical research on this phenomenon. In this review, the recent progress in research on heterosis in plants was reviewed from the aspects of classical genetics, parental genetic distance, quantitative trait loci, transcriptomes, proteomes, epigenetics (DNA methylation, histone modification, and small RNA), and hormone regulation. A regulatory network of various heterosis-related genes under the action of different regulatory factors was summarized. This review lays a foundation for the in-depth study of the molecular and physiological aspects of this phenomenon to promote its effects on increasing the yield of agricultural production.
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Affiliation(s)
- Xilin Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yan Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yaowei Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Ran Gu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
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25
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Xiao Q, Huang Z, Shen Y, Gan Y, Wang Y, Gong S, Lu Y, Luo X, You W, Ke C. Transcriptome analysis reveals the molecular mechanisms of heterosis on thermal resistance in hybrid abalone. BMC Genomics 2021; 22:650. [PMID: 34496767 PMCID: PMC8428104 DOI: 10.1186/s12864-021-07954-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/23/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Heterosis has been exploited for decades in different animals and crops due to it resulting in dramatic increases in yield and adaptability. Hybridization is a classical breeding method that can effectively improve the genetic characteristics of organisms through heterosis. Abalone has become an increasingly economically important aquaculture resource with high commercial value. However, due to changing climate, abalone is now facing serious threats of high temperature in summer. Interspecific hybrid abalone (Haliotis gigantea ♀ × H. discus hannai ♂, SD) has been cultured at large scale in southern China and has been shown high survival rates under heat stress in summer. Therefore, SD has become a good model material for heterosis research, but the molecular basis of heterosis remains elusive. RESULTS Heterosis in thermal tolerance of SD was verified through Arrhenius break temperatures (ABT) of cardiac performance in this study. Then RNA-Sequencing was conducted to obtain gene expression patterns and alternative splicing events at control temperature (20 °C) and heat stress temperature (30 °C). A total of 356 (317 genes), 476 (435genes), and 876 (726 genes) significantly diverged alternative splicing events were identified in H. discus hannai (DD), H. gigantea (SS), and SD in response to heat stress, respectively. In the heat stress groups, 93.37% (20,512 of 21,969) of the expressed genes showed non-additive expression patterns, and over-dominance expression patterns of genes account for the highest proportion (40.15%). KEGG pathway enrichment analysis showed that the overlapping genes among common DEGs and NAGs were significantly enriched in protein processing in the endoplasmic reticulum, mitophagy, and NF-κB signaling pathway. In addition, we found that among these overlap genes, 39 genes had undergone alternative splicing events in SD. These pathways and genes may play an important role in the thermal resistance of hybrid abalone. CONCLUSION More alternative splicing events and non-additive expressed genes were detected in hybrid under heat stress and this may contribute to its thermal heterosis. These results might provide clues as to how hybrid abalone has a better physiological regulation ability than its parents under heat stress, to increase our understanding of heterosis in abalone.
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Affiliation(s)
- Qizhen Xiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Zekun Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Yawei Shen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Yang Gan
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Yi Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Shihai Gong
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Yisha Lu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Xuan Luo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Weiwei You
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, People's Republic of China.
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, People's Republic of 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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Wang L, Zhou A, Li J, Yang M, Bu F, Ge L, Chen L, Huang W. Circadian rhythms driving a fast-paced root clock implicate species-specific regulation in Medicago truncatula. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1537-1554. [PMID: 34009694 DOI: 10.1111/jipb.13138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Abstract
Plants have a hierarchical circadian structure comprising multiple tissue-specific oscillators that operate at different speeds and regulate the expression of distinct sets of genes in different organs. However, the identity of the genes differentially regulated by the circadian clock in different organs, such as roots, and how their oscillations create functional specialization remain unclear. Here, we profiled the diurnal and circadian landscapes of the shoots and roots of Medicago truncatula and identified the conserved regulatory sequences contributing to transcriptome oscillations in each organ. We found that the light-dark cycles strongly affect the global transcriptome oscillation in roots, and many clock genes oscillate only in shoots. Moreover, many key genes involved in nitrogen fixation are regulated by circadian rhythms. Surprisingly, the root clock runs faster than the shoot clock, which is contrary to the hierarchical circadian structure showing a slow-paced root clock in both detached and intact Arabidopsis thaliana (L.) Heynh. roots. Our result provides important clues about the species-specific circadian regulatory mechanism, which is often overlooked, and possibly coordinates the timing between shoots and roots independent of the current prevailing model.
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Affiliation(s)
- Liping Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Anqi Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Mingkang Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Fan Bu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Liangfa Ge
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, 510642, China
| | - Liang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
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28
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Han T, Wang F, Song Q, Ye W, Liu T, Wang L, Chen ZJ. An epigenetic basis of inbreeding depression in maize. SCIENCE ADVANCES 2021; 7:7/35/eabg5442. [PMID: 34452913 PMCID: PMC8397266 DOI: 10.1126/sciadv.abg5442] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/07/2021] [Indexed: 05/12/2023]
Abstract
Inbreeding depression is widespread across plant and animal kingdoms and may arise from the exposure of deleterious alleles and/or loss of overdominant alleles resulting from increased homozygosity, but these genetic models cannot fully explain the phenomenon. Here, we report epigenetic links to inbreeding depression in maize. Teosinte branched1/cycloidea/proliferating cell factor (TCP) transcription factors control plant development. During successive inbreeding among inbred lines, thousands of genomic regions across TCP-binding sites (TBS) are hypermethylated through the H3K9me2-mediated pathway. These hypermethylated regions are accompanied by decreased chromatin accessibility, increased levels of the repressive histone marks H3K27me2 and H3K27me3, and reduced binding affinity of maize TCP-proteins to TBS. Consequently, hundreds of TCP-target genes involved in mitochondrion, chloroplast, and ribosome functions are down-regulated, leading to reduced growth vigor. Conversely, random mating can reverse corresponding hypermethylation sites and TCP-target gene expression, restoring growth vigor. These results support a unique role of reversible epigenetic modifications in inbreeding depression.
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Affiliation(s)
- Tongwen Han
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Fang Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Qingxin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Tieshan Liu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Liming Wang
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Z Jeffrey Chen
- Department of Molecular Biosciences and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA.
