1
|
Kumar M, Rani K. Epigenomics in stress tolerance of plants under the climate change. Mol Biol Rep 2023:10.1007/s11033-023-08539-6. [PMID: 37294468 DOI: 10.1007/s11033-023-08539-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND Climate change has had a tremendous impact on the environment in general as well as agricultural crops grown in these situations as time passed. Agricultural production of crops is less suited and of lower quality due to disturbances in plant metabolism brought on by sensitivity to environmental stresses, which are brought on by climate change. Abiotic stressors that are specific to climate change, including as drought, extremes in temperature, increasing CO2, waterlogging from heavy rain, metal toxicity, and pH changes, are known to negatively affect an array of species. Plants adapt to these challenges by undergoing genome-wide epigenetic changes, which are frequently accompanied by differences in transcriptional gene expression. The sum of a cell's biochemical modifications to its nuclear DNA, post-translational modifications to histones, and variations in the synthesis of non-coding RNAs is called an epigenome. These modifications frequently lead to variations in gene expression that occur without any alteration in the underlying base sequence. EPIGENETIC MECHANISMS AND MARKS The methylation of homologous loci by three different modifications-genomic (DNA methylation), chromatin (histone modifications), and RNA-directed DNA methylation (RdDM)-could be regarded as epigenetic mechanisms that control the regulation of differential gene expression. Stresses from the environment cause chromatin remodelling, which enables plant cells to adjust their expression patterns temporarily or permanently. EPIGENOMICS' CONSEQUENCES FOR GENOME STABILITY AND GENE EXPRESSION: DNA methylation affects gene expression in response to abiotic stressors by blocking or suppressing transcription. Environmental stimuli cause changes in DNA methylation levels, either upward in the case of hypermethylation or downward in the case of hypomethylation. The type of stress response that occurs as a result also affects the degree of DNA methylation alterations. Stress is also influenced by DRM2 and CMT3 methylating CNN, CNG, and CG. Both plant development and stress reactions depend on histone changes. Gene up-regulation is associated with histone tail phosphorylation, ubiquitination, and acetylation, while gene down-regulation is associated with de-acetylation and biotinylation. Plants undergo a variety of dynamic changes to histone tails in response to abiotic stressors. The relevance of these transcripts against stress is highlighted by the accumulation of numerous additional antisense transcripts, a source of siRNAs, caused by abiotic stresses. The study highlights the finding that plants can be protected from a range of abiotic stresses by epigenetic mechanisms such DNA methylation, histone modification, and RNA-directed DNA methylation. TRANSGENERATIONAL INHERITANCE AND SOURCES OF EPIGENETIC VARIATION: Stress results in the formation of epialleles, which are either transient or enduring epigenetic stress memory in plants. After the stress is gone, the stable memory is kept for the duration of the plant's remaining developmental cycles or passed on to the next generations, leading to plant evolution and adaptability. The bulk of epigenetic changes brought on by stress are temporary and return to normal after the stress has passed. Some of the modifications, however, might be long-lasting and transmitted across mitotic or even meiotic cell divisions. Epialleles often have genetic or non-genetic causes. Epialleles can arise spontaneously due to improper methylation state maintenance, short RNA off-target effects, or other non-genetic causes. Developmental or environmental variables that influence the stability of epigenetic states or direct chromatin modifications may also be non-genetic drivers of epigenetic variation. Transposon insertions that change local chromatin and structural rearrangements, such copy number changes that are genetically related or unrelated, are two genetic sources of epialleles. EPIGENOMICS IN CROP IMPROVEMENT To include epigenetics into crop breeding, it is necessary to create epigenetic variation as well as to identify and evaluate