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Zhang H, Zhu JK. Epigenetic gene regulation in plants and its potential applications in crop improvement. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00769-1. [PMID: 39192154 DOI: 10.1038/s41580-024-00769-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2024] [Indexed: 08/29/2024]
Abstract
DNA methylation, also known as 5-methylcytosine, is an epigenetic modification that has crucial functions in plant growth, development and adaptation. The cellular DNA methylation level is tightly regulated by the combined action of DNA methyltransferases and demethylases. Protein complexes involved in the targeting and interpretation of DNA methylation have been identified, revealing intriguing roles of methyl-DNA binding proteins and molecular chaperones. Structural studies and in vitro reconstituted enzymatic systems have provided mechanistic insights into RNA-directed DNA methylation, the main pathway catalysing de novo methylation in plants. A better understanding of the regulatory mechanisms will enable locus-specific manipulation of the DNA methylation status. CRISPR-dCas9-based epigenome editing tools are being developed for this goal. Given that DNA methylation patterns can be stably transmitted through meiosis, and that large phenotypic variations can be contributed by epimutations, epigenome editing holds great promise in crop breeding by creating additional phenotypic variability on the same genetic material.
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Affiliation(s)
- Heng Zhang
- Department of Genetics and Developmental Science, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, China.
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2
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Kumar S, Singh A, Bist CMS, Sharma M. Advancements in genetic techniques and functional genomics for enhancing crop traits and agricultural sustainability. Brief Funct Genomics 2024:elae017. [PMID: 38679487 DOI: 10.1093/bfgp/elae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/03/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
Genetic variability is essential for the development of new crop varieties with economically beneficial traits. The traits can be inherited from wild relatives or induced through mutagenesis. Novel genetic elements can then be identified and new gene functions can be predicted. In this study, forward and reverse genetics approaches were described, in addition to their applications in modern crop improvement programs and functional genomics. By using heritable phenotypes and linked genetic markers, forward genetics searches for genes by using traditional genetic mapping and allele frequency estimation. Despite recent advances in sequencing technology, omics and computation, genetic redundancy remains a major challenge in forward genetics. By analyzing close-related genes, we will be able to dissect their functional redundancy and predict possible traits and gene activity patterns. In addition to these predictions, sophisticated reverse gene editing tools can be used to verify them, including TILLING, targeted insertional mutagenesis, gene silencing, gene targeting and genome editing. By using gene knock-down, knock-up and knock-out strategies, these tools are able to detect genetic changes in cells. In addition, epigenome analysis and editing enable the development of novel traits in existing crop cultivars without affecting their genetic makeup by increasing epiallelic variants. Our understanding of gene functions and molecular dynamics of various biological phenomena has been revised by all of these findings. The study also identifies novel genetic targets in crop species to improve yields and stress tolerances through conventional and non-conventional methods. In this article, genetic techniques and functional genomics are specifically discussed and assessed for their potential in crop improvement.
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Affiliation(s)
- Surender Kumar
- Department of Biotechnology, College of Horticulture, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India
| | - Anupama Singh
- Department of Biotechnology, College of Horticulture, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India
| | - Chander Mohan Singh Bist
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla-171001, Himachal Pradesh, India
| | - Munish Sharma
- Department of Plant Sciences, Central University of Himachal Pradesh, Dharamshala-176215, Himachal Pradesh, India
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Junaid MD, Chaudhry UK, Şanlı BA, Gökçe AF, Öztürk ZN. A review of the potential involvement of small RNAs in transgenerational abiotic stress memory in plants. Funct Integr Genomics 2024; 24:74. [PMID: 38600306 DOI: 10.1007/s10142-024-01354-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
Crop production is increasingly threatened by the escalating weather events and rising temperatures associated with global climate change. Plants have evolved adaptive mechanisms, including stress memory, to cope with abiotic stresses such as heat, drought, and salinity. Stress memory involves priming, where plants remember prior stress exposures, providing enhanced responses to subsequent stress events. Stress memory can manifest as somatic, intergenerational, or transgenerational memory, persisting for different durations. The chromatin, a central regulator of gene expression, undergoes modifications like DNA acetylation, methylation, and histone variations in response to abiotic stress. Histone modifications, such as H3K4me3 and acetylation, play crucial roles in regulating gene expression. Abiotic stresses like drought and salinity are significant challenges to crop production, leading to yield reductions. Plant responses to stress involve strategies like escape, avoidance, and tolerance, each influencing growth stages differently. Soil salinity affects plant growth by disrupting water potential, causing ion toxicity, and inhibiting nutrient uptake. Understanding plant responses to these stresses requires insights into histone-mediated modifications, chromatin remodeling, and the role of small RNAs in stress memory. Histone-mediated modifications, including acetylation and methylation, contribute to epigenetic stress memory, influencing plant adaptation to environmental stressors. Chromatin remodeling play a crucial role in abiotic stress responses, affecting the expression of stress-related genes. Small RNAs; miRNAs and siRNAs, participate in stress memory pathways by guiding DNA methylation and histone modifications. The interplay of these epigenetic mechanisms helps plants adapt to recurring stress events and enhance their resilience. In conclusion, unraveling the epigenetic mechanisms in plant responses to abiotic stresses provides valuable insights for developing resilient agricultural techniques. Understanding how plants utilize stress memory, histone modifications, chromatin remodeling, and small RNAs is crucial for designing strategies to mitigate the impact of climate change on crop production and global food security.
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Affiliation(s)
- Muhammad Daniyal Junaid
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Türkiye, Turkey.
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan.
| | - Usman Khalid Chaudhry
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Türkiye, Turkey
- Pakistan Environmental Protection Agency, Ministry of Climate Change & Environmental Coordination, Islamabad, Pakistan
| | - Beyazıt Abdurrahman Şanlı
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Türkiye, Turkey
| | - Ali Fuat Gökçe
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Türkiye, Turkey
| | - Zahide Neslihan Öztürk
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Türkiye, Turkey
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Rodrigues MGF, Nakanishi ES, Soutello RVG, Diniz FONH. Global methylation in 'Valencia' orange seedlings associated with rootstocks and Huanglongbing. BRAZ J BIOL 2023; 83:e277679. [PMID: 38126644 DOI: 10.1590/1519-6984.277679] [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: 08/17/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Citrus farming is one of the main activities that contributed to the Brazilian trade balance, with citrus seedling being the most important input in the formation of orchards to guarantee high productivity and fruit quality, which fundamentally depends on the chosen genetics. The present study aimed to analyze the existence of epigenetic variability in 'Valencia' orange plants on rootstocks, associated or not with HLB, through the quantification of the global methylation of its genome, in order to support works on genetic improvement and crop production. For this purpose, this work was carried out in greenhouse in a completely randomized experimental design, with 5 treatments and 6 replicates per treatment, each seedling being considered a replicate, namely: T1 = "Valencia" orange grafted onto "Rangpur" lemon, inoculated with HLB; T2 = "Valencia" orange grafted onto "Swingle" citrumelo, inoculated with HLB; T3 = "Valencia" orange grafted onto "Rangpur" lemon, without HLB inoculation ; T4 = "Valencia" orange grafted onto "Swingle" citrumelo, without HLB inoculation ; T5 = "Valencia" orange in free standing. The DNA was extracted from leaves and the ELISA test (Enzyme-Linked Immunosorbent Assay) was carried out, based on the use of receptors sensitive to 5-mC., to measure the relative quantification of global methylation between genomic orange DNAs . Since the control treatment (T5) consists of "Valencia" orange in free standing, it could be inferred that both the normal grafting technique in the seedling formation process and the inoculation of buds infected with HLB are external factors capable of changing the methylation pattern in the evaluated plants, including the DNA demethylation process, causing an adaptive response in association with the expression of genes previously silenced by genome methylation.
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Affiliation(s)
- M G F Rodrigues
- Universidade Estadual Paulista - UNESP, Faculdade de Ciências Agrárias e Tecnológicas - FCAT, Departamento de Produção Vegetal, Dracena, SP, Brasil
| | - E S Nakanishi
- Universidade Estadual Paulista - UNESP, Faculdade de Ciências Agrárias e Tecnológicas - FCAT, Dracena, SP, Brasil
| | - R V G Soutello
- Universidade Estadual Paulista - UNESP, Departamento de Produção Animal, Faculdade de Ciências Agrárias e Tecnológicas - FCAT, Dracena, SP, Brasil
| | - F O N H Diniz
- Universidade Estadual Paulista - UNESP, Faculdade de Engenharia de Ilha Solteira - FEIS, Ilha Solteira, SP, Brasil
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Epigenetic Changes Occurring in Plant Inbreeding. Int J Mol Sci 2023; 24:ijms24065407. [PMID: 36982483 PMCID: PMC10048984 DOI: 10.3390/ijms24065407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
Inbreeding is the crossing of closely related individuals in nature or a plantation or self-pollinating plants, which produces plants with high homozygosity. This process can reduce genetic diversity in the offspring and decrease heterozygosity, whereas inbred depression (ID) can often reduce viability. Inbred depression is common in plants and animals and has played a significant role in evolution. In the review, we aim to show that inbreeding can, through the action of epigenetic mechanisms, affect gene expression, resulting in changes in the metabolism and phenotype of organisms. This is particularly important in plant breeding because epigenetic profiles can be linked to the deterioration or improvement of agriculturally important characteristics.
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Bowerman AF, Byrt CS, Roy SJ, Whitney SM, Mortimer JC, Ankeny RA, Gilliham M, Zhang D, Millar AA, Rebetzke GJ, Pogson BJ. Potential abiotic stress targets for modern genetic manipulation. THE PLANT CELL 2023; 35:139-161. [PMID: 36377770 PMCID: PMC9806601 DOI: 10.1093/plcell/koac327] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/03/2022] [Indexed: 05/06/2023]
Abstract
Research into crop yield and resilience has underpinned global food security, evident in yields tripling in the past 5 decades. The challenges that global agriculture now faces are not just to feed 10+ billion people within a generation, but to do so under a harsher, more variable, and less predictable climate, and in many cases with less water, more expensive inputs, and declining soil quality. The challenges of climate change are not simply to breed for a "hotter drier climate," but to enable resilience to floods and droughts and frosts and heat waves, possibly even within a single growing season. How well we prepare for the coming decades of climate variability will depend on our ability to modify current practices, innovate with novel breeding methods, and communicate and work with farming communities to ensure viability and profitability. Here we define how future climates will impact farming systems and growing seasons, thereby identifying the traits and practices needed and including exemplars being implemented and developed. Critically, this review will also consider societal perspectives and public engagement about emerging technologies for climate resilience, with participatory approaches presented as the best approach.