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Zhang Y, Cheng P, Wang J, Abdalmegeed D, Li Y, Wu M, Dai C, Wan S, Guan R, Pu H, Shen W. Nitric Oxide Is Associated With Heterosis of Salinity Tolerance in Brassica napus L. FRONTIERS IN PLANT SCIENCE 2021; 12:649888. [PMID: 34122475 PMCID: PMC8194068 DOI: 10.3389/fpls.2021.649888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/13/2021] [Indexed: 06/01/2023]
Abstract
Heterosis is most frequently manifested as the superior performance of a hybrid than either of the parents, especially under stress conditions. Nitric oxide (NO) is a well-known gaseous signaling molecule that acts as a functional component during plant growth, development, and defense responses. In this study, the Brassica napus L. hybrid (F1, NJ4375 × MB1942) showed significant heterosis under salt stress, during both germination and post-germination periods. These phenotypes in the hybrid were in parallel with the better performance in redox homeostasis, including alleviation of reactive oxygen species accumulation and lipid peroxidation, and ion homeostasis, evaluated as a lower Na/K ratio in the leaves than parental lines. Meanwhile, stimulation of endogenous NO was more pronounced in hybrid plants, compared with parental lines, which might be mediated by nitrate reductase. Proteomic and biochemical analyses further revealed that protein abundance related to several metabolic processes, including chlorophyll biosynthesis, proline metabolism, and tricarboxylic acid cycle metabolism pathway, was greatly suppressed by salt stress in the two parental lines than in the hybrid. The above responses in hybrid plants were intensified by a NO-releasing compound, but abolished by a NO scavenger, both of which were matched with the changes in chlorophyll and proline contents. It was deduced that the above metabolic processes might play important roles in heterosis upon salt stress. Taken together, we proposed that heterosis derived from F1 hybridization in salt stress tolerance might be mediated by NO-dependent activation of defense responses and metabolic processes.
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Affiliation(s)
- Yihua Zhang
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- Ministry of Agriculture’s Key Laboratory of Cotton and Rapeseed, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Pengfei Cheng
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jun Wang
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Dyaaaldin Abdalmegeed
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ying Li
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mangteng Wu
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Chen Dai
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Shubei Wan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Rongzhan Guan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Huiming Pu
- Ministry of Agriculture’s Key Laboratory of Cotton and Rapeseed, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Wenbiao Shen
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
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A central circadian oscillator confers defense heterosis in hybrids without growth vigor costs. Nat Commun 2021; 12:2317. [PMID: 33875651 PMCID: PMC8055661 DOI: 10.1038/s41467-021-22268-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 03/05/2021] [Indexed: 11/10/2022] Open
Abstract
Plant immunity frequently incurs growth penalties, which known as the trade-off between immunity and growth. Heterosis, the phenotypic superiority of a hybrid over its parents, has been demonstrated for many traits but rarely for disease resistance. Here, we report that the central circadian oscillator, CCA1, confers heterosis for bacterial defense in hybrids without growth vigor costs, and it even significantly enhances the growth heterosis of hybrids under pathogen infection. The genetic perturbation of CCA1 abrogated heterosis for both defense and growth in hybrids. Upon pathogen attack, the expression of CCA1 in F1 hybrids is precisely modulated at different time points during the day by its rhythmic histone modifications. Before dawn of the first infection day, epigenetic activation of CCA1 promotes an elevation of salicylic acid accumulation in hybrids, enabling heterosis for defense. During the middle of every infection day, diurnal epigenetic repression of CCA1 leads to rhythmically increased chlorophyll synthesis and starch metabolism in hybrids, effectively eliminating the immunity-growth heterosis trade-offs in hybrids. There is frequently a trade-off between plant immunity and growth. Here the authors show that the epigenetic control of CCA1, encoding a core component of the circadian oscillator, simultaneously promotes heterosis for both defense and growth in hybrids under pathogen invasion.
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31
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Li Y, Lu Y, Zhou Y, Wei X, Peng Y, Dai Y, Zhang L, Zhu Z. Diurnal transcriptomics analysis reveals the regulatory role of the circadian rhythm in super-hybrid rice LY2186. Genomics 2021; 113:1281-1290. [PMID: 33705889 DOI: 10.1016/j.ygeno.2020.12.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/23/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022]
Abstract
Heterosis, an important biological phenomenon wherein F1 hybrids exhibit better performance than any of their parents, has been widely applied; however, its underlying mechanism remains largely unknown. Here, we studied and compared the dynamic transcriptional profiles of super-hybrid rice LY2186 and its parents at 17 time points during 2 day/night cycles and identified 1552 rhythmic differentially expressed genes (RDGs). Cluster and functional enrichment analyses revealed that the day- and night-phased RDGs were mainly enriched in the photosynthesis and stress response categories, respectively. Regulatory network analysis indicated that circadian-related RDGs are core components in both the day and night phases and extensively regulate downstream genes involved in photosynthesis, starch synthesis, plant hormone signal transduction, and other pathways. Furthermore, among the 282 RDGs mapped onto the quantitative tract loci of small intervals (≤100 genes), 72.3% were significantly enriched in the yield, vigor, and anatomy categories. These findings provide valuable information for exploring heterosis mechanisms further and guiding breeding practices.