epialleles. Epigenome editing or epi-genomic selection may be required for epiallele creation and identification. In order to combat the challenges given by changing environments, these epigenetic mechanisms have generated novel epialleles that can be exploited to develop new crop types that are more climate-resilient. Numerous techniques can be used to alter the epigenome generally or at specific target loci in order to induce the epigenetic alterations necessary for crop development. Technologies like CRISPR/Cas9 and dCas, which have recently advanced, have opened up new avenues for the study of epigenetics. Epialleles could be employed in epigenomics-assisted breeding in addition to sequence-based markers for crop breeding. CONCLUSIONS AND FUTURE PROSPECTUS A few of the exciting questions that still need to be resolved in the area of heritable epigenetic variation include a better understanding of the epigenetic foundation of characteristics, the stability and heritability of epialleles, and the sources of epigenetic variation in crops. Investigating long intergenic non-coding RNAs (lincRNAs) as an epigenetic process might open up a new path to understanding crop plant's ability to withstand abiotic stress. For many of these technologies and approaches to be more applicable and deployable at a lower cost, technological breakthroughs will also be necessary. Breeders will probably need to pay closer attention to crop epialleles and how they can affect future responses to climate changes. The development of epialleles suitable for particular environmental circumstances may be made possible by creating targeted epigenetic changes in pertinent genes and by comprehending the molecular underpinnings of trans generational epigenetic inheritance. More research on a wider variety of plant species is required in order to fully comprehend the mechanisms that produce and stabilise epigenetic variation in crops. In addition to a collaborative and multidisciplinary effort by researchers in many fields of plant science, this will require a greater integration of the epigenomic data gathered in many crops. Before it may be applied generally, more study is required.
Collapse
Affiliation(s)
- Mithlesh Kumar
- AICRN On Potential Crops, ARS Mandor, Agriculture University, Jodhpur, 342 304, Rajasthan, India.
| | - Kirti Rani
- ICAR-National Bureau of Plant Genetic Resources (NBPGR), Regional Station, Jodhpur, 342 003, Rajasthan, India
| |
Collapse
|
2
|
Rajpal VR, Rathore P, Mehta S, Wadhwa N, Yadav P, Berry E, Goel S, Bhat V, Raina SN. Epigenetic variation: A major player in facilitating plant fitness under changing environmental conditions. Front Cell Dev Biol 2022; 10:1020958. [PMID: 36340045 PMCID: PMC9628676 DOI: 10.3389/fcell.2022.1020958] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Recent research in plant epigenetics has increased our understanding of how epigenetic variability can contribute to adaptive phenotypic plasticity in natural populations. Studies show that environmental changes induce epigenetic switches either independently or in complementation with the genetic variation. Although most of the induced epigenetic variability gets reset between generations and is short-lived, some variation becomes transgenerational and results in heritable phenotypic traits. The short-term epigenetic responses provide the first tier of transient plasticity required for local adaptations while transgenerational epigenetic changes contribute to stress memory and help the plants respond better to recurring or long-term stresses. These transgenerational epigenetic variations translate into an additional tier of diversity which results in stable epialleles. In recent years, studies have been conducted on epigenetic variation in natural populations related to various biological processes, ecological factors, communities, and habitats. With the advent of advanced NGS-based technologies, epigenetic studies targeting plants in diverse environments have increased manifold to enhance our understanding of epigenetic responses to environmental stimuli in facilitating plant fitness. Taking all points together in a frame, the present review is a compilation of present-day knowledge and understanding of the role of epigenetics and its fitness benefits in diverse ecological systems in natural populations.
