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Zhan W, Cui L, Yang S, Zhang K, Zhang Y, Yang J. Natural variations of heterosis-related allele-specific expression genes in promoter regions lead to allele-specific expression in maize. BMC Genomics 2024; 25:476. [PMID: 38745122 PMCID: PMC11092226 DOI: 10.1186/s12864-024-10395-y] [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: 03/29/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Heterosis has successfully enhanced maize productivity and quality. Although significant progress has been made in delineating the genetic basis of heterosis, the molecular mechanisms underlying its genetic components remain less explored. Allele-specific expression (ASE), the imbalanced expression between two parental alleles in hybrids, is increasingly being recognized as a factor contributing to heterosis. ASE is a complex process regulated by both epigenetic and genetic variations in response to developmental and environmental conditions. RESULTS In this study, we explored the differential characteristics of ASE by analyzing the transcriptome data of two maize hybrids and their parents under four light conditions. On the basis of allele expression patterns in different hybrids under various conditions, ASE genes were divided into three categories: bias-consistent genes involved in basal metabolic processes in a functionally complementary manner, bias-reversal genes adapting to the light environment, and bias-specific genes maintaining cell homeostasis. We observed that 758 ASE genes (ASEGs) were significantly overlapped with heterosis quantitative trait loci (QTLs), and high-frequency variations in the promoter regions of heterosis-related ASEGs were identified between parents. In addition, 10 heterosis-related ASEGs participating in yield heterosis were selected during domestication. CONCLUSIONS The comprehensive analysis of ASEGs offers a distinctive perspective on how light quality influences gene expression patterns and gene-environment interactions, with implications for the identification of heterosis-related ASEGs to enhance maize yield.
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Affiliation(s)
- Weimin Zhan
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Lianhua Cui
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Shuling Yang
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Kangni Zhang
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yanpei Zhang
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Jianping Yang
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
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2
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Kakoulidou I, Johannes F. DNA methylation remodeling in F1 hybrids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:671-681. [PMID: 36752648 DOI: 10.1111/tpj.16137] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/20/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
F1 hybrids derived from a cross between two inbred parental lines often display widespread changes in DNA methylation patterns relative to their parents. To which extent these changes drive non-additive gene expression levels and phenotypic heterosis in F1 individuals is not fully resolved. Current mechanistic models propose that DNA methylation remodeling in hybrids is the result of epigenetic interactions between parental alleles via small interfering RNA (sRNA). These models have strong empirical support but are limited to genomic regions where the two parental lines differ in DNA methylation status. However, most remodeling events occur in parental regions with similar methylation patterns, and seem to be strongly conditioned by distally acting factors, even in isogenic hybrid systems. The molecular basis of these distal interactions is currently unknown, and will likely emerge as an active area of research in the future. Despite these gaps in our molecular understanding, parental DNA methylation states are statistically associated with heterosis, independent of genetic information, and may serve as biomarkers in crop breeding.
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Affiliation(s)
- Ioanna Kakoulidou
- Plant Epigenomics, Technical University of Munich, Emil-Ramman-Str. 4, 85354, Freising, Germany
| | - Frank Johannes
- Plant Epigenomics, Technical University of Munich, Emil-Ramman-Str. 4, 85354, Freising, Germany
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3
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Kakoulidou I, Piecyk RS, Meyer RC, Kuhlmann M, Gutjahr C, Altmann T, Johannes F. Mapping parental DMRs predictive of local and distal methylome remodeling in epigenetic F1 hybrids. Life Sci Alliance 2024; 7:e202402599. [PMID: 38290756 PMCID: PMC10828516 DOI: 10.26508/lsa.202402599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/01/2024] Open
Abstract
F1 hybrids derived from a cross between two inbred parental lines often display widespread changes in DNA methylation and gene expression patterns relative to their parents. An emerging challenge is to understand how parental epigenomic differences contribute to these events. Here, we generated a large mapping panel of F1 epigenetic hybrids, whose parents are isogenic but variable in their DNA methylation patterns. Using a combination of multi-omic profiling and epigenetic mapping strategies we show that differentially methylated regions in parental pericentromeres act as major reorganizers of hybrid methylomes and transcriptomes, even in the absence of genetic variation. These parental differentially methylated regions are associated with hybrid methylation remodeling events at thousands of target regions throughout the genome, both locally (in cis) and distally (in trans). Many of these distally-induced methylation changes lead to nonadditive expression of nearby genes and associate with phenotypic heterosis. Our study highlights the pleiotropic potential of parental pericentromeres in the functional remodeling of hybrid genomes and phenotypes.
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Affiliation(s)
- Ioanna Kakoulidou
- https://ror.org/02kkvpp62 Plant Epigenomics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Robert S Piecyk
- https://ror.org/02kkvpp62 Plant Epigenomics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Rhonda C Meyer
- https://ror.org/02skbsp27 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Markus Kuhlmann
- https://ror.org/02skbsp27 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Caroline Gutjahr
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Thomas Altmann
- https://ror.org/02skbsp27 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Frank Johannes
- https://ror.org/02kkvpp62 Plant Epigenomics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
- https://ror.org/02kkvpp62 Institute of Advanced Studies, Technical University of Munich, Munich, Germany
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4
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Liu W, He G, Deng XW. Toward understanding and utilizing crop heterosis in the age of biotechnology. iScience 2024; 27:108901. [PMID: 38533455 PMCID: PMC10964264 DOI: 10.1016/j.isci.2024.108901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Abstract
Heterosis, a universal phenomenon in nature, mainly reflected in the superior productivity, quality, and fitness of F1 hybrids compared with their inbred parents, has been exploited in agriculture and greatly benefited human society in terms of food security. However, the flexible and efficient utilization of heterosis has remained a challenge in hybrid breeding systems because of the limitations of "three-line" and "two-line" methods. In the past two decades, rapidly developed biotechnologies have provided unprecedented conveniences for both understanding and utilizing heterosis. Notably, "third-generation" (3G) hybrid breeding technology together with high-throughput sequencing and gene editing greatly promoted the efficiency of hybrid breeding. Here, we review emerging ideas about the genetic or molecular mechanisms of heterosis and the development of 3G hybrid breeding system in the age of biotechnology. In addition, we summarized opportunities and challenges for optimal heterosis utilization in the future.
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Affiliation(s)
- Wenwen Liu
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
| | - Guangming He
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
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5
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Gao Z, Su Y, Chang L, Jiao G, Ou Y, Yang M, Xu C, Liu P, Wang Z, Qi Z, Liu W, Sun L, He G, Deng XW, He H. Increased long-distance and homo-trans interactions related to H3K27me3 in Arabidopsis hybrids. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:208-227. [PMID: 38326968 DOI: 10.1111/jipb.13620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 01/04/2024] [Indexed: 02/09/2024]
Abstract
In plants, the genome structure of hybrids changes compared with their parents, but the effects of these changes in hybrids remain elusive. Comparing reciprocal crosses between Col × C24 and C24 × Col in Arabidopsis using high-throughput chromosome conformation capture assay (Hi-C) analysis, we found that hybrid three-dimensional (3D) chromatin organization had more long-distance interactions relative to parents, and this was mainly located in promoter regions and enriched in genes with heterosis-related pathways. The interactions between euchromatin and heterochromatin were increased, and the compartment strength decreased in hybrids. In compartment domain (CD) boundaries, the distal interactions were more in hybrids than their parents. In the hybrids of CURLY LEAF (clf) mutants clfCol × clfC24 and clfC24 × clfCol , the heterosis phenotype was damaged, and the long-distance interactions in hybrids were fewer than in their parents with lower H3K27me3. ChIP-seq data revealed higher levels of H3K27me3 in the region adjacent to the CD boundary and the same interactional homo-trans sites in the wild-type (WT) hybrids, which may have led to more long-distance interactions. In addition, the differentially expressed genes (DEGs) located in the boundaries of CDs and loop regions changed obviously in WT, and the functional enrichment for DEGs was different between WT and clf in the long-distance interactions and loop regions. Our findings may therefore propose a new epigenetic explanation of heterosis in the Arabidopsis hybrids and provide new insights into crop breeding and yield increase.
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Affiliation(s)
- Zhaoxu Gao
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Yanning Su
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Le Chang
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Guanzhong Jiao
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Yang Ou
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Mei Yang
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Chao Xu
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Pengtao Liu
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Zejia Wang
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Zewen Qi
- College of Grassland Science, Beijing Forestry University, Beijing, 100083, China
| | - Wenwen Liu
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Linhua Sun
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Guangming He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
| | - Hang He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
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6
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Abdulraheem MI, Xiong Y, Moshood AY, Cadenas-Pliego G, Zhang H, Hu J. Mechanisms of Plant Epigenetic Regulation in Response to Plant Stress: Recent Discoveries and Implications. PLANTS (BASEL, SWITZERLAND) 2024; 13:163. [PMID: 38256717 PMCID: PMC10820249 DOI: 10.3390/plants13020163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
Plant stress is a significant challenge that affects the development, growth, and productivity of plants and causes an adverse environmental condition that disrupts normal physiological processes and hampers plant survival. Epigenetic regulation is a crucial mechanism for plants to respond and adapt to stress. Several studies have investigated the role of DNA methylation (DM), non-coding RNAs, and histone modifications in plant stress responses. However, there are various limitations or challenges in translating the research findings into practical applications. Hence, this review delves into the recent recovery, implications, and applications of epigenetic regulation in response to plant stress. To better understand plant epigenetic regulation under stress, we reviewed recent studies published in the last 5-10 years that made significant contributions, and we analyzed the novel techniques and technologies that have advanced the field, such as next-generation sequencing and genome-wide profiling of epigenetic modifications. We emphasized the breakthrough findings that have uncovered specific genes or pathways and the potential implications of understanding plant epigenetic regulation in response to stress for agriculture, crop improvement, and environmental sustainability. Finally, we concluded that plant epigenetic regulation in response to stress holds immense significance in agriculture, and understanding its mechanisms in stress tolerance can revolutionize crop breeding and genetic engineering strategies, leading to the evolution of stress-tolerant crops and ensuring sustainable food production in the face of climate change and other environmental challenges. Future research in this field will continue to unveil the intricacies of epigenetic regulation and its potential applications in crop improvement.