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Affiliation(s)
- Andrew F Bowerman
- ARC Training Centre for Accelerated Future Crops Development, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Caitlin S Byrt
- ARC Training Centre for Accelerated Future Crops Development, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Stuart John Roy
- ARC Training Centre for Accelerated Future Crops Development, University of Adelaide, South Australia, Australia
- School of Agriculture, Food and Wine & Waite Research Institute, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Spencer M Whitney
- ARC Training Centre for Accelerated Future Crops Development, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jenny C Mortimer
- ARC Training Centre for Accelerated Future Crops Development, University of Adelaide, South Australia, Australia
- School of Agriculture, Food and Wine & Waite Research Institute, University of Adelaide, Glen Osmond, South Australia, Australia
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Rachel A Ankeny
- ARC Training Centre for Accelerated Future Crops Development, University of Adelaide, South Australia, Australia
- School of Humanities, University of Adelaide, North Terrace, South Australia, Australia
| | - Matthew Gilliham
- ARC Training Centre for Accelerated Future Crops Development, University of Adelaide, South Australia, Australia
- School of Agriculture, Food and Wine & Waite Research Institute, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Dabing Zhang
- ARC Training Centre for Accelerated Future Crops Development, University of Adelaide, South Australia, Australia
- School of Agriculture, Food and Wine & Waite Research Institute, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Anthony A Millar
- ARC Training Centre for Accelerated Future Crops Development, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Greg J Rebetzke
- CSIRO Agriculture & Food, Canberra, Australian Capital Territory, Australia
| | - Barry J Pogson
- ARC Training Centre for Accelerated Future Crops Development, The Australian National University, Canberra, Australian Capital Territory, Australia
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Garcia A, Gaju O, Bowerman AF, Buck SA, Evans JR, Furbank RT, Gilliham M, Millar AH, Pogson BJ, Reynolds MP, Ruan Y, Taylor NL, Tyerman SD, Atkin OK. Enhancing crop yields through improvements in the efficiency of photosynthesis and respiration. THE NEW PHYTOLOGIST 2023; 237:60-77. [PMID: 36251512 PMCID: PMC10100352 DOI: 10.1111/nph.18545] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/15/2022] [Indexed: 06/06/2023]
Abstract
The rate with which crop yields per hectare increase each year is plateauing at the same time that human population growth and other factors increase food demand. Increasing yield potential (Y p ) of crops is vital to address these challenges. In this review, we explore a component ofY p that has yet to be optimised - that being improvements in the efficiency with which light energy is converted into biomass (ε c ) via modifications to CO2 fixed per unit quantum of light (α), efficiency of respiratory ATP production (ε prod ) and efficiency of ATP use (ε use ). For α, targets include changes in photoprotective machinery, ribulose bisphosphate carboxylase/oxygenase kinetics and photorespiratory pathways. There is also potential forε prod to be increased via targeted changes to the expression of the alternative oxidase and mitochondrial uncoupling pathways. Similarly, there are possibilities to improveε use via changes to the ATP costs of phloem loading, nutrient uptake, futile cycles and/or protein/membrane turnover. Recently developed high-throughput measurements of respiration can serve as a proxy for the cumulative energy cost of these processes. There are thus exciting opportunities to use our growing knowledge of factors influencing the efficiency of photosynthesis and respiration to create a step-change in yield potential of globally important crops.
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Affiliation(s)
- Andres Garcia
- ARC Centre of Excellence in Plant Energy Biology, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
| | - Oorbessy Gaju
- ARC Centre of Excellence in Plant Energy Biology, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- College of Science, Lincoln Institute for Agri‐Food TechnologyUniversity of LincolnLincolnshireLN2 2LGUK
| | - Andrew F. Bowerman
- ARC Centre of Excellence in Plant Energy Biology, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
| | - Sally A. Buck
- ARC Centre of Excellence in Plant Energy Biology, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
| | - John R. Evans
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
- ARC Centre of Excellence for Translational Photosynthesis, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Robert T. Furbank
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
- ARC Centre of Excellence for Translational Photosynthesis, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Matthew Gilliham
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine & Waite Research InstituteUniversity of AdelaideGlen OsmondSA5064Australia
| | - A. Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences & Institute of AgricultureThe University of Western AustraliaCrawleyWA6009Australia
| | - Barry J. Pogson
- ARC Centre of Excellence in Plant Energy Biology, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
| | - Matthew P. Reynolds
- International Maize and Wheat Improvement Center (CIMMYT)Km. 45, Carretera Mexico, El BatanTexcoco56237Mexico
| | - Yong‐Ling Ruan
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
| | - Nicolas L. Taylor
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences & Institute of AgricultureThe University of Western AustraliaCrawleyWA6009Australia
| | - Stephen D. Tyerman
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine & Waite Research InstituteUniversity of AdelaideGlen OsmondSA5064Australia
| | - Owen K. Atkin
- ARC Centre of Excellence in Plant Energy Biology, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
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Katsidi EC, Avramidou EV, Ganopoulos I, Barbas E, Doulis A, Triantafyllou A, Aravanopoulos FA. Genetics and epigenetics of Pinus nigra populations with differential exposure to air pollution. FRONTIERS IN PLANT SCIENCE 2023; 14:1139331. [PMID: 37089661 PMCID: PMC10117940 DOI: 10.3389/fpls.2023.1139331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Forest species in the course of their evolution have experienced several environmental challenges, which since historic times include anthropogenic pollution. The effects of pollution on the genetic and epigenetic diversity in black pine (Pinus nigra) forests were investigated in the Amyntaio - Ptolemais - Kozani Basin, which has been for decades the largest lignite mining and burning center of Greece, with a total installed generating capacity of about 4.5 GW, operating for more than 70 years and resulting in large amounts of primary air pollutant emissions, mainly SO2, NOx and PM10. P. nigra, a biomarker for air pollution and a keystone species of affected natural ecosystems, was examined in terms of phenology (cone and seed parameters), genetics (283 AFLP loci) and epigenetics (606 MSAP epiloci), using two populations (exposed to pollution and control) of the current (mature trees) and future (embryos) stand. It was found that cone, seed, as well as genetic diversity parameters, did not show statistically significant differences between the exposed population and the control. Nevertheless, statistically significant differences were detected at the population epigenetic level. Moreover, there was a further differentiation regarding the intergenerational comparison: while the epigenetic diversity does not substantially change in the two generations assessed in the control population, epigenetic diversity is significantly higher in the embryo population compared to the parental stand in the exposed population. This study sheds a light to genome dynamics in a forest tree population exposed to long term atmospheric pollution burden and stresses the importance of assessing both genetics and epigenetics in biomonitoring applications.
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Affiliation(s)
- Elissavet Ch. Katsidi
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Evangelia V. Avramidou
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioannis Ganopoulos
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Evangelos Barbas
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andreas Doulis
- Laboratory of Plant Biotechnology – Genomic Resources, Hellenic Agricultural Organization DEMETER, Institute of Viticulture, Floriculture and Vegetable Crops, Heraklion, Greece
| | - Athanasios Triantafyllou
- Laboratory of Atmospheric Pollution and Environmental Physics (LALEP), Faculty of Engineering, University of Western Macedonia, Kozani, Greece
| | - Filippos A. Aravanopoulos
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
- *Correspondence: Filippos A. Aravanopoulos,
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El-Shehawi AM, Elseehy MA, Elseehy MM. CpG Methylation of the Proximal Promoter Region Regulates the Expression of NAC6D Gene in Response to High Temperature in Wheat (Triticum aestivum). CYTOL GENET+ 2022. [DOI: 10.3103/s009545272205005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Tonosaki K, Fujimoto R, Dennis ES, Raboy V, Osabe K. Will epigenetics be a key player in crop breeding? FRONTIERS IN PLANT SCIENCE 2022; 13:958350. [PMID: 36247549 PMCID: PMC9562705 DOI: 10.3389/fpls.2022.958350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
If food and feed production are to keep up with world demand in the face of climate change, continued progress in understanding and utilizing both genetic and epigenetic sources of crop variation is necessary. Progress in plant breeding has traditionally been thought to be due to selection for spontaneous DNA sequence mutations that impart desirable phenotypes. These spontaneous mutations can expand phenotypic diversity, from which breeders can select agronomically useful traits. However, it has become clear that phenotypic diversity can be generated even when the genome sequence is unaltered. Epigenetic gene regulation is a mechanism by which genome expression is regulated without altering the DNA sequence. With the development of high throughput DNA sequencers, it has become possible to analyze the epigenetic state of the whole genome, which is termed the epigenome. These techniques enable us to identify spontaneous epigenetic mutations (epimutations) with high throughput and identify the epimutations that lead to increased phenotypic diversity. These epimutations can create new phenotypes and the causative epimutations can be inherited over generations. There is evidence of selected agronomic traits being conditioned by heritable epimutations, and breeders may have historically selected for epiallele-conditioned agronomic traits. These results imply that not only DNA sequence diversity, but the diversity of epigenetic states can contribute to increased phenotypic diversity. However, since the modes of induction and transmission of epialleles and their stability differ from that of genetic alleles, the importance of inheritance as classically defined also differs. For example, there may be a difference between the types of epigenetic inheritance important to crop breeding and crop production. The former may depend more on longer-term inheritance whereas the latter may simply take advantage of shorter-term phenomena. With the advances in our understanding of epigenetics, epigenetics may bring new perspectives for crop improvement, such as the use of epigenetic variation or epigenome editing in breeding. In this review, we will introduce the role of epigenetic variation in plant breeding, largely focusing on DNA methylation, and conclude by asking to what extent new knowledge of epigenetics in crop breeding has led to documented cases of its successful use.
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Affiliation(s)
- Kaoru Tonosaki
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Elizabeth S. Dennis
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Canberra, ACT, Australia
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Victor Raboy
- Independent Researcher Portland, Portland, OR, United States
| | - Kenji Osabe
- Institute of Scientific and Industrial Research (SANKEN), Osaka University, Osaka, Japan
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11
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Analysis of genome and methylation changes in Chinese indigenous chickens over time provides insight into species conservation. Commun Biol 2022; 5:952. [PMID: 36097156 PMCID: PMC9467985 DOI: 10.1038/s42003-022-03907-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/26/2022] [Indexed: 11/08/2022] Open
Abstract
Conservation of natural resources is a vital and challenging task. Numerous animal genetic resources have been effectively conserved worldwide. However, the effectiveness of conservation programmes and the variation information of species have rarely been evaluated. Here, we performed whole-genome and whole-genome bisulfite sequencing of 90 Chinese indigenous chickens, which belonged to the Tibetan, Wenchang and Bian chicken breeds, and have been conserved under different conservation programmes. We observed that low genetic diversity and high DNA methylation variation occurs during ex situ in vivo conservation, while higher genetic diversity and differentiation occurs during in situ conservation. Further analyses revealed that most DNA methylation signatures are unique within ex situ in vivo conservation. Moreover, a high proportion of differentially methylated regions is found in genomic selection regions, suggesting a link between the effects of genomic variation and DNA methylation. Altogether our findings provide valuable information about genetic and DNA methylation variations during different conservation programmes, and hold practical relevance for species conservation. Comparisons of genomic and methylomic changes during the conservation of indigenous chicken breeds in China provide insight into conservation programmes for these breeds and their adaptations to unique environments.
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Kumari P, Khan S, Wani IA, Gupta R, Verma S, Alam P, Alaklabi A. Unravelling the Role of Epigenetic Modifications in Development and Reproduction of Angiosperms: A Critical Appraisal. Front Genet 2022; 13:819941. [PMID: 35664328 PMCID: PMC9157814 DOI: 10.3389/fgene.2022.819941] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/14/2022] [Indexed: 12/28/2022] Open
Abstract
Epigenetics are the heritable changes in gene expression patterns which occur without altering DNA sequence. These changes are reversible and do not change the sequence of the DNA but can alter the way in which the DNA sequences are read. Epigenetic modifications are induced by DNA methylation, histone modification, and RNA-mediated mechanisms which alter the gene expression, primarily at the transcriptional level. Such alterations do control genome activity through transcriptional silencing of transposable elements thereby contributing toward genome stability. Plants being sessile in nature are highly susceptible to the extremes of changing environmental conditions. This increases the likelihood of epigenetic modifications within the composite network of genes that affect the developmental changes of a plant species. Genetic and epigenetic reprogramming enhances the growth and development, imparts phenotypic plasticity, and also ensures flowering under stress conditions without changing the genotype for several generations. Epigenetic modifications hold an immense significance during the development of male and female gametophytes, fertilization, embryogenesis, fruit formation, and seed germination. In this review, we focus on the mechanism of epigenetic modifications and their dynamic role in maintaining the genomic integrity during plant development and reproduction.