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Affiliation(s)
- Yue Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yufei Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoli Wei
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yonggang Peng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Dai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Lei Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Zhen Zhu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
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32
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McClung CR. Circadian Clock Components Offer Targets for Crop Domestication and Improvement. Genes (Basel) 2021; 12:genes12030374. [PMID: 33800720 PMCID: PMC7999361 DOI: 10.3390/genes12030374] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 12/31/2022] Open
Abstract
During plant domestication and improvement, farmers select for alleles present in wild species that improve performance in new selective environments associated with cultivation and use. The selected alleles become enriched and other alleles depleted in elite cultivars. One important aspect of crop improvement is expansion of the geographic area suitable for cultivation; this frequently includes growth at higher or lower latitudes, requiring the plant to adapt to novel photoperiodic environments. Many crops exhibit photoperiodic control of flowering and altered photoperiodic sensitivity is commonly required for optimal performance at novel latitudes. Alleles of a number of circadian clock genes have been selected for their effects on photoperiodic flowering in multiple crops. The circadian clock coordinates many additional aspects of plant growth, metabolism and physiology, including responses to abiotic and biotic stresses. Many of these clock-regulated processes contribute to plant performance. Examples of selection for altered clock function in tomato demonstrate that with domestication, the phasing of the clock is delayed with respect to the light–dark cycle and the period is lengthened; this modified clock is associated with increased chlorophyll content in long days. These and other data suggest the circadian clock is an attractive target during breeding for crop improvement.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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33
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Liu Y, Yuan J, Jia G, Ye W, Jeffrey Chen Z, Song Q. Histone H3K27 dimethylation landscapes contribute to genome stability and genetic recombination during wheat polyploidization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:678-690. [PMID: 33131144 DOI: 10.1111/tpj.15063] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/21/2020] [Accepted: 10/27/2020] [Indexed: 05/02/2023]
Abstract
Bread wheat (Triticum aestivum) is an allohexaploid that was formed via two allopolyploidization events. Growing evidence suggests histone modifications are involved in the response to 'genomic shock' and environmental adaptation during polyploid formation and evolution. However, the role of histone modifications, especially histone H3 lysine-27 dimethylation (H3K27me2), in genome evolution remains elusive. Here we analyzed H3K27me2 and H3K27me3 profiles in hexaploid wheat and its tetraploid and diploid relatives. Although H3K27me3 levels were relatively stable among wheat species with different ploidy levels, H3K27me2 intensities increased concurrent with increased ploidy levels, and H3K27me2 peaks were colocalized with massively amplified DTC transposons (CACTA family) in euchromatin, which may silence euchromatic transposons to maintain genome stability during polyploid wheat evolution. Consistently, the distribution of H3K27me2 is mutually exclusive with another repressive histone mark, H3K9me2, that mainly silences transposons in heterochromatic regions. Remarkably, the regions with low H3K27me2 levels (named H3K27me2 valleys) were associated with the formation of DNA double-strand breaks in genomes of wheat, maize (Zea mays) and Arabidopsis. Our results provide a comprehensive view of H3K27me2 and H3K27me3 distributions during wheat evolution, which support roles for H3K27me2 in silencing euchromatic transposons to maintain genome stability and in modifying genetic recombination landscapes. These genomic insights may empower breeding improvement of crops.
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Affiliation(s)
- Yanfeng Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Jingya Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Guanghong Jia
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Z Jeffrey Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Qingxin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
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Li S, Zhou Y, Yang C, Fan S, Huang L, Zhou T, Wang Q, Zhao R, Tang C, Tao M, Liu S. Comparative analyses of hypothalamus transcriptomes reveal fertility-, growth-, and immune-related genes and signal pathways in different ploidy cyprinid fish. Genomics 2021; 113:595-605. [PMID: 33485949 DOI: 10.1016/j.ygeno.2021.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 01/12/2021] [Accepted: 01/18/2021] [Indexed: 12/23/2022]
Abstract
Triploid crucian carp (TCC) is obtained by hybridization of female diploid red crucian carp (Carassius auratus red var., RCC) and male allotetraploid hybrids. In this study, high-throughput sequencing was used to conduct the transcriptome analysis of the female hypothalamus of diploid RCC, diploid common carp (Cyprinus carpio L., CC) and TCC. The key functional expression genes of the hypothalamus were obtained through functional gene annotation and differential gene expression screening. A total of 71.56 G data and 47,572 genes were obtained through sequencing and genome mapping, respectively. The Fuzzy Analysis Clustering assigned the differentially expressed genes (DEGs) into eight groups, two of which, overdominance expression (6005, 12.62%) and underdominance expression (3849, 8.09%) in TCC were further studied. KEGG enrichment analysis showed that the DEGs in overdominance were mainly enriched in four pathways. The expression of several fertility-related genes was lower levels in TCC, whereas the expression of several growth-related genes and immune-related genes was higher levels in TCC. Besides, 15 DEGs were verified by quantitative real-time PCR (qPCR). The present study can provide a reference for breeding sterility, fast-growth, and disease-resistant varieties by distant hybridization.
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Affiliation(s)
- Shengnan Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Yi Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Conghui Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Siyu Fan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Lu Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Tian Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Qiubei Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Rurong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Chenchen Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha 410081, Hunan, PR China.
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha 410081, Hunan, PR China.
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Ko DK, Brandizzi F. A temporal hierarchy underpins the transcription factor-DNA interactome of the maize UPR. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:254-270. [PMID: 33098715 PMCID: PMC7942231 DOI: 10.1111/tpj.15044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 09/18/2020] [Accepted: 09/23/2020] [Indexed: 05/10/2023]
Abstract
Adverse environmental conditions reduce crop productivity and often increase the load of unfolded or misfolded proteins in the endoplasmic reticulum (ER). This potentially lethal condition, known as ER stress, is buffered by the unfolded protein response (UPR), a set of signaling pathways designed to either recover ER functionality or ignite programmed cell death. Despite the biological significance of the UPR to the life of the organism, the regulatory transcriptional landscape underpinning ER stress management is largely unmapped, especially in crops. To fill this significant knowledge gap, we performed a large-scale systems-level analysis of the protein-DNA interaction (PDI) network in maize (Zea mays). Using 23 promoter fragments of six UPR marker genes in a high-throughput enhanced yeast one-hybrid assay, we identified a highly interconnected network of 262 transcription factors (TFs) associated with significant biological traits and 831 PDIs underlying the UPR. We established a temporal hierarchy of TF binding to gene promoters within the same family as well as across different families of TFs. Cistrome analysis revealed the dynamic activities of a variety of cis-regulatory elements (CREs) in ER stress-responsive gene promoters. By integrating the cistrome results into a TF network analysis, we mapped a subnetwork of TFs associated with a CRE that may contribute to UPR management. Finally, we validated the role of a predicted network hub gene using the Arabidopsis system. The PDIs, TF networks, and CREs identified in our work are foundational resources for understanding transcription-regulatory mechanisms in the stress responses and crop improvement.
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Affiliation(s)
- Dae Kwan Ko
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, Michigan, 48824
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, 48824
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, Michigan, 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, 48824
- Correspondence:
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36
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Li Z, Zhu A, Song Q, Chen HY, Harmon FG, Chen ZJ. Temporal Regulation of the Metabolome and Proteome in Photosynthetic and Photorespiratory Pathways Contributes to Maize Heterosis. THE PLANT CELL 2020; 32:3706-3722. [PMID: 33004616 PMCID: PMC7721322 DOI: 10.1105/tpc.20.00320] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/17/2020] [Accepted: 09/29/2020] [Indexed: 05/04/2023]
Abstract
Heterosis or hybrid vigor is widespread in plants and animals. Although the molecular basis for heterosis has been extensively studied, metabolic and proteomic contributions to heterosis remain elusive. Here we report an integrative analysis of time-series metabolome and proteome data in maize (Zea mays) hybrids and their inbred parents. Many maize metabolites and proteins are diurnally regulated, and many of these show nonadditive abundance in the hybrids, including key enzymes and metabolites involved in carbon assimilation. Compared with robust trait heterosis, metabolic heterosis is relatively mild. Interestingly, most amino acids display negative mid-parent heterosis (MPH), i.e., having lower values than the average of the parents, while sugars, alcohols, and nucleoside metabolites show positive MPH. From the network perspective, metabolites in the photosynthetic pathway show positive MPH, whereas metabolites in the photorespiratory pathway show negative MPH, which corresponds to nonadditive protein abundance and enzyme activities of key enzymes in the respective pathways in the hybrids. Moreover, diurnally expressed proteins that are upregulated in the hybrids are enriched in photosynthesis-related gene-ontology terms. Hybrids may more effectively remove toxic metabolites generated during photorespiration, and thus maintain higher photosynthetic efficiency. These metabolic and proteomic resources provide unique insight into heterosis and its utilization for high yielding maize and other crop plants.