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Affiliation(s)
- Mukhtar Iderawumi Abdulraheem
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Yani Xiong
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Abiodun Yusuff Moshood
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Gregorio Cadenas-Pliego
- Centro de Investigación en Química Aplicada, Blvd. Enrique Reyna 140, Saltillo 25294, Mexico;
| | - Hao Zhang
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
| | - Jiandong Hu
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
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7
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Paril J, Reif J, Fournier-Level A, Pourkheirandish M. Heterosis in crop improvement. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:23-32. [PMID: 37971883 DOI: 10.1111/tpj.16488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 11/19/2023]
Abstract
Heterosis, also known as hybrid vigor, is the phenomenon wherein a progeny exhibits superior traits relative to one or both parents. In terms of crop breeding, this usually refers to the yield advantage of F1 hybrids over both inbred parents. The development of high-yielding hybrid cultivars across a wider range of crops is key to meeting future food demands. However, conventional hybrid breeding strategies are proving to be exceptionally challenging to apply commercially in many self-pollinating crops, particularly wheat and barley. Currently in these crops, the relative performance advantage of hybrids over inbred line cultivars does not outweigh the cost of hybrid seed production. Here, we review the genetic basis of heterosis, discuss the challenges in hybrid breeding, and propose a strategy to recruit multiple heterosis-associated genes to develop lines with improved agronomic characteristics. This strategy leverages modern genetic engineering tools to synthesize supergenes by fusing multiple heterotic alleles across multiple heterosis-associated loci. We outline a plan to assess the feasibility of this approach to improve line performance using barley (Hordeum vulgare) as the model self-pollinating crop species, and a few heterosis-associated genes. The proposed method can be applied to all crops for which heterotic gene combinations can be identified.
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Affiliation(s)
- Jefferson Paril
- Faculty of Science, University of Melbourne, Parkville, Melbourne, Victoria, Australia
- AgriBio, Centre for AgriBioscience, Agriculture Victoria Research, Bundoora, Victoria, Australia
| | - Jochen Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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8
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de Tomás C, Vicient CM. The Genomic Shock Hypothesis: Genetic and Epigenetic Alterations of Transposable Elements after Interspecific Hybridization in Plants. EPIGENOMES 2023; 8:2. [PMID: 38247729 PMCID: PMC10801548 DOI: 10.3390/epigenomes8010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/21/2023] [Accepted: 12/24/2023] [Indexed: 01/23/2024] Open
Abstract
Transposable elements (TEs) are major components of plant genomes with the ability to change their position in the genome or to create new copies of themselves in other positions in the genome. These can cause gene disruption and large-scale genomic alterations, including inversions, deletions, and duplications. Host organisms have evolved a set of mechanisms to suppress TE activity and counter the threat that they pose to genome integrity. These includes the epigenetic silencing of TEs mediated by a process of RNA-directed DNA methylation (RdDM). In most cases, the silencing machinery is very efficient for the vast majority of TEs. However, there are specific circumstances in which TEs can evade such silencing mechanisms, for example, a variety of biotic and abiotic stresses or in vitro culture. Hybridization is also proposed as an inductor of TE proliferation. In fact, the discoverer of the transposons, Barbara McClintock, first hypothesized that interspecific hybridization provides a "genomic shock" that inhibits the TE control mechanisms leading to the mobilization of TEs. However, the studies carried out on this topic have yielded diverse results, showing in some cases a total absence of mobilization or being limited to only some TE families. Here, we review the current knowledge about the impact of interspecific hybridization on TEs in plants and the possible implications of changes in the epigenetic mechanisms.
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Affiliation(s)
| | - Carlos M. Vicient
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain
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9
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Fernie AR, Yan J, Aharoni A, Ma J. Editorial: The past, present and future of The Plant Journal Resource Articles. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:967-973. [PMID: 37943112 DOI: 10.1111/tpj.16515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Affiliation(s)
- Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetics, Huazhong Agricultural District, Wuhan, China
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Jianxian Ma
- Purdue University, 915 S. University St, West Lafayette, IN, USA
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10
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Ding C, Zhang Z. Effective omics tools are still lacking for improvement of stress tolerance in polyploid crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1295528. [PMID: 38023865 PMCID: PMC10646182 DOI: 10.3389/fpls.2023.1295528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Affiliation(s)
- Chao Ding
- Shanxi Center for Testing of Functional Agro-Products, Shanxi Agricultural University, Taiyuan, China
| | - Zhao Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
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11
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Hamid R, Jacob F, Ghorbanzadeh Z, Jafari L, Alishah O. Dynamic roles of small RNAs and DNA methylation associated with heterosis in allotetraploid cotton (Gossypium hirsutum L.). BMC PLANT BIOLOGY 2023; 23:488. [PMID: 37828433 PMCID: PMC10571366 DOI: 10.1186/s12870-023-04495-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND Heterosis is a complex phenomenon wherein the hybrids outperform their parents. Understanding the underlying molecular mechanism by which hybridization leads to higher yields in allopolyploid cotton is critical for effective breeding programs. Here, we integrated DNA methylation, transcriptomes, and small RNA profiles to comprehend the genetic and molecular basis of heterosis in allopolyploid cotton at three developmental stages. RESULTS Transcriptome analysis revealed that numerous DEGs responsive to phytohormones (auxin and salicylic acid) were drastically altered in F1 hybrid compared to the parental lines. DEGs involved in energy metabolism and plant growth were upregulated, whereas DEGs related to basal defense were downregulated. Differences in homoeologous gene expression in F1 hybrid were greatly reduced after hybridization, suggesting that higher levels of parental expression have a vital role in heterosis. Small RNAome and methylome studies showed that the degree of DNA methylation in hybrid is higher when compared to the parents. A substantial number of allele-specific expression genes were found to be strongly regulated by CG allele-specific methylation levels. The hybrid exhibited higher 24-nt-small RNA (siRNA) expression levels than the parents. The regions in the genome with increased levels of 24-nt-siRNA were chiefly related to genes and their flanking regulatory regions, demonstrating a possible effect of these molecules on gene expression. The transposable elements correlated with siRNA clusters in the F1 hybrid had higher methylation levels but lower expression levels, which suggest that these non-additively expressed siRNA clusters, reduced the activity of transposable elements through DNA methylation in the hybrid. CONCLUSIONS These multi-omics data provide insights into how changes in epigenetic mechanisms and gene expression patterns can lead to heterosis in allopolyploid cotton. This makes heterosis a viable tool in cotton breeding.
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Affiliation(s)
- Rasmieh Hamid
- Department of Plant Breeding, Cotton Research Institute of Iran (CRII), Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Iran.
| | - Feba Jacob
- Centre for Plant Biotechnology and Molecular Biology, Kerala Agricultural University, Thrissur, India
| | - Zahra Ghorbanzadeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Leila Jafari
- Horticultural Science Department, Faculty of Agriculture and Natural Resources, University of Hormozgan, Bandar Abbas, Iran
- Research Group of Agroecology in Dryland Areas, University of Hormozgan, Bandar Abbas, Iran
| | - Omran Alishah
- Department of Plant Breeding, Cotton Research Institute of Iran (CRII), Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Iran
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12
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Zhang J, Xie Y, Zhang H, He C, Wang X, Cui Y, Heng Y, Lin Y, Gu R, Wang J, Fu J. Integrated Multi-Omics Reveals Significant Roles of Non-Additively Expressed Small RNAs in Heterosis for Maize Plant Height. Int J Mol Sci 2023; 24:ijms24119150. [PMID: 37298102 DOI: 10.3390/ijms24119150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 06/12/2023] Open
Abstract
Heterosis is a complex biological phenomenon regulated by genetic variations and epigenetic changes. However, the roles of small RNAs (sRNAs), an important epigenetic regulatory element, on plant heterosis are still poorly understood. Here, an integrative analysis was performed with sequencing data from multi-omics layers of maize hybrids and their two homologous parental lines to explore the potential underlying mechanisms of sRNAs in plant height (PH) heterosis. sRNAome analysis revealed that 59 (18.61%) microRNAs (miRNAs) and 64,534 (54.00%) 24-nt small interfering RNAs (siRNAs) clusters were non-additively expressed in hybrids. Transcriptome profiles showed that these non-additively expressed miRNAs regulated PH heterosis through activating genes involved in vegetative growth-related pathways while suppressing those related to reproductive and stress response pathways. DNA methylome profiles showed that non-additive methylation events were more likely to be induced by non-additively expressed siRNA clusters. Genes associated with low-parental expression (LPE) siRNAs and trans-chromosomal demethylation (TCdM) events were enriched in developmental processes as well as nutrients and energy metabolism, whereas genes associated with high-parental expression (HPE) siRNAs and trans-chromosomal methylation (TCM) events were gathered in stress response and organelle organization pathways. Our results provide insights into the expression and regulation patterns of sRNAs in hybrids and help to elucidate their potential targeting pathways contributing to PH heterosis.
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Affiliation(s)
- Jie Zhang
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Molecular Genetics, Guizhou Institute of Tobacco Science, Guiyang 550081, China
| | - Yuxin Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongwei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cheng He
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66502, USA
| | - Xiaoli Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yu Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanfang Heng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yingchao Lin
- Key Laboratory of Molecular Genetics, Guizhou Institute of Tobacco Science, Guiyang 550081, China
| | - Riliang Gu
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jianhua Wang
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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13
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Orantes-Bonilla M, Wang H, Lee HT, Golicz AA, Hu D, Li W, Zou J, Snowdon RJ. Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:113. [PMID: 37071201 PMCID: PMC10113308 DOI: 10.1007/s00122-023-04345-7] [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: 11/03/2022] [Accepted: 03/12/2023] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE Transcriptomic and epigenomic profiling of gene expression and small RNAs during seed and seedling development reveals expression and methylation dominance levels with implications on early stage heterosis in oilseed rape. The enhanced performance of hybrids through heterosis remains a key aspect in plant breeding; however, the underlying mechanisms are still not fully elucidated. To investigate the potential role of transcriptomic and epigenomic patterns in early expression of hybrid vigor, we investigated gene expression, small RNA abundance and genome-wide methylation in hybrids from two distant Brassica napus ecotypes during seed and seedling developmental stages using next-generation sequencing. A total of 31117, 344, 36229 and 7399 differentially expressed genes, microRNAs, small interfering RNAs and differentially methylated regions were identified, respectively. Approximately 70% of the differentially expressed or methylated features displayed parental dominance levels where the hybrid followed the same patterns as the parents. Via gene ontology enrichment and microRNA-target association analyses during seed development, we found copies of reproductive, developmental and meiotic genes with transgressive and paternal dominance patterns. Interestingly, maternal dominance was more prominent in hypermethylated and downregulated features during seed formation, contrasting to the general maternal gamete demethylation reported during gametogenesis in angiosperms. Associations between methylation and gene expression allowed identification of putative epialleles with diverse pivotal biological functions during seed formation. Furthermore, most differentially methylated regions, differentially expressed siRNAs and transposable elements were in regions that flanked genes without differential expression. This suggests that differential expression and methylation of epigenomic features may help maintain expression of pivotal genes in a hybrid context. Differential expression and methylation patterns during seed formation in an F1 hybrid provide novel insights into genes and mechanisms with potential roles in early heterosis.