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Affiliation(s)
- Priyanka Kumari
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Sajid Khan
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Ishfaq Ahmad Wani
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Renu Gupta
- Division of Soil Sciences & Agricultural Chemistry, Faculty of Agriculture Sher e Kashmir University of Agricultural Sciences and Technology, Chatha, India
| | - Susheel Verma
- Department of Botany, University of Jammu, Jammu, India
- *Correspondence: Susheel Verma,
| | - Pravej Alam
- Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University (PSAU), Alkharj, Saudi Arabia
| | - Abdullah Alaklabi
- Department of Biology, College of Science, University of Bisha, Bisha, Saudi Arabia
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13
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Song C, Acuña T, Adler-Agmon M, Rachmilevitch S, Barak S, Fait A. Leveraging a graft collection to develop metabolome-based trait prediction for the selection of tomato rootstocks with enhanced salt tolerance. HORTICULTURE RESEARCH 2022; 9:uhac061. [PMID: 35531316 PMCID: PMC9071376 DOI: 10.1093/hr/uhac061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Grafting has been demonstrated to significantly enhance the salt tolerance of crops. However, breeding efforts to develop enhanced graft combinations are hindered by knowledge-gaps as to how rootstocks mediate scion-response to salt stress. We grafted the scion of cultivated M82 onto rootstocks of 254 tomato accessions and explored the morphological and metabolic responses of grafts under saline conditions (EC = 20 dS m-1) as compared to self-grafted M82 (SG-M82). Correlation analysis and Least Absolute Shrinkage and Selection Operator were performed to address the association between morphological diversification and metabolic perturbation. We demonstrate that grafting the same variety onto different rootstocks resulted in scion phenotypic heterogeneity and emphasized the productivity efficiency of M82 irrespective of the rootstock. Spectrophotometric analysis to test lipid oxidation showed largest variability of malondialdehyde (MDA) equivalents across the population, while the least responsive trait was the ratio of fruit fresh weight to total fresh weight (FFW/TFW). Generally, grafts showed greater values for the traits measured than SG-M82, except for branch number and wild race-originated rootstocks; the latter were associated with smaller scion growth parameters. Highly responsive and correlated metabolites were identified across the graft collection including malate, citrate, and aspartate, and their variance was partly related to rootstock origin. A group of six metabolites that consistently characterized exceptional graft response was observed, consisting of sorbose, galactose, sucrose, fructose, myo-inositol, and proline. The correlation analysis and predictive modelling, integrating phenotype- and leaf metabolite data, suggest a potential predictive relation between a set of leaf metabolites and yield-related traits.
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Affiliation(s)
- Chao Song
- The Albert Katz International School for Desert Studies, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Tania Acuña
- Albert Katz Department of Dryland Biotechnologies, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | | | - Shimon Rachmilevitch
- Albert Katz Department of Dryland Biotechnologies, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Simon Barak
- Albert Katz Department of Dryland Biotechnologies, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Aaron Fait
- Albert Katz Department of Dryland Biotechnologies, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
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14
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Jethva J, Schmidt RR, Sauter M, Selinski J. Try or Die: Dynamics of Plant Respiration and How to Survive Low Oxygen Conditions. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11020205. [PMID: 35050092 PMCID: PMC8780655 DOI: 10.3390/plants11020205] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 05/09/2023]
Abstract
Fluctuations in oxygen (O2) availability occur as a result of flooding, which is periodically encountered by terrestrial plants. Plant respiration and mitochondrial energy generation rely on O2 availability. Therefore, decreased O2 concentrations severely affect mitochondrial function. Low O2 concentrations (hypoxia) induce cellular stress due to decreased ATP production, depletion of energy reserves and accumulation of metabolic intermediates. In addition, the transition from low to high O2 in combination with light changes-as experienced during re-oxygenation-leads to the excess formation of reactive oxygen species (ROS). In this review, we will update our current knowledge about the mechanisms enabling plants to adapt to low-O2 environments, and how to survive re-oxygenation. New insights into the role of mitochondrial retrograde signaling, chromatin modification, as well as moonlighting proteins and mitochondrial alternative electron transport pathways (and their contribution to low O2 tolerance and survival of re-oxygenation), are presented.
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Affiliation(s)
- Jay Jethva
- Department of Plant Developmental Biology and Plant Physiology, Faculty of Mathematics and Natural Sciences, Botanical Institute, Christian-Albrechts University, D-24118 Kiel, Germany; (J.J.); (M.S.)
| | - Romy R. Schmidt
- Department of Plant Biotechnology, Faculty of Biology, University of Bielefeld, D-33615 Bielefeld, Germany;
| | - Margret Sauter
- Department of Plant Developmental Biology and Plant Physiology, Faculty of Mathematics and Natural Sciences, Botanical Institute, Christian-Albrechts University, D-24118 Kiel, Germany; (J.J.); (M.S.)
| | - Jennifer Selinski
- Department of Plant Cell Biology, Botanical Institute, Faculty of Mathematics and Natural Sciences, Christian-Albrechts University, D-24118 Kiel, Germany
- Correspondence: ; Tel.: +49-(0)431-880-4245
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15
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Gupta C, Salgotra RK. Epigenetics and its role in effecting agronomical traits. FRONTIERS IN PLANT SCIENCE 2022; 13:925688. [PMID: 36046583 PMCID: PMC9421166 DOI: 10.3389/fpls.2022.925688] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/11/2022] [Indexed: 05/16/2023]
Abstract
Climate-resilient crops with improved adaptation to the changing climate are urgently needed to feed the growing population. Hence, developing high-yielding crop varieties with better agronomic traits is one of the most critical issues in agricultural research. These are vital to enhancing yield as well as resistance to harsh conditions, both of which help farmers over time. The majority of agronomic traits are quantitative and are subject to intricate genetic control, thereby obstructing crop improvement. Plant epibreeding is the utilisation of epigenetic variation for crop development, and has a wide range of applications in the field of crop improvement. Epigenetics refers to changes in gene expression that are heritable and induced by methylation of DNA, post-translational modifications of histones or RNA interference rather than an alteration in the underlying sequence of DNA. The epigenetic modifications influence gene expression by changing the state of chromatin, which underpins plant growth and dictates phenotypic responsiveness for extrinsic and intrinsic inputs. Epigenetic modifications, in addition to DNA sequence variation, improve breeding by giving useful markers. Also, it takes epigenome diversity into account to predict plant performance and increase crop production. In this review, emphasis has been given for summarising the role of epigenetic changes in epibreeding for crop improvement.
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16
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Ajaykumar H, Ramesh S, Sunitha NC, Anilkumar C. Assessment of natural DNA methylation variation and its association with economically important traits in dolichos bean (Lablab purpureus L. Var. Lignosus) using AMP-PCR assay. J Appl Genet 2021; 62:571-583. [PMID: 34247322 DOI: 10.1007/s13353-021-00648-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 05/30/2021] [Accepted: 06/20/2021] [Indexed: 12/29/2022]
Abstract
As a prelude to exploit DNA methylation-induced variation, we hypothesized the existence of substantial natural DNA methylation variation and its association with economically important traits in dolichos bean, and tested it using amplified methylation polymorphism-polymerase chain reaction (AMP-PCR) assay. DNA methylation patterns such as internal, external, full and non-methylation were amplified in a set of 64 genotypes using 26 customized randomly amplified polymorphic DNA (RAPD) primers containing 5'CCGG3' sequence. The 64 genotypes included 60 germplasm accessions (GA), two advanced breeding lines (ABLs) and two released varieties. The ABLs and released varieties are referred to as improved germplasm accessions (IGA) in this study. The association of DNA methylation patterns with economically important traits such as days to 50% flowering, raceme length, fresh pods plant-1, fresh pod yield plant-1 and 100-fresh seed weight was explored. At least 50 genotypes were polymorphic for DNA methylation patterns at 10 loci generated by seven of the 26 RAPD primers. The GA and IGA differed significantly for total, full and external methylation and the frequency of methylation was higher in GA compared to that in IGA. The genotypes with external methylation produced longer racemes than those with full, internal and non-methylation in that order at polymorphic RAPD-11-242 locus. High pod yielding genotypes had significantly lower frequency of full methylation than low yielding ones. On the contrary, the genotypes that produced heavier fresh seeds harboured higher frequencies of total and externally methylated loci than those that produced lighter fresh seeds.
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Affiliation(s)
- H Ajaykumar
- Department of Genetics and Plant Breeding, College of Agriculture, University of Agricultural Sciences, Bangalore, India
| | - S Ramesh
- Department of Genetics and Plant Breeding, College of Agriculture, University of Agricultural Sciences, Bangalore, India.
| | - N C Sunitha
- Department of Genetics and Plant Breeding, College of Agriculture, University of Agricultural Sciences, Bangalore, India
| | - C Anilkumar
- Department of Genetics and Plant Breeding, College of Agriculture, University of Agricultural Sciences, Bangalore, India.,ICAR-National Rice Research Institute, Cuttack, India
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17
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Yung WS, Li MW, Sze CC, Wang Q, Lam HM. Histone modifications and chromatin remodelling in plants in response to salt stress. PHYSIOLOGIA PLANTARUM 2021; 173:1495-1513. [PMID: 34028035 DOI: 10.1111/ppl.13467] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/04/2021] [Accepted: 05/18/2021] [Indexed: 06/12/2023]
Abstract
In the face of global food security crises, it is necessary to boost agricultural production. One factor hampering the attempts to increase food production is elevated soil salinity, which can be due to salt that is naturally present in the soil or a consequence of excessive or prolonged irrigation or application of fertiliser. In response to environmental stresses, plants activate multiple molecular mechanisms, including the timely activation of stress-responsive transcriptional networks. However, in the case of salt stress, the combined effects of the initial osmotic shock and the subsequent ion-specific stress increase the complexity in the selective regulation of gene expressions involved in restoring or maintaining osmotic balance, ion homeostasis and reactive oxygen species scavenging. Histone modifications and chromatin remodelling are important epigenetic processes that regulate gene expressions by modifying the chromatin status and recruiting transcription regulators. In this review, we have specifically summarised the currently available knowledge on histone modifications and chromatin remodelling in relation to plant responses to salt stress. Current findings have revealed the functional importance of chromatin modifiers in regulating salt tolerance and identified the effector genes affected by epigenetic modifications, although counteraction between modifiers within the same family may occur. Emerging evidence has also illustrated the crosstalk between epigenetic modifications and hormone signalling pathways which involves formation of protein complexes. With an improved understanding of these processes, plant breeders will be able to develop alternative strategies using genome editing technologies for crop improvement.
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Affiliation(s)
- Wai-Shing Yung
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Man-Wah Li
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ching-Ching Sze
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Qianwen Wang
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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18
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Singh D, Chaudhary P, Taunk J, Kumar Singh C, Sharma S, Singh VJ, Singh D, Chinnusamy V, Yadav R, Pal M. Plant epigenomics for extenuation of abiotic stresses: challenges and future perspectives. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6836-6855. [PMID: 34302734 DOI: 10.1093/jxb/erab337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Climate change has escalated abiotic stresses, leading to adverse effects on plant growth and development, eventually having deleterious consequences on crop productivity. Environmental stresses induce epigenetic changes, namely cytosine DNA methylation and histone post-translational modifications, thus altering chromatin structure and gene expression. Stable epigenetic changes are inheritable across generations and this enables plants to adapt to environmental changes (epipriming). Hence, epigenomes serve as a good source of additional tier of variability for development of climate-smart crops. Epigenetic resources such as epialleles, epigenetic recombinant inbred lines (epiRILs), epigenetic quantitative trait loci (epiQTLs), and epigenetic hybrids (epihybrids) can be utilized in epibreeding for improving stress tolerance of crops. Epigenome engineering is also gaining momentum for developing sustainable epimarks associated with important agronomic traits. Different epigenome editing tools are available for creating, erasing, and reading such epigenetic codes in plant genomes. However, epigenome editing is still understudied in plants due to its complex nature. Epigenetic interventions such as epi-fingerprinting can be exploited in the near future for health and quality assessment of crops under stress conditions. Keeping in view the challenges and opportunities associated with this important technology, the present review intends to enhance understanding of stress-induced epigenetic changes in plants and its prospects for development of climate-ready crops.