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Affiliation(s)
- Zhi Li
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Andan Zhu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Qingxin Song
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Helen Y Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Frank G Harmon
- Plant Gene Expression Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, California 94710
- Department of Plant & Microbial Biology, University of California, Berkeley, California 94720
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
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37
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Comparative physiological and transcriptomic analysis of pear leaves under distinct training systems. Sci Rep 2020; 10:18892. [PMID: 33144674 PMCID: PMC7641215 DOI: 10.1038/s41598-020-75794-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 10/19/2020] [Indexed: 12/21/2022] Open
Abstract
Canopy architecture is critical in determining the light interception and distribution, and subsequently the photosynthetic efficiency and productivity. However, the physiological responses and molecular mechanisms by which pear canopy architectural traits impact on photosynthesis remain poorly understood. Here, physiological investigations coupled with comparative transcriptomic analyses were performed in pear leaves under distinct training systems. Compared with traditional freestanding system, flat-type trellis system (DP) showed higher net photosynthetic rate (PN) levels at the most time points throughout the entire monitored period, especially for the interior of the canopy in sunny side. Gene ontology analysis revealed that photosynthesis, carbohydrate derivative catabolic process and fatty acid metabolic process were over-represented in leaves of DP system with open-canopy characteristics. Weighted gene co-expression network analysis uncovered a significant network module positive correlated with PN value. The hub genes (PpFKF1 and PpPRR5) of the module were enriched in circadian rhythm pathway, suggesting a functional role for circadian clock genes in mediating photosynthetic performance under distinct training systems. These results draw a link between pear photosynthetic response and specific canopy architectural traits, and highlight light harvesting and circadian clock network as potential targets for the input signals from the fluctuating light availability under distinct training systems.
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38
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Wang F, Han T, Song Q, Ye W, Song X, Chu J, Li J, Chen ZJ. The Rice Circadian Clock Regulates Tiller Growth and Panicle Development Through Strigolactone Signaling and Sugar Sensing. THE PLANT CELL 2020; 32:3124-3138. [PMID: 32796126 PMCID: PMC7534462 DOI: 10.1105/tpc.20.00289] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/20/2020] [Accepted: 08/12/2020] [Indexed: 05/15/2023]
Abstract
Circadian clocks regulate growth and development in plants and animals, but the role of circadian regulation in crop production is poorly understood. Rice (Oryza sativa) grain yield is largely determined by tillering, which is mediated by physiological and genetic factors. Here we report a regulatory loop that involves the circadian clock, sugar, and strigolactone (SL) pathway to regulate rice tiller-bud and panicle development. Rice CIRCADIAN CLOCK ASSOCIATED1 (OsCCA1) positively regulates expression of TEOSINTE BRANCHED1 (OsTB1, also known as FC1), DWARF14 (D14), and IDEAL PLANT ARCHITECTURE1 (IPA1, also known as OsSPL14) to repress tiller-bud outgrowth. Downregulating and overexpressing OsCCA1 increases and reduces tiller numbers, respectively, whereas manipulating PSEUDORESPONSE REGULATOR1 (OsPPR1) expression results in the opposite effects. OsCCA1 also regulates IPA1 expression to mediate panicle and grain development. Genetic analyses using double mutants and overexpression in the mutants show that OsTB1, D14, and IPA1 act downstream of OsCCA1 Sugars repress OsCCA1 expression in roots and tiller buds to promote tiller-bud outgrowth. The circadian clock integrates sugar responses and the SL pathway to regulate tiller and panicle development, providing insights into improving plant architecture and yield in rice and other cereal crops.
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Affiliation(s)
- Fang Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Tongwen Han
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Qingxin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoguang Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100049, China
| | - Jinfang Chu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100049, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100049, China
| | - Z Jeffrey Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
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39
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MacKinnon KJM, Cole BJ, Yu C, Coomey JH, Hartwick NT, Remigereau MS, Duffy T, Michael TP, Kay SA, Hazen SP. Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation. THE NEW PHYTOLOGIST 2020; 227:1709-1724. [PMID: 32112414 DOI: 10.1111/nph.16507] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
Plants are continuously exposed to diurnal fluctuations in light and temperature, and spontaneous changes in their physical or biotic environment. The circadian clock coordinates regulation of gene expression with a 24 h period, enabling the anticipation of these events. We used RNA sequencing to characterize the Brachypodium distachyon transcriptome under light and temperature cycles, as well as under constant conditions. Approximately 3% of the transcriptome was regulated by the circadian clock, a smaller proportion than reported in most other species. For most transcripts that were rhythmic under all conditions, including many known clock genes, the period of gene expression lengthened from 24 to 27 h in the absence of external cues. To functionally characterize the cyclic transcriptome in B. distachyon, we used Gene Ontology enrichment analysis, and found several terms significantly associated with peak expression at particular times of the day. Furthermore, we identified sequence motifs enriched in the promoters of similarly phased genes, some potentially associated with transcription factors. When considering the overlap in rhythmic gene expression and specific pathway behavior, thermocycles was the prevailing cue that controlled diurnal gene regulation. Taken together, our characterization of the rhythmic B. distachyon transcriptome represents a foundational resource with implications in other grass species.