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Affiliation(s)
- Mauricio Orantes-Bonilla
- Department of Plant Breeding, Land Use and Nutrition, IFZ Research Centre for Biosystems, Justus Liebig University, Giessen, Germany
| | - Hao Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Huey Tyng Lee
- Department of Plant Breeding, Land Use and Nutrition, IFZ Research Centre for Biosystems, Justus Liebig University, Giessen, Germany
| | - Agnieszka A Golicz
- Department of Plant Breeding, Land Use and Nutrition, IFZ Research Centre for Biosystems, Justus Liebig University, Giessen, Germany
| | - Dandan Hu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Wenwen Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Rod J Snowdon
- Department of Plant Breeding, Land Use and Nutrition, IFZ Research Centre for Biosystems, Justus Liebig University, Giessen, Germany.
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14
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Shen E, Zou J, Bao J, Zhu QH. Editorial: The roles of ncRNAs in the genome evolution and cross-kingdom regulation. FRONTIERS IN PLANT SCIENCE 2023; 14:1133096. [PMID: 36818837 PMCID: PMC9936233 DOI: 10.3389/fpls.2023.1133096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Affiliation(s)
- Enhui Shen
- College of Agriculture and Biotechnology, Institute of Crop Science, Zhejiang University, Hangzhou, China
- Center for Bioinformatics and Big Data Technology, The Rural Development Academy, Zhejiang University, Hangzhou, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jiandong Bao
- State Key Laboratory for Managing Biotic and Chemical Treats to the and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Qian-Hao Zhu
- Black Mountain Laboratories, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Canberra, ACT, Australia
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15
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Ma M, Zhong W, Zhang Q, Deng L, Wen J, Yi B, Tu J, Fu T, Zhao L, Shen J. Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrid. FRONTIERS IN PLANT SCIENCE 2023; 14:1123729. [PMID: 36778699 PMCID: PMC9911877 DOI: 10.3389/fpls.2023.1123729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Although utilization of heterosis has largely improved the yield of many crops worldwide, the underlying molecular mechanism of heterosis, particularly for allopolyploids, remains unclear. Here, we compared epigenome and transcriptome data of an elite hybrid and its parental lines in three assessed tissues (seedling, flower bud, and silique) to explore their contribution to heterosis in allopolyploid B. napus. Transcriptome analysis illustrated that a small proportion of non-additive genes in the hybrid compared with its parents, as well as parental expression level dominance, might have a significant effect on heterosis. We identified histone modification (H3K4me3 and H3K27me3) variation between the parents and hybrid, most of which resulted from the differences between parents. H3K4me3 variations were positively correlated with gene expression differences among the hybrid and its parents. Furthermore, H3K4me3 and H3K27me3 were rather stable in hybridization and were mainly inherited additively in the B. napus hybrid. Together, our data revealed that transcriptome reprogramming and histone modification remodeling in the hybrid could serve as valuable resources for better understanding heterosis in allopolyploid crops.
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16
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Identification and Functional Prediction of CircRNAs in Leaves of F1 Hybrid Poplars with Different Growth Potential and Their Parents. Int J Mol Sci 2023; 24:ijms24032284. [PMID: 36768607 PMCID: PMC9916877 DOI: 10.3390/ijms24032284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Circular RNAs (CircRNAs) regulate plant growth and development; however, their role in poplar heterosis is unclear. We identified 3722 circRNAs in poplar leaves, most of which were intergenic (57.2%) and exonic (40.2%). The expression of circRNAs in F1 hybrids with high growth potential was higher than that in those with low growth potential. Non-additive expression of circRNAs and single-parent expression of circRNAs (SPE-circRNAs) might regulate poplar heterosis through microRNA sponging and protein translation, respectively. DECs among F1 hybrids with different growth potentials might regulate the growth potential of poplar via microRNA sponging. Correlation analysis between circRNA expression and its parent gene expression showed that SPE-M circRNA (circRNAs expressed by male parent only) might regulate poplar heterosis by inhibiting parent gene expression, while other circRNAs might regulate poplar heterosis by enhancing parent gene expression. Weighted correlation network analysis of gene/circRNA expression showed that circRNAs mainly regulate poplar heterosis via carbohydrate metabolism, amino acid metabolism, energy metabolism, and material transport. In addition, we identified seven circRNAs that positively or negatively regulate poplar heterosis. Thus, non-additively expressed circRNAs and SPE circRNAs are involved in regulating poplar heterosis, and DECs among F1 hybrids with different growth potentials were involved in regulating poplar growth potential.
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17
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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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18
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Orantes-Bonilla M, Makhoul M, Lee H, Chawla HS, Vollrath P, Langstroff A, Sedlazeck FJ, Zou J, Snowdon RJ. Frequent spontaneous structural rearrangements promote rapid genome diversification in a Brassica napus F1 generation. FRONTIERS IN PLANT SCIENCE 2022; 13:1057953. [PMID: 36466276 PMCID: PMC9716091 DOI: 10.3389/fpls.2022.1057953] [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: 09/30/2022] [Accepted: 10/31/2022] [Indexed: 05/26/2023]
Abstract
In a cross between two homozygous Brassica napus plants of synthetic and natural origin, we demonstrate that novel structural genome variants from the synthetic parent cause immediate genome diversification among F1 offspring. Long read sequencing in twelve F1 sister plants revealed five large-scale structural rearrangements where both parents carried different homozygous alleles but the heterozygous F1 genomes were not identical heterozygotes as expected. Such spontaneous rearrangements were part of homoeologous exchanges or segmental deletions and were identified in different, individual F1 plants. The variants caused deletions, gene copy-number variations, diverging methylation patterns and other structural changes in large numbers of genes and may have been causal for unexpected phenotypic variation between individual F1 sister plants, for example strong divergence of plant height and leaf area. This example supports the hypothesis that spontaneous de novo structural rearrangements after de novo polyploidization can rapidly overcome intense allopolyploidization bottlenecks to re-expand crops genetic diversity for ecogeographical expansion and human selection. The findings imply that natural genome restructuring in allopolyploid plants from interspecific hybridization, a common approach in plant breeding, can have a considerably more drastic impact on genetic diversity in agricultural ecosystems than extremely precise, biotechnological genome modifications.
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Affiliation(s)
- Mauricio Orantes-Bonilla
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Manar Makhoul
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - HueyTyng Lee
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Harmeet Singh Chawla
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Paul Vollrath
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Anna Langstroff
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
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19
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Zhou T, Afzal R, Haroon M, Ma Y, Zhang H, Li L. Dominant complementation of biological pathways in maize hybrid lines is associated with heterosis. PLANTA 2022; 256:111. [PMID: 36352050 DOI: 10.1007/s00425-022-04028-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Allele-specific expressed genes (ASEGs) are widespread in maize hybrid lines and play important roles of complementation of biological pathways in heterosis. Heterosis (hybrid vigor) is an important phenomenon with both theoretical and practical value. However, our understanding of the genetic and molecular mechanisms behind heterosis is still limited. Here, we analyzed a comprehensive dataset of maize (Zea mays L.), including RNA-seq data from three hybrid-parent triplets (HPTs) and acetylated protein data from one HPT. The gene expression patterns exhibited extensive variation between the hybrids and their parents, and a substantial number of allele-specific expressed genes (ASEGs) were identified in the hybrids. Notably, ASEGs from different HPTs were significantly enriched in various conserved pathways. The parental alleles of ASEGs with fewer deleterious single-nucleotide polymorphisms were more likely to be expressed in hybrid lines than other parental alleles. ASEGs were mainly enriched in the functional gene ontology terms protein biosynthesis, photosynthesis, and metabolism. In addition, the ASEGs across the three HPTs were involved in key photosynthetic pathways and might enhance the photosynthetic efficiency of the hybrids. These findings suggest that ASEGs involved in complementary biological pathways in maize hybrids contribute to heterosis, shedding new light on the molecular mechanism of heterosis.