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Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Priya Chaudhary
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Jyoti Taunk
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Shristi Sharma
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Vikram Jeet Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Deepti Singh
- Department of Botany, Meerut College, Meerut, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rajbir Yadav
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Madan Pal
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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19
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Rehman AU, Dang T, Qamar S, Ilyas A, Fatema R, Kafle M, Hussain Z, Masood S, Iqbal S, Shahzad K. Revisiting Plant Heterosis-From Field Scale to Molecules. Genes (Basel) 2021; 12:genes12111688. [PMID: 34828294 PMCID: PMC8619659 DOI: 10.3390/genes12111688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 11/21/2022] Open
Abstract
Heterosis refers to the increase in biomass, stature, fertility, and other characters that impart superior performance to the F1 progeny over genetically diverged parents. The manifestation of heterosis brought an economic revolution to the agricultural production and seed sector in the last few decades. Initially, the idea was exploited in cross-pollinated plants, but eventually acquired serious attention in self-pollinated crops as well. Regardless of harvesting the benefits of heterosis, a century-long discussion is continued to understand the underlying basis of this phenomenon. The massive increase in knowledge of various fields of science such as genetics, epigenetics, genomics, proteomics, and metabolomics persistently provide new insights to understand the reasons for the expression of hybrid vigor. In this review, we have gathered information ranging from classical genetic studies, field experiments to various high-throughput omics and computational modelling studies in order to understand the underlying basis of heterosis. The modern-day science has worked significantly to pull off our understanding of heterosis yet leaving open questions that requires further research and experimentation. Answering these questions would possibly equip today’s plant breeders with efficient tools and accurate choices to breed crops for a sustainable future.
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Affiliation(s)
- Attiq ur Rehman
- Horticulture Technologies, Production Systems Unit, Natural Resources Institute (Luke), Toivonlinnantie 518, 21500 Piikkiö, Finland;
- Department of Agricultural Sciences, Faculty of Agriculture and Forestry, The University of Helsinki, 00790 Helsinki, Finland;
| | - Trang Dang
- Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
- Correspondence:
| | - Shanzay Qamar
- Department of Agricultural Biotechnology, National Institute of Biotechnology and Genetic Engineering, Pakistan Institute of Engineering and Applied Science, Faisalabad 38000, Pakistan;
| | - Amina Ilyas
- Department of Botany, Government College University, Lahore 54000, Pakistan;
| | - Reemana Fatema
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), SE-230 53 Alnarp, Sweden;
- Department of Seed Science and Technology, Ege University, Bornova, Izmir 35100, Turkey
| | - Madan Kafle
- Department of Agricultural Sciences, Faculty of Agriculture and Forestry, The University of Helsinki, 00790 Helsinki, Finland;
| | - Zawar Hussain
- Environmental and Plant Biology Department, Ohio University, Athens, OH 45701, USA;
| | - Sara Masood
- University Institute of Diet and Nutritional Sciences (UIDNS), Faculty of Allied Health Sciences, University of Lahore, Lahore 54000, Pakistan;
| | - Shehyar Iqbal
- IMPLANTEUS Graduate School, Avignon Université, 84000 Avignon, France;
| | - Khurram Shahzad
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur 22620, Pakistan;
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20
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Li X, Marquardt A, Wasson A. Carbon budgeting belowground. THE NEW PHYTOLOGIST 2021; 232:5-7. [PMID: 34216155 DOI: 10.1111/nph.17520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Xiaoqing Li
- CSIRO Agriculture & Food, Black Mountain, Canberra, ACT, 2601, Australia
| | | | - Anton Wasson
- CSIRO Agriculture & Food, St Lucia, Brisbane, QLD, 4067, Australia
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21
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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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22
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Crisp PA, Bhatnagar-Mathur P, Hundleby P, Godwin ID, Waterhouse PM, Hickey LT. Beyond the gene: epigenetic and cis-regulatory targets offer new breeding potential for the future. Curr Opin Biotechnol 2021; 73:88-94. [PMID: 34348216 DOI: 10.1016/j.copbio.2021.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/06/2021] [Indexed: 12/20/2022]
Abstract
For millennia, natural and artificial selection has combined favourable alleles for desirable traits in crop species. While modern plant breeding has achieved steady increases in crop yields over the last century, on the current trajectory we will simply not meet demand by 2045. Novel breeding strategies and sources of genetic variation will be required to sustainably fill predicted yield gaps and meet new consumer preferences. Here, we highlight that stepping up to meet this grand challenge will increasingly require thinking 'beyond the gene'. Significant progress has been made in understanding the contributions of both epigenetic variation and cis-regulatory variation to plant traits. This non-genic variation has great potential in future breeding, synthetic biology and biotechnology applications.
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Affiliation(s)
- Peter A Crisp
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane QLD 4072, Australia.
| | - Pooja Bhatnagar-Mathur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Penny Hundleby
- Crop Transformation Group, Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ian D Godwin
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
| | - Peter M Waterhouse
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD 4001, Australia; Centre of Excellence for Plant Success in Nature and Agriculture, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia.
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23
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Gogolev YV, Ahmar S, Akpinar BA, Budak H, Kiryushkin AS, Gorshkov VY, Hensel G, Demchenko KN, Kovalchuk I, Mora-Poblete F, Muslu T, Tsers ID, Yadav NS, Korzun V. OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security. PLANTS (BASEL, SWITZERLAND) 2021; 10:1423. [PMID: 34371624 PMCID: PMC8309286 DOI: 10.3390/plants10071423] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022]
Abstract
The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require much faster responses and more effective solutions that cannot be achieved through traditional breeding. Further prospects for increasing the efficiency of agriculture are undoubtedly associated with the inclusion in the breeding strategy of new knowledge obtained using high-throughput technologies and new tools in the future to ensure the design of new plant genomes and predict the desired phenotype. This article provides an overview of the current state of research in these areas, as well as the study of soil and plant microbiomes, and the prospective use of their potential in a new field of microbiome engineering. In terms of genomic and phenomic predictions, we also propose an integrated approach that combines high-density genotyping and high-throughput phenotyping techniques, which can improve the prediction accuracy of quantitative traits in crop species.
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Affiliation(s)
- Yuri V. Gogolev
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | | | - Hikmet Budak
- Montana BioAg Inc., Missoula, MT 59802, USA; (B.A.A.); (H.B.)
| | - Alexey S. Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Vladimir Y. Gorshkov
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, 40225 Dusseldorf, Germany;
- Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, 78371 Olomouc, Czech Republic
| | - Kirill N. Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | - Tugdem Muslu
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey;
| | - Ivan D. Tsers
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Narendra Singh Yadav
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Viktor Korzun
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37555 Einbeck, Germany
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Mladenov V, Fotopoulos V, Kaiserli E, Karalija E, Maury S, Baranek M, Segal N, Testillano PS, Vassileva V, Pinto G, Nagel M, Hoenicka H, Miladinović D, Gallusci P, Vergata C, Kapazoglou A, Abraham E, Tani E, Gerakari M, Sarri E, Avramidou E, Gašparović M, Martinelli F. Deciphering the Epigenetic Alphabet Involved in Transgenerational Stress Memory in Crops. Int J Mol Sci 2021; 22:7118. [PMID: 34281171 PMCID: PMC8268041 DOI: 10.3390/ijms22137118] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/16/2021] [Accepted: 06/27/2021] [Indexed: 12/11/2022] Open
Abstract
Although epigenetic modifications have been intensely investigated over the last decade due to their role in crop adaptation to rapid climate change, it is unclear which epigenetic changes are heritable and therefore transmitted to their progeny. The identification of epigenetic marks that are transmitted to the next generations is of primary importance for their use in breeding and for the development of new cultivars with a broad-spectrum of tolerance/resistance to abiotic and biotic stresses. In this review, we discuss general aspects of plant responses to environmental stresses and provide an overview of recent findings on the role of transgenerational epigenetic modifications in crops. In addition, we take the opportunity to describe the aims of EPI-CATCH, an international COST action consortium composed by researchers from 28 countries. The aim of this COST action launched in 2020 is: (1) to define standardized pipelines and methods used in the study of epigenetic mechanisms in plants, (2) update, share, and exchange findings in epigenetic responses to environmental stresses in plants, (3) develop new concepts and frontiers in plant epigenetics and epigenomics, (4) enhance dissemination, communication, and transfer of knowledge in plant epigenetics and epigenomics.
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Affiliation(s)
- Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Sq. Dositeja Obradovića 8, 21000 Novi Sad, Serbia;
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences, Biotechnology & Food Science, Cyprus University of Technology, Lemesos 3036, Cyprus;
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK;
| | - Erna Karalija
- Laboratory for Plant Physiology, Department for Biology, Faculty of Science, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina;
| | - Stephane Maury
- INRAe, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, 45067 Orléans, France;
| | - Miroslav Baranek
- Mendeleum—Insitute of Genetics, Faculty of Horticulture, Mendel University in Brno, Valtická 334, 69144 Lednice, Czech Republic;
| | - Naama Segal
- Israel Oceanographic and Limnological Research, The National Center for Mariculture (NCM), P.O.B. 1212, Eilat 88112, Israel;
| | - Pilar S. Testillano
- Center of Biological Research Margarita Salas, CIB-CSIC, Ramiro de 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;
| | - Glória Pinto
- Centre for Environmental and Marine Studies (CESAM), Biology Department, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Manuela Nagel
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany;
| | - Hans Hoenicka
- Genomic Research Department, Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany;
| | - Dragana Miladinović
- Laboratory for Biotechnology, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia;
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—CS5000833882 Villenave d’Ornon, 33076 Bordeaux, France;
| | - Chiara Vergata
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Aliki Kapazoglou
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-Dimitra (HAO-Dimitra), Sofokli Venizelou 1, Lykovrysi, 14123 Athens, Greece;
| | - Eleni Abraham
- Laboratory of Range Science, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.T.); (M.G.); (E.S.); (E.A.)
| | - Maria Gerakari
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.T.); (M.G.); (E.S.); (E.A.)
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.T.); (M.G.); (E.S.); (E.A.)
| | - Evaggelia Avramidou
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.T.); (M.G.); (E.S.); (E.A.)
| | - Mateo Gašparović
- Chair of Photogrammetry and Remote Sensing, Faculty of Geodesy, University of Zagreb, 10000 Zagreb, Croatia;
| | - Federico Martinelli
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy;
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Reynolds M, Atkin OK, Bennett M, Cooper M, Dodd IC, Foulkes MJ, Frohberg C, Hammer G, Henderson IR, Huang B, Korzun V, McCouch SR, Messina CD, Pogson BJ, Slafer GA, Taylor NL, Wittich PE. Addressing Research Bottlenecks to Crop Productivity. TRENDS IN PLANT SCIENCE 2021; 26:607-630. [PMID: 33893046 DOI: 10.1016/j.tplants.2021.03.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 05/22/2023]
Abstract
Asymmetry of investment in crop research leads to knowledge gaps and lost opportunities to accelerate genetic gain through identifying new sources and combinations of traits and alleles. On the basis of consultation with scientists from most major seed companies, we identified several research areas with three common features: (i) relatively underrepresented in the literature; (ii) high probability of boosting productivity in a wide range of crops and environments; and (iii) could be researched in 'precompetitive' space, leveraging previous knowledge, and thereby improving models that guide crop breeding and management decisions. Areas identified included research into hormones, recombination, respiration, roots, and source-sink, which, along with new opportunities in phenomics, genomics, and bioinformatics, make it more feasible to explore crop genetic resources and improve breeding strategies.