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Affiliation(s)
- Kirk J-M MacKinnon
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, 01003, USA
| | - Benjamin J Cole
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Chang Yu
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
| | - Joshua H Coomey
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, 01003, USA
| | | | - Marie-Stanislas Remigereau
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Tomás Duffy
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | | | - Steve A Kay
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Samuel P Hazen
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
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40
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Liu T, Duan W, Chen Z, Yuan J, Xiao D, Hou X, Li Y. Enhanced photosynthetic activity in pak choi hybrids is associated with increased grana thylakoids in chloroplasts. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:2211-2224. [PMID: 32573878 DOI: 10.1111/tpj.14893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/01/2020] [Accepted: 06/12/2020] [Indexed: 05/12/2023]
Abstract
Increased photosynthetic activity is closely linked to heterosis in plants, but the underlying molecular mechanisms remain elusive. Pak choi (Brassica rapa ssp. chinensis) is a widely grown vegetable in Asia, and the most commercial cultivars are F1 hybrids. Here, the inbred pak choi lines WTC and 2Q, and their reciprocal F1 hybrids WQ and QW, were used to characterize the increased photosynthetic activity in these hybrids at the physiological, cellular and molecular levels. We found that the hybrids had larger leaves, with more grana thylakoids. Additionally, these hybrids had significantly increased net photosynthetic rates (Pn ) under both saturating and low irradiance conditions. These data indicate that the increased photosynthetic activity in pak choi hybrids was associated with an improved photosynthetic mechanism and larger leaves. Next, we obtained genome-wide data using transcriptome and bisulfite sequencing. Gene ontology (GO) analysis showed that the differentially expressed genes among the parents and hybrids were mostly enriched in the 'photosynthesis', 'thylakoid', and 'chloroplast' categories, indicating that the increased number of grana thylakoids contributes to the enhanced photosynthetic capacity in hybrids. Furthermore, we found that the increased number of grana thylakoids was associated with the upregulation of light-harvesting complex of photosystem II 1 (BrLhcb1). Yeast one-hybrid and transient assay showed that the BrLhcb1 promoter was directly bound by CIRCADIAN CLOCK ASSOCIATED 1 (BrCCA1), resulting in increased BrLhcb1 expression and enhanced carbon fixation in hybrids. Finally, our findings provide new insight into molecular mechanisms underlying enhanced photosynthesis in pak choi hybrids.
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Affiliation(s)
- Tongkun Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weike Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Life science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Zhongwen Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jingping Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dong Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
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Inoue K, Takahagi K, Kouzai Y, Koda S, Shimizu M, Uehara-Yamaguchi Y, Nakayama R, Kita T, Onda Y, Nomura T, Matsui H, Nagaki K, Nishii R, Mochida K. Parental legacy and regulatory novelty in Brachypodium diurnal transcriptomes accompanying their polyploidy. NAR Genom Bioinform 2020; 2:lqaa067. [PMID: 33575616 PMCID: PMC7671347 DOI: 10.1093/nargab/lqaa067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 08/15/2020] [Accepted: 08/31/2020] [Indexed: 11/22/2022] Open
Abstract
Polyploidy is a widespread phenomenon in eukaryotes that can lead to phenotypic novelty and has important implications for evolution and diversification. The modification of phenotypes in polyploids relative to their diploid progenitors may be associated with altered gene expression. However, it is largely unknown how interactions between duplicated genes affect their diurnal expression in allopolyploid species. In this study, we explored parental legacy and hybrid novelty in the transcriptomes of an allopolyploid species and its diploid progenitors. We compared the diurnal transcriptomes of representative Brachypodium cytotypes, including the allotetraploid Brachypodium hybridum and its diploid progenitors Brachypodium distachyon and Brachypodium stacei. We also artificially induced an autotetraploid B. distachyon. We identified patterns of homoeolog expression bias (HEB) across Brachypodium cytotypes and time-dependent gain and loss of HEB in B. hybridum. Furthermore, we established that many genes with diurnal expression experienced HEB, while their expression patterns and peak times were correlated between homoeologs in B. hybridum relative to B. distachyon and B. stacei, suggesting diurnal synchronization of homoeolog expression in B. hybridum. Our findings provide insight into the parental legacy and hybrid novelty associated with polyploidy in Brachypodium, and highlight the evolutionary consequences of diurnal transcriptional regulation that accompanied allopolyploidy.
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Affiliation(s)
- Komaki Inoue
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Kotaro Takahagi
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, 244-0813, Japan
- Graduate School of Nanobioscience, Yokohama City University, Kanazawa-ku, Yokohama, 236-0027, Japan
| | - Yusuke Kouzai
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Satoru Koda
- Graduate School of Mathematics, Kyushu University, Fukuoka, 819-0395, Japan
| | - Minami Shimizu
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | | | - Risa Nakayama
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Toshie Kita
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Yoshihiko Onda
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Toshihisa Nomura
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Hidetoshi Matsui
- Faculty of Data Science, Shiga University, Hikone, 522-8522, Japan
| | - Kiyotaka Nagaki
- Institute of Plant Science and Resources, Okayama University,710-0046, Kurashiki, Japan
| | - Ryuei Nishii
- School of Information and Data Science, Nagasaki University, Nagasaki, 852-8131, Japan
| | - Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, 244-0813, Japan
- Graduate School of Nanobioscience, Yokohama City University, Kanazawa-ku, Yokohama, 236-0027, Japan
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama, 230-0045, Japan
- Institute of Plant Science and Resources, Okayama University,710-0046, Kurashiki, Japan
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42
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Sinha P, Singh VK, Saxena RK, Kale SM, Li Y, Garg V, Meifang T, Khan AW, Kim KD, Chitikineni A, Saxena KB, Sameer Kumar CV, Liu X, Xu X, Jackson S, Powell W, Nevo E, Searle IR, Lodha M, Varshney RK. Genome-wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1697-1710. [PMID: 31925873 PMCID: PMC7336283 DOI: 10.1111/pbi.13333] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 12/26/2019] [Indexed: 05/20/2023]
Abstract
Hybrids are extensively used in agriculture to deliver an increase in yield, yet the molecular basis of heterosis is not well understood. Global DNA methylation analysis, transcriptome analysis and small RNA profiling were aimed to understand the epigenetic effect of the changes in gene expression level in the two hybrids and their parental lines. Increased DNA methylation was observed in both the hybrids as compared to their parents. This increased DNA methylation in hybrids showed that majority of the 24-nt siRNA clusters had higher expression in hybrids than the parents. Transcriptome analysis revealed that various phytohormones (auxin and salicylic acid) responsive hybrid-MPV DEGs were significantly altered in both the hybrids in comparison to MPV. DEGs associated with plant immunity and growth were overexpressed whereas DEGs associated with basal defence level were repressed. This antagonistic patterns of gene expression might contribute to the greater growth of the hybrids. It was also noticed that some common as well as unique changes in the regulatory pathways were associated with heterotic growth in both the hybrids. Approximately 70% and 67% of down-regulated hybrid-MPV DEGs were found to be differentially methylated in ICPH 2671 and ICPH 2740 hybrid, respectively. This reflected the association of epigenetic regulation in altered gene expressions. Our findings also revealed that miRNAs might play important roles in hybrid vigour in both the hybrids by regulating their target genes, especially in controlling plant growth and development, defence and stress response pathways. The above finding provides an insight into the molecular mechanism of pigeonpea heterosis.