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Affiliation(s)
- Tao Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rabail Afzal
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Muhammad Haroon
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuting Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongwei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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20
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Jaiswal V, Rawoof A, Gahlaut V, Ahmad I, Chhapekar SS, Dubey M, Ramchiary N. Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heterotic Capsicum F 1 hybrid. iScience 2022; 25:105318. [PMID: 36304106 PMCID: PMC9593261 DOI: 10.1016/j.isci.2022.105318] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/04/2022] [Accepted: 10/06/2022] [Indexed: 11/19/2022] Open
Abstract
Hybrid breeding is one of the efficacious methods of crop improvement. Here, we report our work towards understanding the molecular basis of F1 hybrid heterosis from Capsicum chinense and C. frutescens cross. Bisulfite sequencing identified a total of 70597 CG, 108797 CHG, and 38418 CHH differentially methylated regions (DMRs) across F1 hybrid and parents, and of these, 4891 DMRs showed higher methylation in F1 compared to the mid-parental methylation values (MPMV). Transcriptome analysis showed higher expression of 46–55% differentially expressed genes (DE-Gs) in the F1 hybrid. The qRT-PCR analysis of 24 DE-Gs with negative promoter methylation revealed 91.66% expression similarity with the transcriptome data. A few metabolites and 65–72% enriched genes in metabolite biosynthetic pathways showed overall increased expression in the F1 hybrid compared to parents. These findings, taken together, provided insights into the integrated role of DNA methylation, and genes and metabolites expression in the manifestation of heterosis in Capsicum. Global methylation identified significantly different proportions of mCs in hybrid Of common DMRs, 33.08% showed different methylation in hybrid from the mid-parental value Negatively correlated DEG pDMR-genes were enriched in metabolic pathways Significant higher expression of metabolites and DE-Gs were identified in the F1 hybrid
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Affiliation(s)
- Vandana Jaiswal
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Corresponding author
| | - Abdul Rawoof
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Vijay Gahlaut
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Ilyas Ahmad
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sushil S. Chhapekar
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Department of Horticulture, Chungnam National University, Daejeon 34134, South Korea
| | - Meenakshi Dubey
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi 110042, India
| | - Nirala Ramchiary
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Corresponding author
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21
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Chandana BS, Mahto RK, Singh RK, Ford R, Vaghefi N, Gupta SK, Yadav HK, Manohar M, Kumar R. Epigenomics as Potential Tools for Enhancing Magnitude of Breeding Approaches for Developing Climate Resilient Chickpea. Front Genet 2022; 13:900253. [PMID: 35937986 PMCID: PMC9355295 DOI: 10.3389/fgene.2022.900253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022] Open
Abstract
Epigenomics has become a significant research interest at a time when rapid environmental changes are occurring. Epigenetic mechanisms mainly result from systems like DNA methylation, histone modification, and RNA interference. Epigenetic mechanisms are gaining importance in classical genetics, developmental biology, molecular biology, cancer biology, epidemiology, and evolution. Epigenetic mechanisms play important role in the action and interaction of plant genes during development, and also have an impact on classical plant breeding programs, inclusive of novel variation, single plant heritability, hybrid vigor, plant-environment interactions, stress tolerance, and performance stability. The epigenetics and epigenomics may be significant for crop adaptability and pliability to ambient alterations, directing to the creation of stout climate-resilient elegant crop cultivars. In this review, we have summarized recent progress made in understanding the epigenetic mechanisms in plant responses to biotic and abiotic stresses and have also tried to provide the ways for the efficient utilization of epigenomic mechanisms in developing climate-resilient crop cultivars, especially in chickpea, and other legume crops.
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Affiliation(s)
- B. S. Chandana
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | | | - Rebecca Ford
- Center for Planetary Health and Food Security, Griffith University, Brisbane, QLD, Australia
| | - Niloofar Vaghefi
- School of Agriculture and Food, University of Melbourne, Parkville, VIC, Australia
| | | | | | - Murli Manohar
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Rajendra Kumar
- Indian Agricultural Research Institute (ICAR), New Delhi, India
- *Correspondence: Rajendra Kumar,
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22
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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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23
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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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Chen L, Zhu Y, Ren X, Yao D, Song Y, Fan S, Li X, Zhang Z, Yang S, Zhang J, Zhang J. Heterosis and Differential DNA Methylation in Soybean Hybrids and Their Parental Lines. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11091136. [PMID: 35567137 PMCID: PMC9102035 DOI: 10.3390/plants11091136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/17/2022] [Accepted: 04/20/2022] [Indexed: 05/26/2023]
Abstract
Heterosis is an important biological phenomenon and is widely applied to increase agricultural productivity. However, the underlying molecular mechanisms of heterosis are still unclear. Here we constructed three combinations of reciprocal hybrids of soybean, and subsequently used MethylRAD-seq to detect CCGG and CCWGG (W = A or T) methylation in the whole genome of these hybrids and their parents at the middle development period of contemporary seed. We were able to prove that changes in DNA methylation patterns occurred in immature hybrid seeds and the parental variation was to some degree responsible for differential expression between the reciprocal hybrids. Non-additive differential methylation sites (DMSs) were also identified in large numbers in hybrids. Interestingly, most of these DMSs were hyper-methylated and were more concentrated in gene regions than the natural distribution of the methylated sites. Further analysis of the non-additive DMSs located in gene regions exhibited their participation in various biological processes, especially those related to transcriptional regulation and hormonal function. These results revealed DNA methylation reprogramming pattern in the hybrid soybean, which is associated with phenotypic variation and heterosis initiation.
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Affiliation(s)
- Liangyu Chen
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (L.C.); (Y.Z.); (X.R.); (Y.S.); (S.F.); (X.L.); (Z.Z.)
| | - Yanyu Zhu
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (L.C.); (Y.Z.); (X.R.); (Y.S.); (S.F.); (X.L.); (Z.Z.)
| | - Xiaobo Ren
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (L.C.); (Y.Z.); (X.R.); (Y.S.); (S.F.); (X.L.); (Z.Z.)
| | - Dan Yao
- College of Life Science, Jilin Agricultural University, Changchun 130118, China;
| | - Yang Song
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (L.C.); (Y.Z.); (X.R.); (Y.S.); (S.F.); (X.L.); (Z.Z.)
| | - Sujie Fan
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (L.C.); (Y.Z.); (X.R.); (Y.S.); (S.F.); (X.L.); (Z.Z.)
| | - Xueying Li
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (L.C.); (Y.Z.); (X.R.); (Y.S.); (S.F.); (X.L.); (Z.Z.)
| | - Zhuo Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (L.C.); (Y.Z.); (X.R.); (Y.S.); (S.F.); (X.L.); (Z.Z.)
| | - Songnan Yang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (L.C.); (Y.Z.); (X.R.); (Y.S.); (S.F.); (X.L.); (Z.Z.)
| | - Jian Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (L.C.); (Y.Z.); (X.R.); (Y.S.); (S.F.); (X.L.); (Z.Z.)
- National Crop Variety Approval and Characteristic Identification Station, Jilin Agricultural University, Changchun 130118, China
- Department Biology, University of British Columbia, Okanagan, Kelowna, BC V1V 1V7, Canada
| | - Jun Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (L.C.); (Y.Z.); (X.R.); (Y.S.); (S.F.); (X.L.); (Z.Z.)
- National Crop Variety Approval and Characteristic Identification Station, Jilin Agricultural University, Changchun 130118, China
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Liu W, Zhang Y, He H, He G, Deng XW. From hybrid genomes to heterotic trait output: Challenges and opportunities. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102193. [PMID: 35219140 DOI: 10.1016/j.pbi.2022.102193] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/19/2021] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
Heterosis (or hybrid vigor) has been widely used in crop seed breeding to improve many key economic traits. Nevertheless, the genetic and molecular basis of this important phenomenon has long remained elusive, constraining its flexible and effective exploitation. Advanced genomic approaches are efficient in characterizing the mechanism of heterosis. Here, we review how the omics approaches, including genomic, transcriptomic, and population genetics methods such as genome-wide association studies, can reveal how hybrid genomes outperform parental genomes in plants. This information opens up opportunities for genomic exploration and manipulation of heterosis in crop breeding.
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Affiliation(s)
- Wenwen Liu
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Yilin Zhang
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Hang He
- Peking University Institute of Advanced Agricultural Sciences, 699 Binhu Road, Xiashan Ecological and Economic Development Zone, Weifang, Shandong, 261325, China
| | - Guangming He
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
| | - Xing Wang Deng
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China; Peking University Institute of Advanced Agricultural Sciences, 699 Binhu Road, Xiashan Ecological and Economic Development Zone, Weifang, Shandong, 261325, China.
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Wang P, Gu M, Shao S, Chen X, Hou B, Ye N, Zhang X. Changes in Non-Volatile and Volatile Metabolites Associated with Heterosis in Tea Plants ( Camellia sinensis). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:3067-3078. [PMID: 35199525 DOI: 10.1021/acs.jafc.1c08248] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Heterosis or hybrid vigor is extensively used in plant breeding. However, the contribution of metabolites to heterosis is still elusive. Here, we systematically identified the non-volatile and volatile metabolites of two hybrids and their parents in Camellia sinensis. The metabolomics analysis showed prevalent non-additive accumulation in hybrids, among which the non-additive nucleotides, alkaloids, organic acids, and tannins contribute to the positive heterosis of hybrids, including typical inosine, guanosine, adenosine, caffeine, succinic acid, adipic acid, xylonic acid, and gallic acid. The catechins and free amino acids in hybrids showed negative heterosis compared to its maternal cultivar TGY. Furthermore, the significant accumulation of non-additive terpenes combined with the mild heterosis of other types of volatiles contributes to the aroma of tea plant hybrids. The genetics of volatiles from different parents affect the aroma of hybrids processed into oolong tea. The comprehensive heterosis of these non-additive metabolites may play an important role in the formation of desirable breeding traits for hybrids. Our results provide insights into the utilization of heterosis breeding and the regulation of heterosis metabolites in tea plants.
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Affiliation(s)
- Pengjie Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou 350002, China
| | - Mengya Gu
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou 350002, China
| | - Shuxian Shao
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou 350002, China
| | - Xiaomin Chen
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou 350002, China
| | - Binghao Hou
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou 350002, China
| | - Naixing Ye
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou 350002, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou 350002, China
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Xiao W, Chen B, Wang J, Zou Z, Wang C, Li D, Zhu J, Yu J, Yang H. Integration of mRNA and miRNA Profiling Reveals Heterosis in Oreochromis niloticus × O. aureus Hybrid Tilapia. Animals (Basel) 2022; 12:640. [PMID: 35268207 PMCID: PMC8909811 DOI: 10.3390/ani12050640] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 02/08/2023] Open
Abstract
Heterosis is a widespread biological phenomenon in fishes, in which hybrids have superior traits to parents. However, the underlying molecular basis for heterosis remains uncertain. Heterosis in growth and survival rates is apparent in hybrid tilapia (Oreochromis niloticus ♀ × O. aureus ♂). Comparisons of growth and hematological biochemical characteristics and mRNA and miRNA transcriptional analyses were performed in hybrid and parents tilapia stocks to investigate the underlying molecular basis for heterosis. Growth characteristics and hematological glucose and cholesterol parameters were significantly improved in hybrids. Of 3097 differentially expressed genes (DEGs) and 120 differentially expressed miRNAs (DEMs) identified among three stocks (O. niloticus, O. aureus, and hybrids), 1598 DEGs and 62 DEMs were non-additively expressed in hybrids. Both expression level dominance and overdominance patterns occurred for DEGs and DEMs, indicating that dominance and overdominance models are widespread in the transcriptional and post-transcriptional regulation of genes involved in growth, metabolism, immunity, and antioxidant capacity in hybrid tilapia. Moreover, potential negative regulation networks between DEMs and predicted target DEGs revealed that most DEGs from miRNA-mRNA pairs are up-regulated. Dominance and overdominance models in levels of transcriptome and miRNAome facilitate the integration of advantageous parental alleles into hybrids, contributing to heterosis of growth and improved survival. The present study provides new insights into molecular heterosis in hybrid tilapia, advancing our understanding of the complex mechanisms involved in this phenomenon in aquatic animals.