Collapse
Affiliation(s)
- Vijay Rani Rajpal
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- *Correspondence: Vijay Rani Rajpal, , ; Shailendra Goel, ; Vishnu Bhat, ; Soom Nath Raina,
| | | | - Sahil Mehta
- School of Agricultural Sciences, K.R. Mangalam University, Gurugram, Haryana, India
| | - Nikita Wadhwa
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | | | - Eapsa Berry
- Maharishi Kanad Bhawan, Delhi School of Climate Change and Sustainability, University of Delhi, Delhi, India
| | - Shailendra Goel
- Department of Botany, University of Delhi, Delhi, India
- *Correspondence: Vijay Rani Rajpal, , ; Shailendra Goel, ; Vishnu Bhat, ; Soom Nath Raina,
| | - Vishnu Bhat
- Department of Botany, University of Delhi, Delhi, India
- *Correspondence: Vijay Rani Rajpal, , ; Shailendra Goel, ; Vishnu Bhat, ; Soom Nath Raina,
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
- *Correspondence: Vijay Rani Rajpal, , ; Shailendra Goel, ; Vishnu Bhat, ; Soom Nath Raina,
| |
Collapse
|
3
|
Jiang H, Song Z, Su QW, Wei ZH, Li WC, Jiang ZX, Tian P, Wang ZH, Yang X, Yang MY, Wei XS, Wu ZH. Transcriptomic and metabolomic reveals silicon enhances adaptation of rice under dry cultivation by improving flavonoid biosynthesis, osmoregulation, and photosynthesis. FRONTIERS IN PLANT SCIENCE 2022; 13:967537. [PMID: 35991391 PMCID: PMC9386530 DOI: 10.3389/fpls.2022.967537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Dry cultivation is a new rice crop mode used to alleviate water shortage and develop water-saving agriculture. There is obvious genetic difference compared with drought-tolerant rice. Silicon (Si) plays an important role in plant adaptation to adverse environmental conditions and can significantly improve the drought tolerance and yield of rice. However, the regulatory mechanism via which Si provides plant tolerance or adaptation under dry cultivation is not well understood. The present study investigated the changes in plant growth, photosynthetic gas exchange, and oxidative stress of the rice cultivar "Suijing 18" under dry cultivation. Si improved photosynthetic performance and antioxidant enzyme activity and subsequently reduced lipid peroxidation of rice seedlings, promoted LAI and promoted leaf growth under dry cultivation. Further, transcriptomics combined with quasi-targeted metabolomics detected 1416 and 520 differentially expressed genes (DEGs), 38 and 41 differentially accumulated metabolites (DAMs) in the rice leaves and roots, respectively. Among them, 13 DEGs were involved in flavonoid biosynthesis, promoting the accumulation of flavonoids, anthocyanins, and flavonols in the roots and leaves of rice under dry cultivation. Meanwhile, 14 DEGs were involved in photosynthesis, promoting photosystem I and photosystem II responses, increasing the abundance of metabolites in leaves. On the other hand, 24 DAMs were identified involved in osmoregulatory processes, significantly increasing amino acids and carbohydrates and their derivatives in roots. These results provide new insight into the role of Si in alleviating to adverse environmental, Si enhanced the accumulation of flavonoids and osmoregulatory metabolites, thereby alleviating drought effect on the roots. On the other hand, improving dehydration resistance of leaves, guaranteeing normal photosynthesis and downward transport of organic matter. In conclusion, Si promoted the coordinated action between the above-ground and below-ground plant parts, improved the root/shoot ratio (R/S) of rice and increased the sugar content and enhancing rice adaptability under dry cultivation conditions. The establishment of the system for increasing the yield of rice under dry cultivation provides theoretical and technical support thereby promoting the rapid development of rice in Northeast China, and ensuring national food security.
Collapse
Affiliation(s)
- Hao Jiang
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Ze Song
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Qing-Wang Su
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Zhi-Heng Wei
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Wan-Chun Li
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Zi-Xian Jiang
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Ping Tian
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Zhen-Hui Wang
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Xue Yang
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Mei-Ying Yang
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Xiao-Shuang Wei
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Zhi-Hai Wu
- College of Agronomy, Jilin Agricultural University, Changchun, China
- National Crop Variety Approval and Characteristic Identification Station, Jilin Agricultural University, Changchun, China
| |
Collapse
|
4
|
Luo Z, Xiong J, Xia H, Wang L, Hou G, Li Z, Li J, Zhou H, Li T, Luo L. Pentatricopeptide Repeat Gene-Mediated Mitochondrial RNA Editing Impacts on Rice Drought Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:926285. [PMID: 35928709 PMCID: PMC9343880 DOI: 10.3389/fpls.2022.926285] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/21/2022] [Indexed: 05/27/2023]
Abstract
Mitochondrial RNA editing plays crucial roles in the plant development and environmental adaptation. Pentatricopeptide repeat (PPR) genes, which are involved in the regulating mitochondrial RNA editing, are potential gene resources in the improvement of rice drought tolerance. In this study, we investigated genome-wide mitochondrial RNA editing in response to drought between upland and lowland rice. Responses of mitochondrial RNA editing to drought exhibit site-specific and genotype-specific patterns. We detected 22 and 57 ecotype-differentiated editing sites under well-watered and drought-treated conditions, respectively. Interestingly, the RNA editing efficiency was positively correlated with many agronomic traits, while it was negatively correlated with drought tolerance. We further selected two mitochondrial-localized PPR proteins, PPR035 and PPR406, to validate their functions in drought tolerance. PPR035 regulated RNA editing at rps4-926 and orfX-406, while PPR406 regulated RNA editing at orfX-355. The defectiveness in RNA editing at these sites had no apparent penalties in rice respiration and vegetative growth. Meanwhile, the knockout mutants of ppr035 and ppr406 show enhanced drought- and salt tolerance. PPR035 and PPR406 were under the balancing selection in upland rice and highly differentiated between upland and lowland rice ecotypes. The upland-dominant haplotypes of PPR035 and PPR406 shall contribute to the better drought tolerance in upland rice. They have great prospective in the improvement of rice drought tolerance.