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Affiliation(s)
- Pallavi Sinha
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - Vikas K. Singh
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
- International Rice Research Institute, South‐Asia HubPatancheruIndia
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - Sandip M. Kale
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
- The Leibniz Institute of Plant Genetics and Crop Plant ResearchGaterslebenGermany
| | | | - Vanika Garg
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | | | - Aamir W. Khan
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - Kyung Do Kim
- University of GeorgiaAthensUSA
- Myongji UniversityYonginRepublic of Korea
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - K. B. Saxena
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - C. V. Sameer Kumar
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | | | - Xun Xu
- BGI‐ShenzhenShenzhenChina
| | | | | | | | | | - Mukesh Lodha
- Centre for Cellular and Molecular Biology (CSIR)HyderabadIndia
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
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43
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Lai X, Bendix C, Yan L, Zhang Y, Schnable JC, Harmon FG. Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs. BMC Genomics 2020; 21:428. [PMID: 32586356 PMCID: PMC7315539 DOI: 10.1186/s12864-020-06824-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/12/2020] [Indexed: 11/17/2022] Open
Abstract
Background The circadian clock drives endogenous 24-h rhythms that allow organisms to adapt and prepare for predictable and repeated changes in their environment throughout the day-night (diurnal) cycle. Many components of the circadian clock in Arabidopsis thaliana have been functionally characterized, but comparatively little is known about circadian clocks in grass species including major crops like maize and sorghum. Results Comparative research based on protein homology and diurnal gene expression patterns suggests the function of some predicted clock components in grasses is conserved with their Arabidopsis counterparts, while others have diverged in function. Our analysis of diurnal gene expression in three panicoid grasses sorghum, maize, and foxtail millet revealed conserved and divergent evolution of expression for core circadian clock genes and for the overall transcriptome. We find that several classes of core circadian clock genes in these grasses differ in copy number compared to Arabidopsis, but mostly exhibit conservation of both protein sequence and diurnal expression pattern with the notable exception of maize paralogous genes. We predict conserved cis-regulatory motifs shared between maize, sorghum, and foxtail millet through identification of diurnal co-expression clusters for a subset of 27,196 orthologous syntenic genes. In this analysis, a Cochran–Mantel–Haenszel based method to control for background variation identified significant enrichment for both expected and novel 6–8 nucleotide motifs in the promoter regions of genes with shared diurnal regulation predicted to function in common physiological activities. Conclusions This study illustrates the divergence and conservation of circadian clocks and diurnal regulatory networks across syntenic orthologous genes in panacoid grass species. Further, conserved local regulatory sequences contribute to the architecture of these diurnal regulatory networks that produce conserved patterns of diurnal gene expression.
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Affiliation(s)
- Xianjun Lai
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, USA.,College of Agricultural Sciences, Xichang University, Liangshan, Xichang, 615000, China
| | - Claire Bendix
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA.,Plant Gene Expression Center, USDA-ARS, Albany, CA, 94710, USA
| | - Lang Yan
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, USA.,College of Agricultural Sciences, Xichang University, Liangshan, Xichang, 615000, China
| | - Yang Zhang
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, USA
| | - James C Schnable
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, USA.
| | - Frank G Harmon
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA. .,Plant Gene Expression Center, USDA-ARS, Albany, CA, 94710, USA.
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44
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Kebrom TH, McKinley BA, Mullet JE. Shade signals alter the expression of circadian clock genes in newly-formed bioenergy sorghum internodes. PLANT DIRECT 2020; 4:e00235. [PMID: 32607464 PMCID: PMC7315773 DOI: 10.1002/pld3.235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 06/11/2023]
Abstract
Stem internodes of bioenergy sorghum inbred R.07020 are longer at high plant density (shade) than at low plant density (control). Initially, the youngest newly-formed subapical stem internodes of shade-treated and control plants are comparable in length. However, full-length internodes of shade-treated plants are three times longer than the internodes of the control plants. To identify the early molecular events associated with internode elongation in response to shade, we analyzed the transcriptome of the newly-formed internodes of shade-treated and control plants sampled between 4 and 6 hr after the start of the light period (14 hr light/10 hr dark). Sorghum genes homologous to the Arabidopsis shade marker genes ATHB2 and PIL1 were not differentially expressed. The results indicate that shade signals promote internode elongation indirectly because sorghum internodes are not illuminated and grow while enclosed with leaf sheaths. Sorghum genes homologous to the Arabidopsis morning-phased circadian clock genes LHY, RVE, and LNK were downregulated and evening-phased genes such as TOC1, PRR5, and GI were upregulated in young internodes in response to shade. We hypothesize that a change in the function or patterns of expression of the circadian clock genes is the earliest molecular event associated with internode elongation in response to shade in bioenergy sorghum. Increased expression of CycD1, which promotes cell division, and decreased expression of cell wall-loosening and MBF1-like genes, which promote cell expansion, suggest that shade signals promote internode elongation in bioenergy sorghum in part through increasing cell number by delaying transition from cell division to cell expansion.
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Affiliation(s)
- Tesfamichael H. Kebrom
- Cooperative Agricultural Research CenterCollege of Agriculture and Human SciencesPrairie View A&M UniversityPrairie ViewTXUSA
- Center for Computational Systems BiologyCollege of EngineeringPrairie View A&M UniversityPrairie ViewTXUSA
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Brian A. McKinley
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - John E. Mullet
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
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45
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Zhu A, Wang A, Zhang Y, Dennis ES, Peacock WJ, Greaves AIK. Early Establishment of Photosynthesis and Auxin Biosynthesis Plays a Key Role in Early Biomass Heterosis in Brassica napus (Canola) Hybrids. PLANT & CELL PHYSIOLOGY 2020; 61:1134-1143. [PMID: 32215572 DOI: 10.1093/pcp/pcaa038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/16/2020] [Indexed: 05/26/2023]
Abstract
Heterosis or hybrid vigor has been used widely for more than a decade in Canola (Brassica napus) production. Canola hybrids show heterosis in a variety of traits compared to parents, including increased biomass at the early stages of seedling establishment, which is a critical developmental step that impacts future plant growth and seed yield. In this study, we examined transcriptomes of two parental lines, Garnet (Gar) and NX0052 (0052), and their reciprocal hybrids, Gar/0052, at 4 and 8 days after sowing (DAS). In hybrids, early seedling biomass heterosis is correlated with earlier expression of genes in photosynthesis pathways relative to parents. The hybrids also showed early expression of genes in the auxin biosynthesis pathway, consistent with the higher auxin concentrations detected in hybrid seedlings at 4 DAS. Auxin is a key phytohormone that regulates plant development promoting cell expansion and cell proliferation. Consistent with the increased levels of auxin, hybrids have larger and more palisade cells than the parents at the same time point. We propose a possible mechanism of early biomass heterosis through the early establishment of photosynthesis and auxin biosynthesis, providing insights into how transcriptional changes in hybrids are translated into phenotypical heterosis. This finding could be utilized in future Canola breeding to identify hybrid combinations with the superior early seedling establishment and strong levels of hybrid vigor in later plant development.