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Affiliation(s)
- Wei Xiao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China; (W.X.); (J.W.)
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (B.C.); (Z.Z.); (D.L.); (J.Z.); (J.Y.)
| | - Binglin Chen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (B.C.); (Z.Z.); (D.L.); (J.Z.); (J.Y.)
| | - Jun Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China; (W.X.); (J.W.)
| | - Zhiying Zou
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (B.C.); (Z.Z.); (D.L.); (J.Z.); (J.Y.)
| | - Chenghui Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China; (W.X.); (J.W.)
| | - Dayu Li
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (B.C.); (Z.Z.); (D.L.); (J.Z.); (J.Y.)
| | - Jinglin Zhu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (B.C.); (Z.Z.); (D.L.); (J.Z.); (J.Y.)
| | - Jie Yu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (B.C.); (Z.Z.); (D.L.); (J.Z.); (J.Y.)
| | - Hong Yang
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (B.C.); (Z.Z.); (D.L.); (J.Z.); (J.Y.)
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Li D, Lu X, Zhu Y, Pan J, Zhou S, Zhang X, Zhu G, Shang Y, Huang S, Zhang C. The multi-omics basis of potato heterosis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:671-687. [PMID: 34963038 DOI: 10.1111/jipb.13211] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Heterosis is a fundamental biological phenomenon characterized by the superior performance of hybrids over their parents. Although tremendous progress has been reported in seed crops, the molecular mechanisms underlying heterosis in clonally propagated crops are largely unknown. Potato (Solanum tuberosum L.) is the most important tuber crop and an ongoing revolution is transforming potato from a clonally propagated tetraploid crop into a seed-propagated diploid hybrid potato. In our previous study, we developed the first generation of highly homozygous inbred lines of potato and hybrids with strong heterosis. Here, we integrated transcriptome, metabolome, and DNA methylation data to explore the genetic and molecular basis of potato heterosis at three developmental stages. We found that the initial establishment of heterosis in diploid potato was mainly due to dominant complementation. Flower color, male fertility, and starch and sucrose metabolism showed obvious gene dominant complementation in hybrids, and hybrids devoted more energy to primary metabolism for rapid growth. In addition, we identified ~2 700 allele-specific expression genes at each stage, which likely function in potato heterosis and might be regulated by CHH allele-specific methylation level. Our multi-omics analysis provides insight into heterosis in potato and facilitates the exploitation of heterosis in potato breeding.
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Affiliation(s)
- Dawei Li
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
| | - Xiaoyue Lu
- Yunnan Key Laboratory of Potato Biology, The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Yanhui Zhu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
| | - Jun Pan
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
| | - Shaoqun Zhou
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
| | - Xinyan Zhang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
| | - Guangtao Zhu
- Yunnan Key Laboratory of Potato Biology, The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Yi Shang
- Yunnan Key Laboratory of Potato Biology, The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Sanwen Huang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
| | - Chunzhi Zhang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
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GC content of plant genes is linked to past gene duplications. PLoS One 2022; 17:e0261748. [PMID: 35025913 PMCID: PMC8758071 DOI: 10.1371/journal.pone.0261748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 12/09/2021] [Indexed: 11/24/2022] Open
Abstract
The frequency of G and C nucleotides in genomes varies from species to species, and sometimes even between different genes in the same genome. The monocot grasses have a bimodal distribution of genic GC content absent in dicots. We categorized plant genes from 5 dicots and 4 monocot grasses by synteny to related species and determined that syntenic genes have significantly higher GC content than non-syntenic genes at their 5`-end in the third position within codons for all 9 species. Lower GC content is correlated with gene duplication, as lack of synteny to distantly related genomes is associated with past interspersed gene duplications. Two mutation types can account for biased GC content, mutation of methylated C to T and gene conversion from A to G. Gene conversion involves non-reciprocal exchanges between homologous alleles and is not detectable when the alleles are identical or heterozygous for presence-absence variation, both likely situations for genes duplicated to new loci. Gene duplication can cause production of siRNA which can induce targeted methylation, elevating mC→T mutations. Recently duplicated plant genes are more frequently methylated and less likely to undergo gene conversion, each of these factors synergistically creating a mutational environment favoring AT nucleotides. The syntenic genes with high GC content in the grasses compose a subset that have undergone few duplications, or for which duplicate copies were purged by selection. We propose a “biased gene duplication / biased mutation” (BDBM) model that may explain the origin and trajectory of the observed link between duplication and genic GC bias. The BDBM model is supported by empirical data based on joint analyses of 9 angiosperm species with their genes categorized by duplication status, GC content, methylation levels and functional classes.
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Hu Y, Xiong J, Shalby N, Zhuo C, Jia Y, Yang QY, Tu J. Comparison of dynamic 3D chromatin architecture uncovers heterosis for leaf size in Brassica napus. J Adv Res 2022; 42:289-301. [PMID: 36513419 PMCID: PMC9788941 DOI: 10.1016/j.jare.2022.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/28/2021] [Accepted: 01/02/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Heterosis is the major event driving plant development and promoting crop breeding, but the molecular bases for this phenomenon remain elusive. OBJECTIVES We aim to explore the effect of three-dimensional (3D) chromatin architecture on the underlying mechanism of heterosis. METHODS Here, we constructed the North Carolina II (NC-II) population to select superior and inferior heterosis sets by comparing mid-parent heterosis (MPH) in Brassica napus. To decipher the impact of 3D chromatin architecture on the underlying mechanism of heterosis, we combined genetics, transcriptomics and 3D genomics approaches. RESULTS We suggest that F1 hybrids with superior heterosis tend to contain more transcriptionally active A compartments compared with F1 hybrids with inferior heterosis, and approximately 19-21% compartment significantly altered in the F1 hybrids relative to the parental lines. Further analyses show that chromatin compartments correlate with genetic variance among parents, which may form the basis for differentially active chromatin compartments. Having more A compartments in F1 hybrids confers a more accessible chromatin circumstance, which promotes a higher proportion of highly expressed ELD (expression level dominance) genes in superior heterosis F1 hybrids (46-64%) compared with inferior heterosis F1 hybrids (22-31%). Moreover, genes related to hormones which affect plant growth, are more up-regulated with changes of 3D genome architecture, and we validate that increased hormone content contributes to cell proliferation and expansion by influencing the key genes of cell cycle thereby promoting leaf size. CONCLUSION Dynamic 3D chromatin architecture correlates with genetic variance among parents and contributes to heterosis in Brassica napus.
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Affiliation(s)
- Yue Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China,Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, 430070 Wuhan, China
| | - Jie Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China
| | - Nesma Shalby
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China
| | - Chenjian Zhuo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yupeng Jia
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China,Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, 430070 Wuhan, China
| | - Qing-Yong Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China,Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, 430070 Wuhan, China,Corresponding authors at: National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China (Q.-Y. Yang).
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China,Corresponding authors at: National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China (Q.-Y. Yang).
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Xie D, Ye P, Ma Y, Li Y, Liu X, Sarkies P, Zhao Z. Genetic exchange with an outcrossing sister species causes severe genome-wide dysregulation in a selfing Caenorhabditis nematode. Genome Res 2022; 32:2015-2027. [PMID: 36351773 PMCID: PMC9808620 DOI: 10.1101/gr.277205.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022]
Abstract
Different modes of reproduction evolve rapidly, with important consequences for genome composition. Selfing species often occupy a similar niche as their outcrossing sister species with which they are able to mate and produce viable hybrid progeny, raising the question of how they maintain genomic identity. Here, we investigate this issue by using the nematode Caenorhabditis briggsae, which reproduces as a hermaphrodite, and its outcrossing sister species Caenorhabditis nigoni We hypothesize that selfing species might develop some barriers to prevent gene intrusions through gene regulation. We therefore examined gene regulation in the hybrid F2 embryos resulting from reciprocal backcrosses between F1 hybrid progeny and C. nigoni or C. briggsae F2 hybrid embryos with ∼75% of their genome derived from C. briggsae (termed as bB2) were inviable, whereas those with ∼75% of their genome derived from C. nigoni (termed as nB2) were viable. Misregulation of transposable elements, coding genes, and small regulatory RNAs was more widespread in the bB2 compared with the nB2 hybrids, which is a plausible explanation for the differential phenotypes between the two hybrids. Our results show that regulation of the C. briggsae genome is strongly affected by genetic exchanges with its outcrossing sister species, C. nigoni, whereas regulation of the C. nigoni genome is more robust on genetic exchange with C. briggsae The results provide new insights into how selfing species might maintain their identity despite genetic exchanges with closely related outcrossing species.