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Affiliation(s)
- Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mexico, El Batan, Texcoco, Mexico.
| | - Owen K Atkin
- Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University Canberra, Acton, ACT 2601, Australia.
| | - Malcolm Bennett
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Leicestershire, LE12 5RD, UK.
| | - Mark Cooper
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Ian C Dodd
- The Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - M John Foulkes
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Leicestershire, LE12 5RD, UK
| | - Claus Frohberg
- BASF BBC-Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Gent, Belgium
| | - Graeme Hammer
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Bingru Huang
- Department of Plant Biology and Pathology, Rutgers University, 59 Dudley Road, New Brunswick, NJ 08901, USA.
| | | | - Susan R McCouch
- Plant Breeding & Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14850, USA.
| | - Carlos D Messina
- Corteva Agriscience, 7250 NW 62nd Avenue, Johnston, IA 50310, USA.
| | - Barry J Pogson
- Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University Canberra, Acton, ACT 2601, Australia
| | - Gustavo A Slafer
- Department of Crop and Forest Sciences, University of Lleida, AGROTECNIO, CERCA Center, Av. R. Roure 191, 25198 Lleida, Spain; ICREA, Catalonian Institution for Research and Advanced Studies, Barcelona, Spain.
| | - Nicolas L Taylor
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Peter E Wittich
- Syngenta Seeds B.V., Westeinde 62, 1601 BK, Enkhuizen, The Netherlands.
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26
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Technow F, Podlich D, Cooper M. Back to the future: Implications of genetic complexity for the structure of hybrid breeding programs. G3 (BETHESDA, MD.) 2021; 11:6265599. [PMID: 33950172 PMCID: PMC8495936 DOI: 10.1093/g3journal/jkab153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/28/2021] [Indexed: 11/14/2022]
Abstract
Commercial hybrid breeding operations can be described as decentralized networks of smaller, more or less isolated breeding programs. There is further a tendency for the disproportionate use of successful inbred lines for generating the next generation of recombinants, which has led to a series of significant bottlenecks, particularly in the history of the North American and European maize germplasm. Both the decentralization and the disproportionate contribution of inbred lines reduce effective population size and constrain the accessible genetic space. Under these conditions, long-term response to selection is not expected to be optimal under the classical infinitesimal model of quantitative genetics. In this study, we therefore aim to propose a rationale for the success of large breeding operations in the context of genetic complexity arising from the structure and properties of interactive genetic networks. For this, we use simulations based on the NK model of genetic architecture. We indeed found that constraining genetic space through program decentralization and disproportionate contribution of parental inbred lines, is required to expose additive genetic variation and thus facilitate heritable genetic gains under high levels of genetic complexity. These results introduce new insights into why the historically grown structure of hybrid breeding programs was successful in improving the yield potential of hybrid crops over the last century. We also hope that a renewed appreciation for “why things worked” in the past can guide the adoption of novel technologies and the design of future breeding strategies for navigating biological complexity.
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Affiliation(s)
- Frank Technow
- Plant Breeding, Corteva Agriscience, Tavistock, ON, N0B 2R0, Canada
| | - Dean Podlich
- Systems and Innovation for Breeding and Seed Products, Corteva Agriscience, Johnston, IA, 50131, USA
| | - Mark Cooper
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4067, Australia
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27
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Mohd Saad NS, Severn-Ellis AA, Pradhan A, Edwards D, Batley J. Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment. Front Genet 2021; 12:600789. [PMID: 33679880 PMCID: PMC7930750 DOI: 10.3389/fgene.2021.600789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022] Open
Abstract
Meeting the needs of a growing world population in the face of imminent climate change is a challenge; breeding of vegetable and oilseed Brassica crops is part of the race in meeting these demands. Available genetic diversity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of diversity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient Brassica crops. During the past two decades, an increasing number of high-quality nuclear and organellar Brassica genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with diversity, is set to lead the way in Brassica improvement; however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient Brassica varieties ready for climate change.
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Affiliation(s)
| | | | | | | | - Jacqueline Batley
- School of Biological Sciences Western Australia and UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia
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28
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Srikant T, Drost HG. How Stress Facilitates Phenotypic Innovation Through Epigenetic Diversity. FRONTIERS IN PLANT SCIENCE 2021; 11:606800. [PMID: 33519857 PMCID: PMC7843580 DOI: 10.3389/fpls.2020.606800] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/16/2020] [Indexed: 05/14/2023]
Abstract
Climate adaptation through phenotypic innovation will become the main challenge for plants during global warming. Plants exhibit a plethora of mechanisms to achieve environmental and developmental plasticity by inducing dynamic alterations of gene regulation and by maximizing natural variation through large population sizes. While successful over long evolutionary time scales, most of these mechanisms lack the short-term adaptive responsiveness that global warming will require. Here, we review our current understanding of the epigenetic regulation of plant genomes, with a focus on stress-response mechanisms and transgenerational inheritance. Field and laboratory-scale experiments on plants exposed to stress have revealed a multitude of temporally controlled, mechanistic strategies integrating both genetic and epigenetic changes on the genome level. We analyze inter- and intra-species population diversity to discuss how methylome differences and transposon activation can be harnessed for short-term adaptive efforts to shape co-evolving traits in response to qualitatively new climate conditions and environmental stress.
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Affiliation(s)
| | - Hajk-Georg Drost
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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29
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Li G, Chen T, Feng B, Peng S, Tao L, Fu G. Respiration, Rather Than Photosynthesis, Determines Rice Yield Loss Under Moderate High-Temperature Conditions. FRONTIERS IN PLANT SCIENCE 2021; 12:678653. [PMID: 34249047 PMCID: PMC8264589 DOI: 10.3389/fpls.2021.678653] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/03/2021] [Indexed: 05/11/2023]
Abstract
Photosynthesis is an important biophysical and biochemical reaction that provides food and oxygen to maintain aerobic life on earth. Recently, increasing photosynthesis has been revisited as an approach for reducing rice yield losses caused by high temperatures. We found that moderate high temperature causes less damage to photosynthesis but significantly increases respiration. In this case, the energy production efficiency is enhanced, but most of this energy is allocated to maintenance respiration, resulting in an overall decrease in the energy utilization efficiency. In this perspective, respiration, rather than photosynthesis, may be the primary contributor to yield losses in a high-temperature climate. Indeed, the dry matter weight and yield could be enhanced if the energy was mainly allocated to the growth respiration. Therefore, we proposed that engineering smart rice cultivars with a highly efficient system of energy production, allocation, and utilization could effectively solve the world food crisis under high-temperature conditions.
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Affiliation(s)
- Guangyan Li
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- Crop Production and Physiology Center (CPPC), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tingting Chen
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Baohua Feng
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Shaobing Peng
- Crop Production and Physiology Center (CPPC), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Longxing Tao
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- *Correspondence: Longxing Tao,
| | - Guanfu Fu
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- Guanfu Fu,
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30
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Mona Mohamed Elseehy. Differential Transgeneration Methylation of Exogenous Promoters in T1 Transgenic Wheat (Triticum aestivum). CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720050151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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31
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Varotto S, Tani E, Abraham E, Krugman T, Kapazoglou A, Melzer R, Radanović A, Miladinović D. Epigenetics: possible applications in climate-smart crop breeding. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5223-5236. [PMID: 32279074 PMCID: PMC7475248 DOI: 10.1093/jxb/eraa188] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/09/2020] [Indexed: 05/23/2023]
Abstract
To better adapt transiently or lastingly to stimuli from the surrounding environment, the chromatin states in plant cells vary to allow the cells to fine-tune their transcriptional profiles. Modifications of chromatin states involve a wide range of post-transcriptional histone modifications, histone variants, DNA methylation, and activity of non-coding RNAs, which can epigenetically determine specific transcriptional outputs. Recent advances in the area of '-omics' of major crops have facilitated identification of epigenetic marks and their effect on plant response to environmental stresses. As most epigenetic mechanisms are known from studies in model plants, we summarize in this review recent epigenetic studies that may be important for improvement of crop adaptation and resilience to environmental changes, ultimately leading to the generation of stable climate-smart crops. This has paved the way for exploitation of epigenetic variation in crop breeding.
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Affiliation(s)
- Serena Varotto
- Department of Agronomy, Food, Natural Resources, Animals, and the Environment, University of Padova, Agripolis, Viale dell’Università, Padova, Italy
| | - Eleni Tani
- Department of Crop Science, Laboratory of Plant Breeding and Biometry, Agricultural University of Athens, Athens, Greece
| | - Eleni Abraham
- Laboratory of Range Science, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Aliki Kapazoglou
- Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Department of Vitis, Hellenic Agricultural Organization-Demeter (HAO-Demeter), Lykovrysi, Greece
| | - Rainer Melzer
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin, Ireland
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32
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Chen C, Zheng Z, Bao Y, Zhang H, Richards CL, Li J, Chen Y, Zhao Y, Shen Z, Fu C. Comparisons of Natural and Cultivated Populations of Corydalis yanhusuo Indicate Divergent Patterns of Genetic and Epigenetic Variation. FRONTIERS IN PLANT SCIENCE 2020; 11:985. [PMID: 32719703 PMCID: PMC7347962 DOI: 10.3389/fpls.2020.00985] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
Epigenetic variation may contribute to traits that are important in domestication, but how patterns of genetic and epigenetic variation differ between cultivated and wild plants remains poorly understood. In particular, we know little about how selection may shape epigenetic variation in natural and cultivated populations. In this study, we investigated 11 natural populations and 6 major cultivated populations using amplified fragment length polymorphism (AFLP) and methylation-sensitive AFLP (MS-AFLP or MSAP) markers to identify patterns of genetic and epigenetic diversity among Corydalis yanhusuo populations. We further explored correlations among genetic, epigenetic, alkaloidal, and climatic factors in natural and cultivated C. yanhusuo. We found support for a single origin for all cultivated populations, from a natural population which was differentiated from the other natural populations. The magnitude of F ST based on AFLP was significantly correlated with that for MSAP in pairwise comparisons in both natural and cultivated populations, suggesting a relationship between genetic and epigenetic variation in C. yanhusuo. This relationship was further supported by dbRDA (distance-based redundancy analyses) where some of the epigenetic variation could be explained by genetic variation in natural and cultivated populations. Genetic variation was slightly higher in natural than cultivated populations, and exceeded epigenetic variation in both types of populations. However, epigenetic differentiation exceeded that of genetic differentiation among cultivated populations, while the reverse was observed among natural populations. The differences between wild and cultivated plants may be partly due to processes inherent to cultivation and in particular the differences in mode of reproduction. The importance of epigenetic compared to genetic modifications is thought to vary depending on reproductive strategies, and C. yanhusuo usually reproduces sexually in natural environments, while the cultivated C. yanhusuo are propagated clonally. In addition, alkaloid content of C. yanhusuo varied across cultivated populations, and alkaloid content was significantly correlated to climatic variation, but also to genetic (6.89%) and even more so to epigenetic (14.09%) variation in cultivated populations. Our study demonstrates that epigenetic variation could be important in cultivation of C. yanhusuo and serve as a source of variation for response to environmental conditions.