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Affiliation(s)
- Anyu Zhu
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, Australian Capital Territory 2600, Australia
| | - Aihua Wang
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, Australian Capital Territory 2600, Australia
| | - You Zhang
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, Australian Capital Territory 2600, Australia
- School of Life Sciences, Faculty of Science, University of Technology, Sydney, New South Wales 2007, Australia
| | - Elizabeth S Dennis
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, Australian Capital Territory 2600, Australia
- School of Life Sciences, Faculty of Science, University of Technology, Sydney, New South Wales 2007, Australia
| | - W James Peacock
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, Australian Capital Territory 2600, Australia
- School of Life Sciences, Faculty of Science, University of Technology, Sydney, New South Wales 2007, Australia
| | - And Ian K Greaves
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, Australian Capital Territory 2600, Australia
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46
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Zhang C, Wang H, Xu Y, Zhang S, Wang J, Hu B, Hou X, Li Y, Liu T. Enhanced Relative Electron Transport Rate Contributes to Increased Photosynthetic Capacity in Autotetraploid Pak Choi. PLANT & CELL PHYSIOLOGY 2020; 61:761-774. [PMID: 31904850 DOI: 10.1093/pcp/pcz238] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 12/26/2019] [Indexed: 06/10/2023]
Abstract
Autopolyploids often show growth advantages over their diploid progenitors because of their increased photosynthetic activity; however, the underlying molecular basis of such mechanism remains elusive. In this study, we aimed to characterize autotetraploid pak choi (Brassica rapa ssp. chinensis) at the physiological, cellular and molecular levels. Autotetraploid pak choi has thicker leaves than its diploid counterparts, with relatively larger intercellular spaces and cell size and greater grana thylakoid height. Photosynthetic data showed that the relative electron transport rate (rETR) was markedly higher in autotetraploid than in diploid pak choi. Transcriptomic data revealed that the expressions of genes involved in 'photosynthesis' biological process and 'thylakoids' cellular component were mainly regulated in autotetraploids. Overall, our findings suggested that the increased rETR in the thylakoids contributed to the increased photosynthetic capacity of autotetraploid leaves. Furthermore, we found that the enhanced rETR is associated with increased BrPetC expression, which is likely altered by histone modification. The ectopic expression of BrPetC in Arabidopsis thaliana led to increased rETR and biomass, which were decreased in BrPetC-silenced pak choi. Autotetraploid pak choi also shows altered hormone levels, which was likely responsible for the increased drought resistance and the impaired powdery mildew resistance of this lineage. Our findings further our understanding on how autotetraploidy provides growth advantages to plants.
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Affiliation(s)
- Changwei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Department of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Huiyu Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Department of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanyuan Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Department of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuning Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Department of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianjun Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Department of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Bing Hu
- Department of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Department of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Department of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Tongkun Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Department of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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47
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Shi Y, Zhao X, Guo S, Dong S, Wen Y, Han Z, Jin W, Chen Y. ZmCCA1a on Chromosome 10 of Maize Delays Flowering of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2020; 11:78. [PMID: 32153606 PMCID: PMC7044342 DOI: 10.3389/fpls.2020.00078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/20/2020] [Indexed: 06/01/2023]
Abstract
Maize (Zea mays) is a major cereal crop that originated at low latitudes, and thus photoperiod sensitivity is an important barrier to the use of tropical/subtropical germplasm in temperate regions. However, studies of the mechanisms underlying circadian regulation in maize are at an early stage. In this study we cloned ZmCCA1a on chromosome 10 of maize by map-based cloning. The gene is homologous to the Myb transcription factor genes AtCCA1/AtLHY in Arabidopsis thaliana; the deduced Myb domain of ZmCCA1a showed high similarity with that of AtCCA1/AtLHY and ZmCCA1b. Transiently or constitutively expressed ZmCCA1a-YFPs were localized to nuclei of Arabidopsis mesophyll protoplasts, agroinfiltrated tobacco leaves, and leaf and root cells of transgenic seedlings of Arabidopsis thaliana. Unlike AtCCA1/AtLHY, ZmCCA1a did not form homodimers nor interact with ZmCCA1b. Transcripts of ZmCCA1a showed circadian rhythm with peak expression around sunrise in maize inbred lines CML288 (photoperiod sensitive) and Huangzao 4 (HZ4; photoperiod insensitive). Under short days, transcription of ZmCCA1a in CML288 and HZ4 was repressed compared with that under long days, whereas the effect of photoperiod on ZmCCA1a expression was moderate in HZ4. In ZmCCA1a-overexpressing A. thaliana (ZmCCA1a-ox) lines, the circadian rhythm was disrupted under constant light and flowering was delayed under long days, but the hypocotyl length was not affected. In addition, expression of endogenous AtCCA1/AtLHY and the downstream genes AtGI, AtCO, and AtFt was repressed in ZmCCA1a-ox seedlings. The present results suggest that the function of ZmCCA1a is similar, at least in part, to that of AtCCA1/AtLHY and ZmCCA1b, implying that ZmCCA1a is likely to be an important component of the circadian clock pathway in maize.