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Affiliation(s)
- Dongying Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Pohao Ye
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yiming Ma
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yongbin Li
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xiao Liu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Peter Sarkies
- Department of Biochemistry, University of Oxford, Oxford, OX1 4BH, United Kingdom
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, China;,State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
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Wang Q, Yan T, Long Z, Huang LY, Zhu Y, Xu Y, Chen X, Pak H, Li J, Wu D, Xu Y, Hua S, Jiang L. Prediction of heterosis in the recent rapeseed (Brassica napus) polyploid by pairing parental nucleotide sequences. PLoS Genet 2021; 17:e1009879. [PMID: 34735437 PMCID: PMC8608326 DOI: 10.1371/journal.pgen.1009879] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/22/2021] [Accepted: 10/15/2021] [Indexed: 11/19/2022] Open
Abstract
The utilization of heterosis is a successful strategy in increasing yield for many crops. However, it consumes tremendous manpower to test the combining ability of the parents in fields. Here, we applied the genomic-selection (GS) strategy and developed models that significantly increase the predictability of heterosis by introducing the concept of a regional parental genetic-similarity index (PGSI) and reducing dimension in the calculation matrix in a machine-learning approach. Overall, PGSI negatively affected grain yield and several other traits but positively influenced the thousand-seed weight of the hybrids. It was found that the C subgenome of rapeseed had a greater impact on heterosis than the A subgenome. We drew maps with overviews of quantitative-trait loci that were responsible for the heterosis (h-QTLs) of various agronomic traits. Identifications and annotations of genes underlying high impacting h-QTLs were provided. Using models that we elaborated, combining abilities between an Ogu-CMS-pool member and a potential restorer can be simulated in silico, sidestepping laborious work, such as testing crosses in fields. The achievements here provide a case of heterosis prediction in polyploid genomes with relatively large genome sizes. Oilseed rape (Brassica napus) is of significant economic interest worldwide, providing high-quality oil with excellent health-promoting properties. It represents an excellent model of a successful recent polyploid that rapidly became an important crop worldwide. The utilization of hybridization, leading to hybrid vigor, or heterosis, is a successful strategy in increasing yield and vigor for many field crops including rapeseed (Brassica napus). However, the procedure of using classical breeding methods remains slow and laborious, illustrating the need for predictive and innovative methods. Here, we have achieved a significant breakthrough by using genome selection and significantly advanced models to predict the heterosis by pairing genome-wide nucleotides of parents. We provided maps with overviews of quantitative trait loci that were responsible for the heterosis of various agronomic traits. The research used deep resequencing (>30x) data of the entire polyploidy rapeseed genome, providing a successful case for the prediction of heterosis in polyploid genomes with relatively large genome sizes. Moreover, we provided the genetic information (SNPs) of 1007 core accessions of this species in the public domain for testing combinations with high heterosis using our predicting model for rapeseed breeders all over the world.
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Affiliation(s)
- Qian Wang
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Tao Yan
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Zhengbiao Long
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Luna Yue Huang
- Department of Agricultural and Resource Economics, University of California, Berkeley, California, United States of America
| | - Yang Zhu
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Ying Xu
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Xiaoyang Chen
- Institute of Crop Science, Jinhua Academy of Agricultural Sciences, Jinhua, China
| | - Haksong Pak
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Jiqiang Li
- Institute of Crop Science, Zhangye Academy of Agricultural Sciences, Zhangye, China
| | - Dezhi Wu
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Yang Xu
- Agricultural College, Yangzhou University, Yangzhou, China
- * E-mail: (YX); (SH); (LJ)
| | - Shuijin Hua
- Institute of Crop and Nuclear Agricultural Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- * E-mail: (YX); (SH); (LJ)
| | - Lixi Jiang
- Institute of Crop Science, Zhejiang University, Hangzhou, China
- * E-mail: (YX); (SH); (LJ)
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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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Shu HY, Zhou H, Mu HL, Wu SH, Jiang YL, Yang Z, Hao YY, Zhu J, Bao WL, Cheng SH, Zhu GP, Wang ZW. Integrated Analysis of mRNA and Non-coding RNA Transcriptome in Pepper ( Capsicum chinense) Hybrid at Seedling and Flowering Stages. Front Genet 2021; 12:685788. [PMID: 34490032 PMCID: PMC8417703 DOI: 10.3389/fgene.2021.685788] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/26/2021] [Indexed: 01/22/2023] Open
Abstract
Pepper is an important vegetable in the world. In this work, mRNA and ncRNA transcriptome profiles were applied to understand the heterosis effect on the alteration in the gene expression at the seedling and flowering stages between the hybrid and its parents in Capsicum chinense. Our phenotypic data indicated that the hybrid has dominance in leaf area, plant scope, plant height, and fruit-related traits. Kyoto Encyclopedia of Genes and Genomes analysis showed that nine members of the plant hormone signal transduction pathway were upregulated in the seedling and flowering stages of the hybrid, which was supported by weighted gene coexpression network analysis and that BC332_23046 (auxin response factor 8), BC332_18317 (auxin-responsive protein IAA20), BC332_13398 (ethylene-responsive transcription factor), and BC332_27606 (ethylene-responsive transcription factor WIN1) were candidate hub genes, suggesting the important potential role of the plant hormone signal transduction in pepper heterosis. Furthermore, some transcription factor families, including bHLH, MYB, and HSF were greatly over-dominant. We also identified 2,525 long ncRNAs (lncRNAs), 47 micro RNAs (miRNAs), and 71 circle RNAs (circRNAs) in the hybrid. In particular, downregulation of miR156, miR169, and miR369 in the hybrid suggested their relationship with pepper growth vigor. Moreover, we constructed some lncRNA–miRNA–mRNA regulatory networks that showed a multi-dimension to understand the ncRNA relationship with heterosis. These results will provide guidance for a better understanding of the molecular mechanism involved in pepper heterosis.
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Affiliation(s)
- Huang-Ying Shu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - He Zhou
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Hai-Ling Mu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Shu-Hua Wu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Yi-Li Jiang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Zhuang Yang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Yuan-Yuan Hao
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Jie Zhu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Wen-Long Bao
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Shan-Han Cheng
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Guo-Peng Zhu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
| | - Zhi-Wei Wang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, China
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Yang Q, Nong X, Xu J, Huang F, Wang F, Wu J, Zhang C, Liu C. Unraveling the Genetic Basis of Fertility Restoration for Cytoplasmic Male Sterile Line WNJ01A Originated From Brassica juncea in Brassica napus. FRONTIERS IN PLANT SCIENCE 2021; 12:721980. [PMID: 34531887 PMCID: PMC8438535 DOI: 10.3389/fpls.2021.721980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
Crosses that lead to heterosis have been widely used in the rapeseed (Brassica napus L.) industry. Cytoplasmic male sterility (CMS)/restorer-of-fertility (Rf) systems represent one of the most useful tools for rapeseed production. Several CMS types and their restorer lines have been identified in rapeseed, but there are few studies on the mechanisms underlying fertility restoration. Here, we performed morphological observation, map-based cloning, and transcriptomic analysis of the F2 population developed by crossing the CMS line WNJ01A with its restorer line Hui01. Paraffin-embedded sections showed that the sporogenous cell stage was the critical pollen degeneration period, with major sporogenous cells displaying loose and irregular arrangement in sterile anthers. Most mitochondrial electron transport chain (mtETC) complex genes were upregulated in fertile compared to sterile buds. Using bulked segregant analysis (BSA)-seq to analyze mixed DNA pools from sterile and fertile F2 buds, respectively, we identified a 6.25 Mb candidate interval where Rfw is located. Using map-based cloning experiments combined with bacterial artificial chromosome (BAC) clone sequencing, the candidate interval was reduced to 99.75 kb and two pentatricopeptide repeat (PPR) genes were found among 28 predicted genes in this interval. Transcriptome sequencing showed that there were 1679 DEGs (1023 upregulated and 656 downregulated) in fertile compared to sterile F2 buds. The upregulated differentially expressed genes (DEGs) were enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) lysine degradation pathway and phenylalanine metabolism, and the downregulated DEGs were enriched in cutin, suberine, and wax biosynthesis. Furthermore, 44 DEGs were involved in pollen and anther development, such as tapetum, microspores, and pollen wall development. All of them were upregulated except a few such as POE1 genes (which encode Pollen Ole e I allergen and extensin family proteins). There were 261 specifically expressed DEGs (9 and 252 in sterile and fertile buds, respectively). Regarding the fertile bud-specific upregulated DEGs, the ubiquitin-proteasome pathway was enriched. The top four hub genes in the protein-protein interaction network (BnaA09g56400D, BnaA10g18210D, BnaA10g18220D, and BnaC09g41740D) encode RAD23d proteins, which deliver ubiquitinated substrates to the 26S proteasome. These findings provide evidence on the pathways regulated by Rfw and improve our understanding of fertility restoration.
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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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Kakoulidou I, Avramidou EV, Baránek M, Brunel-Muguet S, Farrona S, Johannes F, Kaiserli E, Lieberman-Lazarovich M, Martinelli F, Mladenov V, Testillano PS, Vassileva V, Maury S. Epigenetics for Crop Improvement in Times of Global Change. BIOLOGY 2021; 10:766. [PMID: 34439998 PMCID: PMC8389687 DOI: 10.3390/biology10080766] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022]
Abstract
Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity-naturally, genetically, chemically, or environmentally induced-can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change.
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Affiliation(s)
- Ioanna Kakoulidou
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
| | - Evangelia V. Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-Dimitra (ELGO-DIMITRA), 11528 Athens, Greece;
| | - Miroslav Baránek
- Faculty of Horticulture, Mendeleum—Institute of Genetics, Mendel University in Brno, Valtická 334, 69144 Lednice, Czech Republic;
| | - Sophie Brunel-Muguet
- UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, UNICAEN, INRAE, Normandie Université, CEDEX, F-14032 Caen, France;
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, National University of Ireland (NUI) Galway, H91 TK33 Galway, Ireland;
| | - Frank Johannes
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
- Institute for Advanced Study, Technical University of Munich, Lichtenberg Str. 2a, 85748 Garching, Germany
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK;
| | - Michal Lieberman-Lazarovich
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel;
| | - Federico Martinelli
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Sq. Dositeja Obradovića 8, 21000 Novi Sad, Serbia;
| | - Pilar S. Testillano
- Pollen Biotechnology of Crop Plants Group, Centro de Investigaciones Biológicas Margarita Salas-(CIB-CSIC), Ramiro Maeztu 9, 28040 Madrid, Spain;
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bldg. 21, 1113 Sofia, Bulgaria;
| | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE, EA1207 USC1328, Université d’Orléans, F-45067 Orléans, France
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Biological pathway expression complementation contributes to biomass heterosis in Arabidopsis. Proc Natl Acad Sci U S A 2021; 118:2023278118. [PMID: 33846256 DOI: 10.1073/pnas.2023278118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The mechanisms underlying heterosis have long remained a matter of debate, despite its agricultural importance. How changes in transcriptional networks during plant development are relevant to the continuous manifestation of growth vigor in hybrids is intriguing and unexplored. Here, we present an integrated high-resolution analysis of the daily dynamic growth phenotypes and transcriptome atlases of young Arabidopsis seedlings (parental ecotypes [Col-0 and Per-1] and their F1 hybrid). Weighted gene coexpression network analysis uncovered divergent expression patterns between parents of the network hub genes, in which genes related to the cell cycle were more highly expressed in one parent (Col-0), whereas those involved in photosynthesis were more highly expressed in the other parent (Per-1). Notably, the hybrid exhibited spatiotemporal high-parent-dominant expression complementation of network hub genes in the two pathways during seedling growth. This suggests that the integrated capacities of cell division and photosynthesis contribute to hybrid growth vigor, which could be enhanced by temporal advances in the progression of leaf development in the hybrid relative to its parents. Altogether, this study provides evidence of expression complementation between fundamental biological pathways in hybrids and highlights the contribution of expression dominance in heterosis.