Collapse
Affiliation(s)
- Zhi Luo
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Jie Xiong
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Hui Xia
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Lei Wang
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Guihua Hou
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Zhaoyang Li
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Jing Li
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Hengling Zhou
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Tianfei Li
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Lijun Luo
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| |
Collapse
|
5
|
Zhang G, Li N, Zhang D, Li Z, Zhang A, Guo X. Exploring japonica rice epigenetic diversity in the main production regions of Heilongjiang Province. Sci Rep 2022; 12:4592. [PMID: 35301398 PMCID: PMC8931079 DOI: 10.1038/s41598-022-08683-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/11/2022] [Indexed: 11/23/2022] Open
Abstract
As a major epigenetic modification, DNA methylation plays an important role in coordinating plant responses to environmental changes. Methylation-sensitive amplified polymorphism (MSAP) technology was used in this study to investigate the epigenetic diversity of fifty japonica rice samples from five regions in Heilongjiang Province, China. In addition, the phenotypic indicators of japonica rice samples and the environmental conditions of the sampling sites were investigated and analysed. Based on the MSAP analysis technique, using eight pairs of selective primers, we identified a total of 551 amplified loci, of which 267 (48.5%) were classified as methylation loci. The methylation status and levels of the japonica rice genome in different regions differed significantly (p < 0.05). The results of the analysis of molecular variance (AMOVA) revealed that most of the molecular variation (91%) came from within the groups (regions) and was caused by individual variation within the region. Furthermore, the results of principal coordinates analysis (PCoA), cluster analysis, and population structure analysis indicated that there was no obvious correlation between the epigenetic differences and geographical locations, which may have been due to the limited range of sampling sites. When environmental factors, phenotypic indicators, and epigenetic data analysis are combined, it is easy to conclude that japonica rice grown in the same latitudinal region has increased epigenetic and phenotypic similarities due to similar climatic conditions and production practices.
Collapse
Affiliation(s)
- Guifang Zhang
- National Coarse Cereal Engineering Technology Research Center, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China
| | - Nuo Li
- College of Food Science, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China
| | - Dongjie Zhang
- National Coarse Cereal Engineering Technology Research Center, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China. .,College of Food Science, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China.
| | - Zhijiang Li
- College of Food Science, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China
| | - Aiwu Zhang
- College of Food Science, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China
| | - Xijuan Guo
- College of Food Science, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China
| |
Collapse
|
6
|
In Response to Abiotic Stress, DNA Methylation Confers EpiGenetic Changes in Plants. PLANTS 2021; 10:plants10061096. [PMID: 34070712 PMCID: PMC8227271 DOI: 10.3390/plants10061096] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 02/07/2023]
Abstract
Epigenetics involves the heritable changes in patterns of gene expression determined by developmental and abiotic stresses, i.e., drought, cold, salinity, trace metals, and heat. Gene expression is driven by changes in DNA bases, histone proteins, the biogenesis of ncRNA, and changes in the nucleotide sequence. To cope with abiotic stresses, plants adopt certain changes driven by a sophisticated biological system. DNA methylation is a primary mechanism for epigenetic variation, which can induce phenotypic alterations in plants under stress. Some of the stress-driven changes in plants are temporary, while some modifications may be stable and inheritable to the next generations to allow them to cope with such extreme stress challenges in the future. In this review, we discuss the pivotal role of epigenetically developed phenotypic characteristics in plants as an evolutionary process participating in adaptation and tolerance responses to abiotic and biotic stresses that alter their growth and development. We emphasize the molecular process underlying changes in DNA methylation, differential variation for different species, the roles of non-coding RNAs in epigenetic modification, techniques for studying DNA methylation, and its role in crop improvement in tolerance to abiotic stress (drought, salinity, and heat). We summarize DNA methylation as a significant future research priority for tailoring crops according to various challenging environmental issues.