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Affiliation(s)
- Chen Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zhi Zheng
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yiqiong Bao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Hanchao Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Christina L. Richards
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
- Plant Evolutionary Ecology Group, University of Tübingen, Tübingen, Germany
| | - Jinghui Li
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, and College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yahua Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yunpeng Zhao
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, and College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Chengxin Fu
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, and College of Life Sciences, Zhejiang University, Hangzhou, China
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K. Srivastava R, Bollam S, Pujarula V, Pusuluri M, Singh RB, Potupureddi G, Gupta R. Exploitation of Heterosis in Pearl Millet: A Review. PLANTS (BASEL, SWITZERLAND) 2020; 9:E807. [PMID: 32605134 PMCID: PMC7412370 DOI: 10.3390/plants9070807] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 01/06/2023]
Abstract
The phenomenon of heterosis has fascinated plant breeders ever since it was first described by Charles Darwin in 1876 in the vegetable kingdom and later elaborated by George H Shull and Edward M East in maize during 1908. Heterosis is the phenotypic and functional superiority manifested in the F1 crosses over the parents. Various classical complementation mechanisms gave way to the study of the underlying potential cellular and molecular mechanisms responsible for heterosis. In cereals, such as maize, heterosis has been exploited very well, with the development of many single-cross hybrids that revolutionized the yield and productivity enhancements. Pearl millet (Pennisetum glaucum (L.) R. Br.) is one of the important cereal crops with nutritious grains and lower water and energy footprints in addition to the capability of growing in some of the harshest and most marginal environments of the world. In this highly cross-pollinating crop, heterosis was exploited by the development of a commercially viable cytoplasmic male-sterility (CMS) system involving a three-lines breeding system (A-, B- and R-lines). The first set of male-sterile lines, i.e., Tift 23A and Tift18A, were developed in the early 1960s in Tifton, Georgia, USA. These provided a breakthrough in the development of hybrids worldwide, e.g., Tift 23A was extensively used by Punjab Agricultural University (PAU), Ludhiana, India, for the development of the first single-cross pearl millet hybrid, named Hybrid Bajra 1 (HB 1), in 1965. Over the past five decades, the pearl millet community has shown tremendous improvement in terms of cytoplasmic and nuclear diversification of the hybrid parental lines, which led to a progressive increase in the yield and adaptability of the hybrids that were developed, resulting in significant genetic gains. Lately, the whole genome sequencing of Tift 23D2B1 and re-sequencing of circa 1000 genomes by a consortium led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) has been a significant milestone in the development of cutting-edge genetic and genomic resources in pearl millet. Recently, the application of genomics and molecular technologies has provided better insights into genetic architecture and patterns of heterotic gene pools. Development of whole-genome prediction models incorporating heterotic gene pool models, mapped traits and markers have the potential to take heterosis breeding to a new level in pearl millet. This review discusses advances and prospects in various fronts of heterosis for pearl millet.
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Affiliation(s)
- Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad TS 502324, India; (S.B.); (V.P.); (M.P.); (R.B.S.); (G.P.)
| | | | | | | | | | | | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad TS 502324, India; (S.B.); (V.P.); (M.P.); (R.B.S.); (G.P.)
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Corbin KR, Bolt B, Rodríguez López CM. Breeding for Beneficial Microbial Communities Using Epigenomics. Front Microbiol 2020; 11:937. [PMID: 32477316 PMCID: PMC7242621 DOI: 10.3389/fmicb.2020.00937] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 04/20/2020] [Indexed: 02/03/2023] Open
Affiliation(s)
- Kendall R Corbin
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States.,Biosystems and Agricultural Engineering, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
| | - Bridget Bolt
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
| | - Carlos M Rodríguez López
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
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López-García CM, Ruíz-Herrera LF, López-Bucio JS, Huerta-Venegas PI, Peña-Uribe CA, de la Cruz HR, López-Bucio J. ALTERED MERISTEM PROGRAM 1 promotes growth and biomass accumulation influencing guard cell aperture and photosynthetic efficiency in Arabidopsis. PROTOPLASMA 2020; 257:573-582. [PMID: 31823020 DOI: 10.1007/s00709-019-01458-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
ALTERED MERISTEM PROGRAM 1 (AMP1) encodes a putative glutamate-carboxypeptidase important for plant growth and development. In this study, by comparing the growth of Arabidopsis wild-type, amp1-10 and amp1-13 mutants, and AMP1-GFP/OX2- and AMP1-GFP/OX7-overexpressing seedlings in vitro and in soil, we uncover the role of AMP1 in biomass accumulation in Arabidopsis. AMP1-overexpressing plants had longer primary roots and increased lateral root number and density than the WT, which correlated with improved root, shoot, and total biomass accumulation. AMP1-overexpressing seedlings had an enhanced rate of growth of primary roots, and accordingly, sucrose supplementation restored primary root growth and promoted lateral root formation in amp1 mutants, while reproductive development, fruit size, and seed content were also modified according to disruption or overexpression of AMP1. We further found that AMP1 plays an important role for stomatal development, guard cell functioning, and carbon assimilation. These data help explain the pleiotropic functions of AMP1 in both root and shoot system development, possibly acting in a sugar-dependent manner for regulation of root architecture, biomass accumulation, and seed production.
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Affiliation(s)
- Claudia Marina López-García
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo. Edificio A1´, Ciudad Universitaria, C. P. 58030, Morelia, Michoacán, Mexico
| | - León Francisco Ruíz-Herrera
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo. Edificio A1´, Ciudad Universitaria, C. P. 58030, Morelia, Michoacán, Mexico
| | - Jesús Salvador López-Bucio
- CONACYT, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo. Edificio B3, Ciudad Universitaria, C. P. 58030, Morelia, Michoacán, Mexico
| | - Pedro Iván Huerta-Venegas
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo. Edificio A1´, Ciudad Universitaria, C. P. 58030, Morelia, Michoacán, Mexico
| | - César Arturo Peña-Uribe
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo. Edificio A1´, Ciudad Universitaria, C. P. 58030, Morelia, Michoacán, Mexico
| | - Homero Reyes de la Cruz
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo. Edificio A1´, Ciudad Universitaria, C. P. 58030, Morelia, Michoacán, Mexico
| | - José López-Bucio
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo. Edificio A1´, Ciudad Universitaria, C. P. 58030, Morelia, Michoacán, Mexico.
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Lin L, Wu C, Wang J, Liao M, Yang D, Deng H, Lv X, Xia H, Liang D, Deng Q. Effects of reciprocal hybridization on cadmium accumulation in F1 hybrids of two Solanum photeinocarpum ecotypes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:7120-7129. [PMID: 31883078 DOI: 10.1007/s11356-019-07446-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 12/18/2019] [Indexed: 06/10/2023]
Abstract
In this study, farmland and mining ecotypes of Solanum photeinocarpum (a potential cadmium (Cd) hyperaccumulator plant) were reciprocally hybridized each other, and the Cd accumulation characteristics of the F1 hybrids were studied. In pot experiments, higher biomasses and Cd extraction abilities were found for two S. photeinocarpum F1 hybrids than for the parents, but the Cd contents in various organs were lower in the hybrids than the parents. However, the differences between the Cd contents in the two hybrids were not significant. The antioxidant enzyme (superoxide dismutase and peroxidase) activities were higher for the S. photeinocarpum F1 hybrids than the parents. Less DNA methylation was found in the hybrids than the parents because more demethylation occurred in the hybrids than the parents. The biomass, Cd content, and Cd extraction ability effects in field experiments were similar to the effects in the pot experiments. It was concluded that reciprocally hybridizing different S. photeinocarpum ecotypes improved the ability of S. photeinocarpum to be used to phytoremediate contaminated land.
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Affiliation(s)
- Lijin Lin
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Caifang Wu
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jin Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ming'an Liao
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Daiyu Yang
- Ya'an Poverty Alleviation and Immigration Bureau, Ya'an, 625000, China
| | - Honghong Deng
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiulan Lv
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hui Xia
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dong Liang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qunxian Deng
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
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Silva FB, Costa AC, Müller C, Nascimento KT, Batista PF, Vital RG, Megguer CA, Jakelaitis A, Domingos M. Dipteryx alata, a tree native to the Brazilian Cerrado, is sensitive to the herbicide nicosulfuron. ECOTOXICOLOGY (LONDON, ENGLAND) 2020; 29:217-225. [PMID: 32030573 DOI: 10.1007/s10646-019-02154-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
The expansion of land use for agricultural interests and the excessive use of herbicides are among the causes of biodiversity losses in the Brazilian Cerrado biome. Therefore, we aimed to test the hypothesis that Dipteryx alata Vogel, a common species in this biome, is sensitive to nicosulfuron because of its high phytotoxicity. We evaluated physiological, biochemical and morphological responses in D. alata plants exposed to increasing doses of the herbicide. Young plants were transplanted to 10 L pots containing substrate composed of soil and sand (2:1) after fertilization. After an acclimation period, the following doses of nicosulfuron were applied: 0 (control), 6, 12, 24, 48, and 60 g a.e. ha-1. The experiment was conducted in a randomized block design factorial scheme with six doses of nicosulfuron, three evaluation times, and five replicates per treatment. The effects of the herbicide were assessed by measuring gas exchange, chlorophyll a fluorescence, photosynthetic pigments, membrane permeability, antioxidant enzymes and acetolactate synthase. Nicosulfuron altered the photosynthetic machinery and enzymatic metabolism of D. alata. Reductions in physiological traits, increased catalase and ascorbate peroxidase activities, enhanced malondialdehyde concentrations rate of electrolyte leakage and decreased acetolactate synthase activity in response to nicosulfuron all suggest that D. alata is sensitive to this herbicide.
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Affiliation(s)
- Fábia Barbosa Silva
- Instituto Federal de Educação, Ciência e Tecnologia Goiano-Campus Rio Verde, Caixa Postal 66, Rio Verde, GO, 75901-9 70, Brazil
- Laboratório de Estudo de Plantas sob Estresse, Universidade de Sao Paulo, Escola Superior de Agricultura "Luiz de Queiroz", Caixa Postal 9, Piracicaba, SP, 13418-900, Brazil
| | - Alan Carlos Costa
- Instituto Federal de Educação, Ciência e Tecnologia Goiano-Campus Rio Verde, Caixa Postal 66, Rio Verde, GO, 75901-9 70, Brazil.
| | - Caroline Müller
- Instituto Federal de Educação, Ciência e Tecnologia Goiano-Campus Rio Verde, Caixa Postal 66, Rio Verde, GO, 75901-9 70, Brazil
| | - Kelly Telles Nascimento
- Instituto Federal de Educação, Ciência e Tecnologia Goiano-Campus Rio Verde, Caixa Postal 66, Rio Verde, GO, 75901-9 70, Brazil
| | - Priscila Ferreira Batista
- Instituto Federal de Educação, Ciência e Tecnologia Goiano-Campus Rio Verde, Caixa Postal 66, Rio Verde, GO, 75901-9 70, Brazil
| | - Roberto Gomes Vital
- Instituto Federal de Educação, Ciência e Tecnologia Goiano-Campus Rio Verde, Caixa Postal 66, Rio Verde, GO, 75901-9 70, Brazil
| | - Clarice Aparecida Megguer
- Instituto Federal de Educação, Ciência e Tecnologia Goiano-Campus Morrinhos, Caixa Postal 92, Morrinhos, GO, 75650-000, Brazil
| | - Adriano Jakelaitis
- Instituto Federal de Educação, Ciência e Tecnologia Goiano-Campus Rio Verde, Caixa Postal 66, Rio Verde, GO, 75901-9 70, Brazil
| | - Marisa Domingos
- Instituto de Botânica, Núcleo de Pesquisa em Ecologia, Caixa Postal 68041, São Paulo, SP, 04045-972, Brazil
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Posch BC, Kariyawasam BC, Bramley H, Coast O, Richards RA, Reynolds MP, Trethowan R, Atkin OK. Exploring high temperature responses of photosynthesis and respiration to improve heat tolerance in wheat. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5051-5069. [PMID: 31145793 DOI: 10.1093/jxb/erz257] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 05/21/2019] [Indexed: 06/09/2023]
Abstract
High temperatures account for major wheat yield losses annually and, as the climate continues to warm, these losses will probably increase. Both photosynthesis and respiration are the main determinants of carbon balance and growth in wheat, and both are sensitive to high temperature. Wheat is able to acclimate photosynthesis and respiration to high temperature, and thus reduce the negative affects on growth. The capacity to adjust these processes to better suit warmer conditions stands as a potential avenue toward reducing heat-induced yield losses in the future. However, much remains to be learnt about such phenomena. Here, we review what is known of high temperature tolerance in wheat, focusing predominantly on the high temperature responses of photosynthesis and respiration. We also identify the many unknowns that surround this area, particularly with respect to the high temperature response of wheat respiration and the consequences of this for growth and yield. It is concluded that further investigation into the response of photosynthesis and respiration to high temperature could present several methods of improving wheat high temperature tolerance. Extending our knowledge in this area could also lead to more immediate benefits, such as the enhancement of current crop models.