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Luo JH, Wang M, Jia GF, He Y. Transcriptome-wide analysis of epitranscriptome and translational efficiency associated with heterosis in maize. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2933-2946. [PMID: 33606877 PMCID: PMC8023220 DOI: 10.1093/jxb/erab074] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/12/2021] [Indexed: 05/14/2023]
Abstract
Heterosis has been extensively utilized to increase productivity in crops, yet the underlying molecular mechanisms remain largely elusive. Here, we generated transcriptome-wide profiles of mRNA abundance, m6A methylation, and translational efficiency from the maize F1 hybrid B73×Mo17 and its two parental lines to ascertain the contribution of each regulatory layer to heterosis at the seedling stage. We documented that although the global abundance and distribution of m6A remained unchanged, a greater number of genes had gained an m6A modification in the hybrid. Superior variations were observed at the m6A modification and translational efficiency levels when compared with mRNA abundance between the hybrid and parents. In the hybrid, the vast majority of genes with m6A modification exhibited a non-additive expression pattern, the percentage of which was much higher than that at levels of mRNA abundance and translational efficiency. Non-additive genes involved in different biological processes were hierarchically coordinated by discrete combinations of three regulatory layers. These findings suggest that transcriptional and post-transcriptional regulation of gene expression make distinct contributions to heterosis in hybrid maize. Overall, this integrated multi-omics analysis provides a valuable portfolio for interpreting transcriptional and post-transcriptional regulation of gene expression in hybrid maize, and paves the way for exploring molecular mechanisms underlying hybrid vigor.
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Affiliation(s)
- Jin-Hong Luo
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China
| | - Min Wang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China
| | - Gui-Fang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yan He
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China
- Correspondence:
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Li P, Su T, Zhang D, Wang W, Xin X, Yu Y, Zhao X, Yu S, Zhang F. Genome-wide analysis of changes in miRNA and target gene expression reveals key roles in heterosis for Chinese cabbage biomass. HORTICULTURE RESEARCH 2021; 8:39. [PMID: 33642594 PMCID: PMC7917107 DOI: 10.1038/s41438-021-00474-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 12/05/2020] [Accepted: 12/12/2020] [Indexed: 05/12/2023]
Abstract
Heterosis is a complex phenomenon in which hybrids show better phenotypic characteristics than their parents do. Chinese cabbage (Brassica rapa L. spp. pekinensis) is a popular leafy crop species, hybrids of which are widely used in commercial production; however, the molecular basis of heterosis for biomass of Chinese cabbage is poorly understood. We characterized heterosis in a Chinese cabbage F1 hybrid cultivar and its parental lines from the seedling stage to the heading stage; marked heterosis of leaf weight and biomass yield were observed. Small RNA sequencing revealed 63 and 50 differentially expressed microRNAs (DEMs) at the seedling and early-heading stages, respectively. The expression levels of the majority of miRNA clusters in the F1 hybrid were lower than the mid-parent values (MPVs). Using degradome sequencing, we identified 1,819 miRNA target genes. Gene ontology (GO) analyses demonstrated that the target genes of the MPV-DEMs and low parental expression level dominance (ELD) miRNAs were significantly enriched in leaf morphogenesis, leaf development, and leaf shaping. Transcriptome analysis revealed that the expression levels of photosynthesis and chlorophyll synthesis-related MPV-DEGs (differentially expressed genes) were significantly different in the F1 hybrid compared to the parental lines, resulting in increased photosynthesis capacity and chlorophyll content in the former. Furthermore, expression of genes known to regulate leaf development was also observed at the seedling stage. Arabidopsis plants overexpressing BrGRF4.2 and bra-miR396 presented increased and decreased leaf sizes, respectively. These results provide new insight into the regulation of target genes and miRNA expression patterns in leaf size and heterosis for biomass of B. rapa.
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Affiliation(s)
- Peirong Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Tongbing Su
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Deshuang Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Weihong Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Xiaoyun Xin
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Yangjun Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Xiuyun Zhao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China
| | - Shuancang Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China.
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China.
| | - Fenglan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, 100097, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, China.
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, China.
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Analysis of Transcriptional Changes in Different Brassica napus Synthetic Allopolyploids. Genes (Basel) 2021; 12:genes12010082. [PMID: 33440604 PMCID: PMC7827416 DOI: 10.3390/genes12010082] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 11/23/2022] Open
Abstract
Allopolyploidy is an evolutionary and mechanistically intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the gene expression patterns of eight F2 synthetic Brassica napus using RNA sequencing. We found that B. napus allopolyploid formation was accompanied by extensive changes in gene expression. A comparison between F2 and the parent shows a certain proportion of differentially expressed genes (DEG) and activation\silent gene, and the two genomes (female parent (AA)\male parent (CC) genomes) showed significant differences in response to whole-genome duplication (WGD); non-additively expressed genes represented a small portion, while Gene Ontology (GO) enrichment analysis showed that it played an important role in responding to WGD. Besides, genome-wide expression level dominance (ELD) was biased toward the AA genome, and the parental expression pattern of most genes showed a high degree of conservation. Moreover, gene expression showed differences among eight individuals and was consistent with the results of a cluster analysis of traits. Furthermore, the differential expression of waxy synthetic pathways and flowering pathway genes could explain the performance of traits. Collectively, gene expression of the newly formed allopolyploid changed dramatically, and this was different among the selfing offspring, which could be a prominent cause of the trait separation. Our data provide novel insights into the relationship between the expression of differentially expressed genes and trait segregation and provide clues into the evolution of allopolyploids.
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Cooper RD, Shaffer HB. Allele-specific expression and gene regulation help explain transgressive thermal tolerance in non-native hybrids of the endangered California tiger salamander (Ambystoma californiense). Mol Ecol 2021; 30:987-1004. [PMID: 33338297 DOI: 10.1111/mec.15779] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/30/2020] [Accepted: 12/11/2020] [Indexed: 01/26/2023]
Abstract
Hybridization between native and non-native species is an ongoing global conservation threat. Hybrids that exhibit traits and tolerances that surpass parental values are of particular concern, given their potential to outperform native species. Effective management of hybrid populations requires an understanding of both physiological performance and the underlying mechanisms that drive transgressive hybrid traits. Here, we explore several aspects of the hybridization between the endangered California tiger salamander (Ambystoma californiense; CTS) and the introduced barred tiger salamander (Ambystoma mavortium; BTS). We assayed critical thermal maximum (CTMax) to compare the ability of CTS, BTS and F1 hybrids to tolerate acute thermal stress, and found that hybrids exhibit a wide range of CTMax values, with 33% (4/12) able to tolerate temperatures greater than either parent. We then quantified the genomic response, measured at the RNA transcript level, of each salamander, to explore the mechanisms underlying thermal tolerance strategies. We found that CTS and BTS have strikingly different values and tissue-specific patterns of overall gene expression, with hybrids expressing intermediate values. F1 hybrids display abundant and variable degrees of allele-specific expression (ASE), likely arising from extensive compensatory evolution in gene regulatory mechanisms between CTS and BTS. We found evidence that the proportion of genes with allelic imbalance in individual hybrids correlates with their CTMax, suggesting a link between ASE and expanded thermal tolerance that may contribute to the success of hybrid salamanders in California. Future climate change may further complicate management of CTS if hybrid salamanders are better equipped to deal with rising temperatures.
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Affiliation(s)
- Robert D Cooper
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
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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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Selva C, Riboni M, Baumann U, Würschum T, Whitford R, Tucker MR. Hybrid breeding in wheat: how shaping floral biology can offer new perspectives. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:675-694. [PMID: 32534601 DOI: 10.1071/fp19372] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/21/2020] [Indexed: 06/11/2023]
Abstract
Hybrid breeding in wheat (Triticum aestivum L.) has the potential to deliver major yield increases. This is a requisite to guarantee food security for increasing population demands and to counterbalance the effects of extreme environmental conditions. Successful hybrid breeding in wheat relies on forced outcrossing while preventing self-pollination. To achieve this, research has been directed towards identifying and improving fertility control systems. To maximise cross-pollination and seed set, however, fertility control systems need to be complemented by breeding phenotypically distinct male and female lines. This review summarises existing and novel male sterility systems for wheat hybridisation. We also consider the genetic resources that can be used to alter wheat's floral development and spike morphology, with a focus on the genetic variation already available. Exploiting these resources can lead to enhanced outcrossing, a key requirement in the progress towards hybrid wheat breeding.
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Affiliation(s)
- Caterina Selva
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Matteo Riboni
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Ute Baumann
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Tobias Würschum
- State Plant Breeding Institute, University of Hohenheim, 70593 Stuttgart, Germany
| | - Ryan Whitford
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia; and Corresponding authors. ;
| | - Matthew R Tucker
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia; and Corresponding authors. ;
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45
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Qiu T, Liu Z, Liu B. The effects of hybridization and genome doubling in plant evolution via allopolyploidy. Mol Biol Rep 2020; 47:5549-5558. [PMID: 32572735 DOI: 10.1007/s11033-020-05597-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/17/2020] [Indexed: 12/19/2022]
Abstract
Polyploidy is a pervasive and recurring phenomenon across the tree of life, which occurred at variable time scales, ecological amplitudes and cell types, and is especially prominent in the evolutionary histories of plants. Importantly, many of the world's most important crops and noxious invasive weeds are recent polyploids. Polyploidy includes two major types, autopolyploidy, referring to doubling of a single species genome, and allopolyploidy referring to doubling of two or more merged genomes via biological hybridization of distinct but related species. The prevalence of both types of polyploidy implies that both genome doubling alone and doubling coupled with hybridization confer selective advantages over their diploid progenitors under specific circumstances. In cases of allopolyploidy, the two events, genome doubling and hybridization, have both advantages and disadvantages. Accumulated studies have established that, in allopolyploidy, some advantage(s) of doubling may compensate for the disadvantage(s) of hybridity and vice versa, although further study is required to validate generality of this trend. Some studies have also revealed a variety of non-Mendelian genetic and genomic consequences induced by doubling and hybridization separately or concertedly in nascent allopolyploidy; however, the significance of which to the immediate establishment and longer-term evolutionary success of allopolyploid species remain to be empirically demonstrated and ecologically investigated. This review aims to summarize recent advances in our understanding of the roles of hybridization and genome doubling, in separation and combination, in the evolution of allopolyploid genomes, as well as fruitful future research directions that are emerging from these studies.