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Affiliation(s)
- Yong Shi
- College of Agronomy/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Xiyong Zhao
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Sha Guo
- College of Agronomy/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Shifeng Dong
- College of Agronomy/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Yanpeng Wen
- College of Agronomy/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Zanping Han
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
| | - Weihuan Jin
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yanhui Chen
- College of Agronomy/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
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48
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Shahzad K, Zhang X, Guo L, Qi T, Tang H, Zhang M, Zhang B, Wang H, Qiao X, Feng J, Wu J, Xing C. Comparative transcriptome analysis of inbred lines and contrasting hybrids reveals overdominance mediate early biomass vigor in hybrid cotton. BMC Genomics 2020; 21:140. [PMID: 32041531 PMCID: PMC7011360 DOI: 10.1186/s12864-020-6561-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 02/06/2020] [Indexed: 12/11/2022] Open
Abstract
Background Heterosis breeding is the most useful method for yield increase around the globe. Heterosis is an intriguing process to develop superior offspring to either parent in the desired character. The biomass vigor produced during seedling emergence stage has a direct influence on yield heterosis in plants. Unfortunately, the genetic basis of early biomass vigor in cotton is poorly understood. Results Three stable performing F1 hybrids varying in yield heterosis named as high, medium and low hybrids with their inbred parents were used in this study. Phenotypically, these hybrids established noticeable biomass heterosis during the early stage of seedling growth in the field. Transcriptome analysis of root and leaf revealed that hybrids showed many differentially expressed genes (DEGs) relative to their parents, while the comparison of inbred parents showed limited number of DEGs indicating similarity in their genetic constitution. Further analysis indicated expression patterns of most DEGs were overdominant in both tissues of hybrids. According to GO results, functions of overdominance genes in leaf were enriched for chloroplast, membrane, and protein binding, whereas functions of overdominance genes in root were enriched for plasma membrane, extracellular region, and responses to stress. We found several genes of circadian rhythm pathway related to LATE ELONGATED HYPOCOTYL (LHY) showed downregulated overdominant expressions in both tissues of hybrids. In addition to circadian rhythm, several leaf genes related to Aux/IAA regulation, and many root genes involved in peroxidase activity also showed overdominant expressions in hybrids. Twelve genes involved in circadian rhythm plant were selected to perform qRT-PCR analysis to confirm the accuracy of RNA-seq results. Conclusions Through genome-wide comparative transcriptome analysis, we strongly predict that overdominance at gene expression level plays a pivotal role in early biomass vigor of hybrids. The combinational contribution of circadian rhythm and other metabolic process may control vigorous growth in hybrids. Our result provides an important foundation for dissecting molecular mechanisms of biomass vigor in hybrid cotton.
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Affiliation(s)
- Kashif Shahzad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China
| | - Xuexian Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China
| | - Liping Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China
| | - Tingxiang Qi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China
| | - Huini Tang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China
| | - Meng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China
| | - Bingbing Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China
| | - Hailin Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China
| | - Xiuqin Qiao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China
| | - Juanjuan Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China
| | - Jianyong Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China.
| | - Chaozhu Xing
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, China.
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Interaction between the Circadian Clock and Regulators of Heat Stress Responses in Plants. Genes (Basel) 2020; 11:genes11020156. [PMID: 32024106 PMCID: PMC7074488 DOI: 10.3390/genes11020156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 01/29/2020] [Accepted: 01/29/2020] [Indexed: 02/07/2023] Open
Abstract
The circadian clock is found ubiquitously in nature, and helps organisms coordinate internal biological processes with environmental cues that inform the time of the day or year. Both temperature stress and the clock affect many important biological processes in plants. Specifically, clock-controlled gene regulation and growth are impacted by a compromised clock or heat stress. The interactions linking these two regulatory pathways include several rhythmic transcription factors that are important for coordinating the appropriate response to temperature stress. Here we review the current understanding of clock control of the regulators involved in heat stress responses in plants.
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50
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Liu H, Wang Q, Chen M, Ding Y, Yang X, Liu J, Li X, Zhou C, Tian Q, Lu Y, Fan D, Shi J, Zhang L, Kang C, Sun M, Li F, Wu Y, Zhang Y, Liu B, Zhao XY, Feng Q, Yang J, Han B, Lai J, Zhang XS, Huang X. Genome-wide identification and analysis of heterotic loci in three maize hybrids. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:185-194. [PMID: 31199059 PMCID: PMC6920156 DOI: 10.1111/pbi.13186] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/01/2019] [Accepted: 06/04/2019] [Indexed: 05/18/2023]
Abstract
Heterosis, or hybrid vigour, is a predominant phenomenon in plant genetics, serving as the basis of crop hybrid breeding, but the causative loci and genes underlying heterosis remain unclear in many crops. Here, we present a large-scale genetic analysis using 5360 offsprings from three elite maize hybrids, which identifies 628 loci underlying 19 yield-related traits with relatively high mapping resolutions. Heterotic pattern investigations of the 628 loci show that numerous loci, mostly with complete-incomplete dominance (the major one) or overdominance effects (the secondary one) for heterozygous genotypes and nearly equal proportion of advantageous alleles from both parental lines, are the major causes of strong heterosis in these hybrids. Follow-up studies for 17 heterotic loci in an independent experiment using 2225 F2 individuals suggest most heterotic effects are roughly stable between environments with a small variation. Candidate gene analysis for one major heterotic locus (ub3) in maize implies that there may exist some common genes contributing to crop heterosis. These results provide a community resource for genetics studies in maize and new implications for heterosis in plants.
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Affiliation(s)
- Hongjun Liu
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Qin Wang
- Shanghai Key Laboratory of Plant Molecular SciencesCollege of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Mengjiao Chen
- Shanghai Key Laboratory of Plant Molecular SciencesCollege of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Yahui Ding
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Xuerong Yang
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Jie Liu
- Shanghai Key Laboratory of Plant Molecular SciencesCollege of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Xiaohan Li
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Congcong Zhou
- National Center for Gene ResearchCAS Center for Excellence of Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Qilin Tian
- National Center for Gene ResearchCAS Center for Excellence of Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Yiqi Lu
- National Center for Gene ResearchCAS Center for Excellence of Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Danlin Fan
- National Center for Gene ResearchCAS Center for Excellence of Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Junpeng Shi
- State Key Laboratory of Agrobiotechnology and National Maize Improvement CenterDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Lin Zhang
- College of AgricultureNortheast Agricultural UniversityHarbinChina
| | - Congbin Kang
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Mingfei Sun
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Fangyuan Li
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Yujian Wu
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Yongzhong Zhang
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai'anChina
| | - Baoshen Liu
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai'anChina
| | - Xiang Yu Zhao
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Qi Feng
- National Center for Gene ResearchCAS Center for Excellence of Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Jinliang Yang
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Bin Han
- National Center for Gene ResearchCAS Center for Excellence of Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology and National Maize Improvement CenterDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Xian Sheng Zhang
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular SciencesCollege of Life SciencesShanghai Normal UniversityShanghaiChina
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