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Affiliation(s)
- Bradley C Posch
- ARC Centre of Excellence in Plant Energy Biology, Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Buddhima C Kariyawasam
- ARC Centre of Excellence in Plant Energy Biology, Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Helen Bramley
- Plant Breeding Institute, Sydney Institute of Agriculture & School of Life and Environmental Sciences, The University of Sydney, Narrabri, NSW, Australia
| | - Onoriode Coast
- ARC Centre of Excellence in Plant Energy Biology, Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | | | - Matthew P Reynolds
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | - Richard Trethowan
- Plant Breeding Institute, Sydney Institute of Agriculture & School of Life and Environmental Sciences, The University of Sydney, Narrabri, NSW, Australia
| | - Owen K Atkin
- ARC Centre of Excellence in Plant Energy Biology, Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, Australia
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Coast O, Shah S, Ivakov A, Gaju O, Wilson PB, Posch BC, Bryant CJ, Negrini ACA, Evans JR, Condon AG, Silva-Pérez V, Reynolds MP, Pogson BJ, Millar AH, Furbank RT, Atkin OK. Predicting dark respiration rates of wheat leaves from hyperspectral reflectance. PLANT, CELL & ENVIRONMENT 2019; 42:2133-2150. [PMID: 30835839 DOI: 10.1111/pce.13544] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 02/18/2019] [Accepted: 02/24/2019] [Indexed: 05/22/2023]
Abstract
Greater availability of leaf dark respiration (Rdark ) data could facilitate breeding efforts to raise crop yield and improve global carbon cycle modelling. However, the availability of Rdark data is limited because it is cumbersome, time consuming, or destructive to measure. We report a non-destructive and high-throughput method of estimating Rdark from leaf hyperspectral reflectance data that was derived from leaf Rdark measured by a destructive high-throughput oxygen consumption technique. We generated a large dataset of leaf Rdark for wheat (1380 samples) from 90 genotypes, multiple growth stages, and growth conditions to generate models for Rdark . Leaf Rdark (per unit leaf area, fresh mass, dry mass or nitrogen, N) varied 7- to 15-fold among individual plants, whereas traits known to scale with Rdark , leaf N, and leaf mass per area (LMA) only varied twofold to fivefold. Our models predicted leaf Rdark , N, and LMA with r2 values of 0.50-0.63, 0.91, and 0.75, respectively, and relative bias of 17-18% for Rdark and 7-12% for N and LMA. Our results suggest that hyperspectral model prediction of wheat leaf Rdark is largely independent of leaf N and LMA. Potential drivers of hyperspectral signatures of Rdark are discussed.
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Affiliation(s)
- Onoriode Coast
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
| | - Shahen Shah
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
- The University of Agriculture Peshawar, Peshawar, 25130, Pakistan
| | - Alexander Ivakov
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
| | - Oorbessy Gaju
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
| | - Philippa B Wilson
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
| | - Bradley C Posch
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
| | - Callum J Bryant
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
| | - Anna Clarissa A Negrini
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
| | - John R Evans
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
| | - Anthony G Condon
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
- CSIRO Agriculture, Canberra, Australian Capital Territory, 2601, Australia
| | - Viridiana Silva-Pérez
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
- CSIRO Agriculture, Canberra, Australian Capital Territory, 2601, Australia
| | - Matthew P Reynolds
- International Maize and Wheat Improvement Centre (CIMMYT), México, 06600, Mexico
| | - Barry J Pogson
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Robert T Furbank
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
- CSIRO Agriculture, Canberra, Australian Capital Territory, 2601, Australia
| | - Owen K Atkin
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
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The use of MSAP reveals epigenetic diversity of the invasive clonal populations of Arundo donax L. PLoS One 2019; 14:e0215096. [PMID: 30964932 PMCID: PMC6456200 DOI: 10.1371/journal.pone.0215096] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/26/2019] [Indexed: 12/18/2022] Open
Abstract
Among the most widespread plant species with clonal reproduction Arundo donax L. represents one of most studied one characterized by very low genetic biodiversity. Although it is a perennial rhizomatous tall grass native to eastern and southern Asia, it spreads only asexually in the invaded range all over the world thriving very well in a large array of pedo-climatic conditions. This ability to morphologically or physiologically adapt to a broad array of conditions could be attributed to epigenetic mechanisms. To shade light on this relevant issue, 96 stems of A. donax from spontaneous populations distributed across the Italian invaded range (island of Sardinia, Northern and Southern Italy) were analysed. Leaf DNAs were extracted and processed through AFLPs and MSAPs for defining either genetic and epigenetic profiles. Both analyses clearly showed that the A. donax populations of Sardinia island are genetically distinct from those of Italian mainland; AFLPs showed an extremely low genetic biodiversity due to vegetative reproduction, whilst, epi-biodiversity, estimated through MSAP marker, increased within the analyzed populations. These results suggest that the capability of A. donax to invade and thrive in diverse environmental conditions can be, at least, partially attributed to a higher epigenetic variability. Therefore, the different DNA methylation status may have significant and important biological meaning, in particular, in the case of invasive clonal plants such as A. donax, also for the biodiversity definition, and MSAP marker can be considered an useful and cost effective marker to reveal it.
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Raju SKK, Shao M, Sanchez R, Xu Y, Sandhu A, Graef G, Mackenzie S. An epigenetic breeding system in soybean for increased yield and stability. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1836-1847. [PMID: 29570925 PMCID: PMC6181216 DOI: 10.1111/pbi.12919] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/20/2018] [Accepted: 02/24/2018] [Indexed: 05/17/2023]
Abstract
Epigenetic variation has been associated with a wide range of adaptive phenotypes in plants, but there exist few direct means for exploiting this variation. RNAi suppression of the plant-specific gene, MutS HOMOLOG1 (MSH1), in multiple plant species produces a range of developmental changes accompanied by modulation of defence, phytohormone and abiotic stress response pathways along with methylome repatterning. This msh1-conditioned developmental reprogramming is retained independent of transgene segregation, giving rise to transgene-null 'memory' effects. An isogenic memory line crossed to wild type produces progeny families displaying increased variation in adaptive traits that respond to selection. This study investigates amenability of the MSH1 system for inducing agronomically valuable epigenetic variation in soybean. We developed MSH1 epi-populations by crossing with msh1-acquired soybean memory lines. Derived soybean epi-lines showed increase in variance for multiple yield-related traits including pods per plant, seed weight and maturity time in both glasshouse and field trials. Selected epi-F2:4 and epi-F2:5 lines showed an increase in seed yield over wild type. By epi-F2:6, we observed a return of MSH1-derived enhanced growth back to wild-type levels. Epi-populations also showed evidence of reduced epitype-by-environment (e × E) interaction, indicating higher yield stability. Transcript profiling of epi-lines identified putative signatures of enhanced growth behaviour across generations. Genes related to cell cycle, abscisic acid biosynthesis and auxin response, particularly SMALL AUXIN UP RNAs (SAURs), were differentially expressed in epi-F2:4 lines that showed increased yield when compared to epi-F2:6 . These data support the potential of MSH1-derived epigenetic variation in plant breeding for enhanced yield and yield stability.
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Affiliation(s)
| | - Mon‐Ray Shao
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Robersy Sanchez
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
- Present address:
Departments of Biology and Plant SciencePennsylvania State UniversityUniversity ParkPAUSA
| | - Ying‐Zhi Xu
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Ajay Sandhu
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
- Present address:
SyngentaWoodlandCAUSA
| | - George Graef
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Sally Mackenzie
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
- Present address:
Departments of Biology and Plant SciencePennsylvania State UniversityUniversity ParkPAUSA
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Shen Y, Zhang J, Liu Y, Liu S, Liu Z, Duan Z, Wang Z, Zhu B, Guo YL, Tian Z. DNA methylation footprints during soybean domestication and improvement. Genome Biol 2018; 19:128. [PMID: 30201012 PMCID: PMC6130073 DOI: 10.1186/s13059-018-1516-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/22/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In addition to genetic variation, epigenetic variation plays an important role in determining various biological processes. The importance of natural genetic variation to crop domestication and improvement has been widely investigated. However, the contribution of epigenetic variation in crop domestication at population level has rarely been explored. RESULTS To understand the impact of epigenetics on crop domestication, we investigate the variation of DNA methylation during soybean domestication and improvement by whole-genome bisulfite sequencing of 45 soybean accessions, including wild soybeans, landraces, and cultivars. Through methylomic analysis, we identify 5412 differentially methylated regions (DMRs). These DMRs exhibit characters distinct from those of genetically selected regions. In particular, they have significantly higher genetic diversity. Association analyses suggest only 22.54% of DMRs can be explained by local genetic variations. Intriguingly, genes in the DMRs that are not associated with any genetic variation are enriched in carbohydrate metabolism pathways. CONCLUSIONS This study provides a valuable map of DNA methylation across diverse accessions and dissects the relationship between DNA methylation variation and genetic variation during soybean domestication, thus expanding our understanding of soybean domestication and improvement.
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Affiliation(s)
- Yanting Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Jixiang Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Zhi Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Zheng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Baoge Zhu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
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43
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Hao DC, Xiao PG. Deep in shadows: Epigenetic and epigenomic regulations of medicinal plants. CHINESE HERBAL MEDICINES 2018. [DOI: 10.1016/j.chmed.2018.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Gakière B, Fernie AR, Pétriacq P. More to NAD + than meets the eye: A regulator of metabolic pools and gene expression in Arabidopsis. Free Radic Biol Med 2018; 122:86-95. [PMID: 29309893 DOI: 10.1016/j.freeradbiomed.2018.01.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/22/2017] [Accepted: 01/03/2018] [Indexed: 10/18/2022]
Abstract
Since its discovery more than a century ago, nicotinamide adenine dinucleotide (NAD+) is recognised as a fascinating cornerstone of cellular metabolism. This ubiquitous energy cofactor plays vital roles in metabolic pathways and regulatory processes, a fact emphasised by the essentiality of a balanced NAD+ metabolism for normal plant growth and development. Research on the role of NAD in plants has been predominantly carried out in the model plant Arabidopsis thaliana (Arabidopsis) with emphasis on the redox properties and cellular signalling functions of the metabolite. This review examines the current state of knowledge concerning how NAD can regulate both metabolic pools and gene expression in Arabidopsis. Particular focus is placed on recent studies highlighting the complexity of metabolic regulations involving NAD, more particularly in the mitochondrial compartment, and of signalling roles with respect to interactions with environmental fluctuations most specifically those involving plant immunity.