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Affiliation(s)
- Tian Qiu
- School of Life Sciences, Changchun Normal University, Changchun, 130032, China.,Key Laboratory of Molecular Epigenetics, Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Zhiyuan Liu
- College of Computer Science and Technology, Changchun University, Changchun, 130022, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Northeast Normal University, Changchun, 130024, China.
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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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47
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Shahzad K, Zhang X, Guo L, Qi T, Bao L, Zhang M, Zhang B, Wang H, Tang H, Qiao X, Feng J, Wu J, Xing C. Comparative transcriptome analysis between inbred and hybrids reveals molecular insights into yield heterosis of upland cotton. BMC PLANT BIOLOGY 2020; 20:239. [PMID: 32460693 PMCID: PMC7251818 DOI: 10.1186/s12870-020-02442-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/13/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND Utilization of heterosis has greatly improved the productivity of many crops worldwide. Understanding the potential molecular mechanism about how hybridization produces superior yield in upland cotton is critical for efficient breeding programs. RESULTS In this study, high, medium, and low hybrids varying in the level of yield heterosis were screened based on field experimentation of different years and locations. Phenotypically, high hybrid produced a mean of 14% more seed cotton yield than its better parent. Whole-genome RNA sequencing of these hybrids and their four inbred parents was performed using different tissues of the squaring stage. Comparative transcriptomic differences in each hybrid parent triad revealed a higher percentage of differentially expressed genes (DEGs) in each tissue. Expression level dominance analysis identified majority of hybrids DEGs were biased towards parent like expressions. An array of DEGs involved in ATP and protein binding, membrane, cell wall, mitochondrion, and protein phosphorylation had more functional annotations in hybrids. Sugar metabolic and plant hormone signal transduction pathways were most enriched in each hybrid. Further, these two pathways had most mapped DEGs on known seed cotton yield QTLs. Integration of transcriptome, QTLs, and gene co-expression network analysis discovered genes Gh_A03G1024, Gh_D08G1440, Gh_A08G2210, Gh_A12G2183, Gh_D07G1312, Gh_D08G1467, Gh_A03G0889, Gh_A08G2199, and Gh_D05G0202 displayed a complex regulatory network of many interconnected genes. qRT-PCR of these DEGs was performed to ensure the accuracy of RNA-Seq data. CONCLUSIONS Through genome-wide comparative transcriptome analysis, the current study identified nine key genes and pathways associated with biological process of yield heterosis in upland cotton. Our results and data resources provide novel insights and will be useful for dissecting the molecular mechanism of yield heterosis in 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, 38 Huanghe Dadao, Anyang, 455000 Henan 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, 38 Huanghe Dadao, Anyang, 455000 Henan 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, 38 Huanghe Dadao, Anyang, 455000 Henan 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, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Lisheng Bao
- Jinhua Department of Economic Special Technology Promotion, Jinhua, 321017 Zhejiang 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, 38 Huanghe Dadao, Anyang, 455000 Henan 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, 38 Huanghe Dadao, Anyang, 455000 Henan 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, 38 Huanghe Dadao, Anyang, 455000 Henan 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, 38 Huanghe Dadao, Anyang, 455000 Henan 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, 38 Huanghe Dadao, Anyang, 455000 Henan 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, 38 Huanghe Dadao, Anyang, 455000 Henan 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, 38 Huanghe Dadao, Anyang, 455000 Henan 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, 38 Huanghe Dadao, Anyang, 455000 Henan China
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Heterosis Breeding in Eggplant ( Solanum melongena L.): Gains and Provocations. PLANTS 2020; 9:plants9030403. [PMID: 32213925 PMCID: PMC7154857 DOI: 10.3390/plants9030403] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/17/2020] [Accepted: 03/20/2020] [Indexed: 01/15/2023]
Abstract
Heterosis (or hybrid vigor) results in a hybrid’s phenotypic superiority over its founder parents for quantitative and qualitative traits. Hybrid vigor is defined by mechanisms such as dominant complementation, over-dominance, and epistasis. Eggplant (Solanum melongena L.) is an essential vegetable crop and a good source of dietary minerals, vitamins, and anthocyanins, with a high oxygen radical absorbance capacity and low caloric value. Given the economic and nutritional significance of eggplants, breeding efforts focus on developing high-yielding varieties—mostly F1 hybrids—with important traits. Studies indicate the successful exploitation of heterosis in the eggplant for a considerable improvement with respect to quantitative traits. In this direction, estimating heterosis for yield-related traits could well be useful for examining the most beneficial hybrid mix with the exploitation of top-quality hybrid. This review examines the current perception of the breeding and molecular aspects of heterosis in eggplants and cites several studies describing the mechanisms. Rendering and combining recent genomics, epigenetic, proteomic, and metabolomics studies present new prospects towards the understanding of the regulatory events of heterosis involved in the evolution and the domestication of the eggplant ideotype.
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Lunardon A, Johnson NR, Hagerott E, Phifer T, Polydore S, Coruh C, Axtell MJ. Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants. Genome Res 2020; 30:497-513. [PMID: 32179590 PMCID: PMC7111516 DOI: 10.1101/gr.256750.119] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/27/2020] [Indexed: 01/25/2023]
Abstract
Plant endogenous small RNAs (sRNAs) are important regulators of gene expression. There are two broad categories of plant sRNAs: microRNAs (miRNAs) and endogenous short interfering RNAs (siRNAs). MicroRNA loci are relatively well-annotated but compose only a small minority of the total sRNA pool; siRNA locus annotations have lagged far behind. Here, we used a large data set of published and newly generated sRNA sequencing data (1333 sRNA-seq libraries containing more than 20 billion reads) and a uniform bioinformatic pipeline to produce comprehensive sRNA locus annotations of 47 diverse plants, yielding more than 2.7 million sRNA loci. The two most numerous classes of siRNA loci produced mainly 24- and 21-nucleotide (nt) siRNAs, respectively. Most often, 24-nt-dominated siRNA loci occurred in intergenic regions, especially at the 5′-flanking regions of protein-coding genes. In contrast, 21-nt-dominated siRNA loci were most often derived from double-stranded RNA precursors copied from spliced mRNAs. Genic 21-nt-dominated loci were especially common from disease resistance genes, including from a large number of monocots. Individual siRNA sequences of all types showed very little conservation across species, whereas mature miRNAs were more likely to be conserved. We developed a web server where our data and several search and analysis tools are freely accessible.
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Affiliation(s)
- Alice Lunardon
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Nathan R Johnson
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Emily Hagerott
- Department of Biology, Knox College, Galesburg, Illinois 61401, USA
| | - Tamia Phifer
- Department of Biology, Knox College, Galesburg, Illinois 61401, USA
| | - Seth Polydore
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Ceyda Coruh
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Michael J Axtell
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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50
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Ghaleb MAA, Li C, Shahid MQ, Yu H, Liang J, Chen R, Wu J, Liu X. Heterosis analysis and underlying molecular regulatory mechanism in a wide-compatible neo-tetraploid rice line with long panicles. BMC PLANT BIOLOGY 2020; 20:83. [PMID: 32085735 PMCID: PMC7035737 DOI: 10.1186/s12870-020-2291-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 02/14/2020] [Indexed: 05/07/2023]
Abstract
BACKGROUND Neo-tetraploid rice, which is a new germplasm developed from autotetraploid rice, has a powerful biological and yield potential and could be used for commercial utilization. The length of panicle, as a part of rice panicle architecture, contributes greatly to high yield. However, little information about long panicle associated with heterosis or hybrid vigor is available in neo-tetraploid rice. RESULTS In the present study, we developed a neo-tetraploid rice line, Huaduo 8 (H8), with long panicles and harboring wide-compatibility genes for pollen and embryo sac fertility. All the hybrids generated by H8 produced significant high-parent yield heterosis and displayed long panicles similar to H8. RNA-seq analysis detected a total of 4013, 7050, 6787 and 6195 differentially expressed genes uniquely belonging to F1 and specifically (DEGFu-sp) associated with leaf, sheath, main panicle axis and spikelet in the two hybrids, respectively. Of these DEGFu-sp, 279 and 89 genes were involved in kinase and synthase, and 714 cloned genes, such as GW8, OsGA20ox1, Ghd8, GW6a, and LP1, were identified and validated by qRT-PCR. A total of 2925 known QTLs intervals, with an average of 1~100 genes per interval, were detected in both hybrids. Of these, 109 yield-related QTLs were associated with seven important traits in rice. Moreover, 1393 non-additive DEGs, including 766 up-regulated and 627 down-regulated, were detected in both hybrids. Importantly, eight up-regulated genes associated with panicle were detected in young panicles of the two hybrids compared to their parents by qRT-PCR. Re-sequencing analysis depicted that LP (a gene controlling long panicle) sequence of H8 was different from many other neo-tetraploid rice and most of the diploid and autotetraploid lines. The qRT-PCR results showed that LP was up-regulated in the hybrid compared to its parents at very young stage of panicle development. CONCLUSIONS These results suggested that H8 could overcome the intersubspecific autotetraploid hybrid rice sterility caused by embryo sac and pollen sterility loci. Notably, long panicles of H8 showed dominance phenomenon and played an important role in yield heterosis, which is a complex molecular mechanism. The neo-tetraploid rice is a useful germplasm to attain high yield of polyploid rice.
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Affiliation(s)
- Mohammed Abdullah Abdulraheem Ghaleb
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Cong Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Hang Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Junhong Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Ruoxin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642 China
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