Collapse
|
7
|
Li H, Yang X, Wang Q, Chen J, Shi T. Distinct methylome patterns contribute to ecotypic differentiation in the growth of the storage organ of a flowering plant (sacred lotus). Mol Ecol 2021; 30:2831-2845. [PMID: 33899994 DOI: 10.1111/mec.15933] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 12/27/2022]
Abstract
DNA methylation is an epigenetic modification involved in phenotypic diversity, plant development, and environmental responses. However, the mechanisms of DNA methylation underpinning the adaption of lotus (Nelumbo nucifera) ecotypes to high and low latitudes remain unsolved, especially adaptive evolution of their storage organs. Tropical and temperate lotus ecotypes have thin and enlarged rhizomes which are adapted to low and high latitudes, respectively. Here, we investigated the DNA methylomes and transcriptomes of rhizomes of the temperate and tropical lotus to address this issue. Compared with that of the tropical lotus, the DNA of the temperate lotus was significantly more hypermethylated, indicating an increase in global DNA methylation in the lotus, with rhizome enlargement. Meanwhile, genes associated with differentially methylated regions in their promoters tended to be differentially expressed between the two ecotypes. Interestingly, the genes with their expression negatively correlated with methylation levels in their promoters and genomic regions displayed significantly higher transposon coverage, while the genes showing a significant positive correlation between expression and methylation showed lesser transposon coverage. Further, we identified that DNA methylation, especially in the promoter region, was significantly correlated with the expression of many starch-biosynthetic, gibberellin-, and brassinosteroid-signalling genes associated with rhizome differentiation. Overall, our study unveiled that distinct global and local methylation patterns between the two lotus ecotypes contribute to their expression differences and adaptive phenotypic divergence of their storage organs, highlighting the role of DNA methylation in shaping the ecotypic differentiation of lotus.
Collapse
Affiliation(s)
- Hui Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xingyu Yang
- Wuhan Institute of Landscape Architecture, Wuhan, China
| | - Qingfeng Wang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.,Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Jinming Chen
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Tao Shi
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| |
Collapse
|
8
|
Saban JM, Watson-Lazowski A, Chapman MA, Taylor G. The methylome is altered for plants in a high CO 2 world: Insights into the response of a wild plant population to multigenerational exposure to elevated atmospheric [CO 2 ]. GLOBAL CHANGE BIOLOGY 2020; 26:6474-6492. [PMID: 32902071 DOI: 10.1111/gcb.15249] [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] [Received: 11/08/2019] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Unravelling plant responses to rising atmospheric CO2 concentration ([CO2 ]) has largely focussed on plastic functional attributes to single generation [CO2 ] exposure. Quantifying the consequences of long-term, decadal multigenerational exposure to elevated [CO2 ] and the genetic changes that may underpin evolutionary mechanisms with [CO2 ] as a driver remain largely unexplored. Here, we investigated both plastic and evolutionary plant responses to elevated [CO2 ] by applying multi-omic technologies using populations of Plantago lanceolata L., grown in naturally high [CO2 ] for many generations in a CO2 spring. Seed from populations at the CO2 spring and an adjacent control site (ambient [CO2 ]) were grown in a common environment for one generation, and then offspring were grown in ambient or elevated [CO2 ] growth chambers. Low overall genetic differentiation between the CO2 spring and control site populations was found, with evidence of weak selection in exons. We identified evolutionary divergence in the DNA methylation profiles of populations derived from the spring relative to the control population, providing the first evidence that plant methylomes may respond to elevated [CO2 ] over multiple generations. In contrast, growth at elevated [CO2 ] for a single generation induced limited methylome remodelling (an order of magnitude fewer differential methylation events than observed between populations), although some of this appeared to be stably transgenerationally inherited. In all, 59 regions of the genome were identified where transcripts exhibiting differential expression (associated with single generation or long-term natural exposure to elevated [CO2 ]) co-located with sites of differential methylation or with single nucleotide polymorphisms exhibiting significant inter-population divergence. This included genes in pathways known to respond to elevated [CO2 ], such as nitrogen use efficiency and stomatal patterning. This study provides the first indication that DNA methylation may contribute to plant adaptation to future atmospheric [CO2 ] and identifies several areas of the genome that are targets for future study.