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Affiliation(s)
- Bertrand Gakière
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ. Paris-Sud, Univ. Evry, Univ. Paris-Diderot, Univ. Paris-Saclay, Bâtiment 630 Rue Noetzlin, 91192 Gif-sur-Yvette cedex, France; Plateforme Métabolisme Métabolome, Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ. Paris-Sud, Univ. Evry, Univ. Paris-Diderot, Univ. ParisSaclay, Bâtiment 630 Rue Noetzlin, 91192 Gif-sur-Yvette cedex, France
| | - Alisdair R Fernie
- Max-Planck-Institute for Molecular Plant Physiology, Wissenschaftspark Golm, 14476 Potsdam-Golm, Germany
| | - Pierre Pétriacq
- biOMICS Facility, Department of Animal and Plant Sciences, The University of Sheffield, S10 2TN Sheffield, United Kingdom; UMR 1332 Biologie du Fruit et Pathologie, INRA Bordeaux & Université de Bordeaux, F-33883 Villenave d'Ornon, France.
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45
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Sollars ESA, Buggs RJA. Genome-wide epigenetic variation among ash trees differing in susceptibility to a fungal disease. BMC Genomics 2018; 19:502. [PMID: 29954338 PMCID: PMC6022711 DOI: 10.1186/s12864-018-4874-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 06/18/2018] [Indexed: 11/10/2022] Open
Abstract
Background European ash trees (Fraxinus excelsior) are currently threatened by ash dieback (ADB) caused by the fungus Hymenoscyphus fraxineus but a small percentage of the population possesses natural low susceptibility. The genome of a European ash tree has recently been sequenced. Here, we present whole genome DNA methylation data for two F. excelsior genotypes with high susceptibility to ADB, and two genotypes with low susceptibility, each clonally replicated. We also include two genotypes of Manchurian ash (F. mandshurica), an ash species which has co-evolved with H. fraxineus and also has low susceptibility to ADB. Results In F. excelsior, we find an average methylation level of 76.2% in the CG context, 52.0% in the CHG context, and 13.9% in the CHH context; similar levels to those of tomato. We find higher methylation in transposable elements as opposed to non-mobile elements, and high densities of Non-Differentially Methylation Positions (N-DMPs) in genes with housekeeping functions. Of genes putatively duplicated in whole genome duplication (WGD) events, an average of 25.9% are differentially methylated in at least one cytosine context, potentially indicative of unequal silencing. Variability in methylation patterns exists among clonal replicates, and this is only slightly less than the variability found between different genotypes. Of twenty genes previously found to have expression levels associated with ADB susceptibility, we find only two of these have differential methylation between high and low susceptibility F. excelsior trees. In addition, we identify 1683 significant Differentially Methylated Regions (DMRs) (q-value< 0.001) between the high and low susceptibility genotypes of F. excelsior trees, of which 665 remain significant when F. mandshurica samples are added to the low susceptibility group. Conclusions We find a higher frequency of differentially methylated WGD-derived gene duplicates in ash than other plant species previously studied. We also identify a set of genes with differential methylation between genotypes and species with high versus low susceptibility to ADB. This provides valuable foundational data for future work on the role that epigenetics may play in gene dosage compensation and susceptibility to ADB in ash. Electronic supplementary material The online version of this article (10.1186/s12864-018-4874-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elizabeth S A Sollars
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Richard J A Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK. .,Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AB, UK.
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46
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Finnegan EJ, Ford B, Wallace X, Pettolino F, Griffin PT, Schmitz RJ, Zhang P, Barrero JM, Hayden MJ, Boden SA, Cavanagh CA, Swain SM, Trevaskis B. Zebularine treatment is associated with deletion of FT-B1 leading to an increase in spikelet number in bread wheat. PLANT, CELL & ENVIRONMENT 2018; 41:1346-1360. [PMID: 29430678 DOI: 10.1111/pce.13164] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/16/2018] [Accepted: 01/21/2018] [Indexed: 05/09/2023]
Abstract
The number of rachis nodes (spikelets) on a wheat spike is a component of grain yield that correlates with flowering time. The genetic basis regulating flowering in cereals is well understood, but there are reports that flowering time can be modified at a high frequency by selective breeding, suggesting that it may be regulated by both epigenetic and genetic mechanisms. We investigated the role of DNA methylation in regulating spikelet number and flowering time by treating a semi-spring wheat with the demethylating agent, Zebularine. Three lines with a heritable increase in spikelet number were identified. The molecular basis for increased spikelet number was not determined in 2 lines, but the phenotype showed non-Mendelian inheritance, suggesting that it could have an epigenetic basis. In the remaining line, the increased spikelet phenotype behaved as a Mendelian recessive trait and late flowering was associated with a deletion encompassing the floral promoter, FT-B1. Deletion of FT-B1 delayed the transition to reproductive growth, extended the duration of spike development, and increased spikelet number under different temperature regimes and photoperiod. Transiently disrupting DNA methylation can generate novel flowering behaviour in wheat, but these changes may not be sufficiently stable for use in breeding programs.
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Affiliation(s)
| | - Brett Ford
- CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | | | | | - Patrick T Griffin
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, New South Wales, 2570, Australia
| | - Jose M Barrero
- CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Matthew J Hayden
- Agriculture Victoria Research, Agribio Center, Bundoora, Victoria, 3083, Australia
| | - Scott A Boden
- CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | | | - Steve M Swain
- CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Ben Trevaskis
- CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
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47
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Seifert F, Thiemann A, Schrag TA, Rybka D, Melchinger AE, Frisch M, Scholten S. Small RNA-based prediction of hybrid performance in maize. BMC Genomics 2018; 19:371. [PMID: 29783940 PMCID: PMC5963143 DOI: 10.1186/s12864-018-4708-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 04/22/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Small RNA (sRNA) sequences are known to have a broad impact on gene regulation by various mechanisms. Their performance for the prediction of hybrid traits has not yet been analyzed. Our objective was to analyze the relation of parental sRNA expression with the performance of their hybrids, to develop a sRNA-based prediction approach, and to compare it to more common SNP and mRNA transcript based predictions using a factorial mating scheme of a maize hybrid breeding program. RESULTS Correlation of genomic differences and messenger RNA (mRNA) or sRNA expression differences between parental lines with hybrid performance of their hybrids revealed that sRNAs showed an inverse relationship in contrast to the other two data types. We associated differences for SNPs, mRNA and sRNA expression between parental inbred lines with the performance of their hybrid combinations and developed two prediction approaches using distance measures based on associated markers. Cross-validations revealed parental differences in sRNA expression to be strong predictors for hybrid performance for grain yield in maize, comparable to genomic and mRNA data. The integration of both positively and negatively associated markers in the prediction approaches enhanced the prediction accurary. The associated sRNAs belong predominantly to the canonical size classes of 22- and 24-nt that show specific genomic mapping characteristics. CONCLUSION Expression profiles of sRNA are a promising alternative to SNPs or mRNA expression profiles for hybrid prediction, especially for plant species without reference genome or transcriptome information. The characteristics of the sRNAs we identified suggest that association studies based on breeding populations facilitate the identification of sRNAs involved in hybrid performance.
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Affiliation(s)
- Felix Seifert
- Developmental Biology, Biocenter Klein Flottbek, University of Hamburg, 22609 Hamburg, Germany
| | - Alexander Thiemann
- Developmental Biology, Biocenter Klein Flottbek, University of Hamburg, 22609 Hamburg, Germany
| | - Tobias A. Schrag
- Institute for Plant Breeding, Seed Science and Population Genetics, Quantitative Genetics and Genomics of Crops, University of Hohenheim, Fruwirthstrasse 21, 70599 Stuttgart, Germany
| | - Dominika Rybka
- Developmental Biology, Biocenter Klein Flottbek, University of Hamburg, 22609 Hamburg, Germany
| | - Albrecht E. Melchinger
- Institute for Plant Breeding, Seed Science and Population Genetics, Quantitative Genetics and Genomics of Crops, University of Hohenheim, Fruwirthstrasse 21, 70599 Stuttgart, Germany
| | - Matthias Frisch
- Institute of Agronomy and Plant Breeding II, Justus Liebig University, 35392 Giessen, Germany
| | - Stefan Scholten
- Developmental Biology, Biocenter Klein Flottbek, University of Hamburg, 22609 Hamburg, Germany
- Institute for Plant Breeding, Seed Science and Population Genetics, Quantitative Genetics and Genomics of Crops, University of Hohenheim, Fruwirthstrasse 21, 70599 Stuttgart, Germany
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49
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Zhu X, Pan L, Xiao T, Ren X, Liu Z. Exogenous niacin treatment increases NADPH oxidase in kiwifruit. BRAZ J BIOL 2018; 78:686-690. [PMID: 29412249 DOI: 10.1590/1519-6984.173709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/27/2017] [Indexed: 11/22/2022] Open
Abstract
Kiwifruit are a popular fruit worldwide; however, plant growth is threatened by abiotic stresses such as drought and high temperatures. Niacin treatment in plants has been shown to increase NADPH levels, thus enhancing abiotic stresses tolerance. Here, we evaluate the effect of niacin solution spray treatment on NADPH levels in the kiwifruit cultivars Hayward and Xuxiang. We found that spray treatment with niacin solution promoted NADPH and NADP+ levels and decreased both O2·- production and H2O2 contents in leaves during a short period. In fruit, NADPH contents increased during early development, but decreased later. However, no effect on NADP+ levels has been observed throughout fruit development. In summary, this report suggests that niacin may be used to increase NADPH oxidases, thus increasing stress-tolerance in kiwifruit during encounter of short-term stressful conditions.
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Affiliation(s)
- X Zhu
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.,Institute of Economic Crop Research, Shiyan Academy of Agricultural Sciences, Shiyan, 442714, Hubei, China
| | - L Pan
- Institute of Economic Crop Research, Shiyan Academy of Agricultural Sciences, Shiyan, 442714, Hubei, China
| | - T Xiao
- Institute of Economic Crop Research, Shiyan Academy of Agricultural Sciences, Shiyan, 442714, Hubei, China
| | - X Ren
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Z Liu
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
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50
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Ma K, Sun L, Cheng T, Pan H, Wang J, Zhang Q. Epigenetic Variance, Performing Cooperative Structure with Genetics, Is Associated with Leaf Shape Traits in Widely Distributed Populations of Ornamental Tree Prunus mume. FRONTIERS IN PLANT SCIENCE 2018; 9:41. [PMID: 29441078 PMCID: PMC5797549 DOI: 10.3389/fpls.2018.00041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/09/2018] [Indexed: 05/23/2023]
Abstract
Increasing evidence shows that epigenetics plays an important role in phenotypic variance. However, little is known about epigenetic variation in the important ornamental tree Prunus mume. We used amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) techniques, and association analysis and sequencing to investigate epigenetic variation and its relationships with genetic variance, environment factors, and traits. By performing leaf sampling, the relative total methylation level (29.80%) was detected in 96 accessions of P. mume. And the relative hemi-methylation level (15.77%) was higher than the relative full methylation level (14.03%). The epigenetic diversity (I∗ = 0.575, h∗ = 0.393) was higher than the genetic diversity (I = 0.484, h = 0.319). The cultivated population displayed greater epigenetic diversity than the wild populations in both southwest and southeast China. We found that epigenetic variance and genetic variance, and environmental factors performed cooperative structures, respectively. In particular, leaf length, width and area were positively correlated with relative full methylation level and total methylation level, indicating that the DNA methylation level played a role in trait variation. In total, 203 AFLP and 423 MSAP associated markers were detected and 68 of them were sequenced. Homologous analysis and functional prediction suggested that the candidate marker-linked genes were essential for leaf morphology development and metabolism, implying that these markers play critical roles in the establishment of leaf length, width, area, and ratio of length to width.
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Affiliation(s)
- Kaifeng Ma
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
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