Collapse
Affiliation(s)
- Jasmine M Saban
- School of Biological Sciences, University of Southampton, Southampton, UK
| | | | - Mark A Chapman
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Gail Taylor
- School of Biological Sciences, University of Southampton, Southampton, UK
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| |
Collapse
|
9
|
Luo Z, Xiong J, Xia H, Ma X, Gao M, Wang L, Liu G, Yu X, Luo L. Transcriptomic divergence between upland and lowland ecotypes contributes to rice adaptation to a drought-prone agroecosystem. Evol Appl 2020; 13:2484-2496. [PMID: 33005236 PMCID: PMC7513727 DOI: 10.1111/eva.13054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 06/04/2020] [Accepted: 06/09/2020] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTION Transcriptomic divergence drives plant ecological adaptation. Upland rice is differentiated in drought tolerance from lowland rice during its adaptation to the drought-prone environment. They provide a good system to learn the evolution of drought tolerance in rice. METHODS AND RESULTS We estimate morphological differences between the two rice ecotypes under well-watered and drought conditions, as well as their genetic and transcriptomic divergences by the high-throughput sequencing. Upland rice possesses higher expression diversity than lowland rice does. Thousands of genes exhibit expression divergences between the two rice ecotypes, which contributes to their morphological differences in drought tolerance. These transcriptomic divergences contribute to drought adaptation of upland rice during its domestication. Mutations in transcriptional regulatory regions, which cause presence and absence of cis-elements, are the cause of expression divergence. About 15.3% transcriptionally selected genes also receive sequence-based selection in upland or lowland ecotype. Some highly differentiated genes promote the transcriptomic divergence between rice ecotypes via gene co-expression network. In addition, we also detected transcriptomic trade-offs between drought tolerance and productivity. DISCUSSION Many key genes, which promote transcriptomic adaptation to drought in upland rice, have great prospective in breeding water-saving and drought-resistant rice. Meanwhile, appropriate strategies are required in breeding to overcome the potential transcriptomic trade-off.
Collapse
Affiliation(s)
- Zhi Luo
- College of Plant Sciences & Technology Huazhong Agricultural University Wuhan China
- Shanghai Agrobiological Gene Center Shanghai China
| | - Jie Xiong
- College of Plant Sciences & Technology Huazhong Agricultural University Wuhan China
- Shanghai Agrobiological Gene Center Shanghai China
| | - Hui Xia
- College of Plant Sciences & Technology Huazhong Agricultural University Wuhan China
- Shanghai Agrobiological Gene Center Shanghai China
| | - Xiaosong Ma
- Shanghai Agrobiological Gene Center Shanghai China
| | - Min Gao
- College of Plant Sciences & Technology Huazhong Agricultural University Wuhan China
- Shanghai Agrobiological Gene Center Shanghai China
| | - Lei Wang
- Shanghai Agrobiological Gene Center Shanghai China
| | - Guolan Liu
- Shanghai Agrobiological Gene Center Shanghai China
| | - Xinqiao Yu
- Shanghai Agrobiological Gene Center Shanghai China
| | - Lijun Luo
- College of Plant Sciences & Technology Huazhong Agricultural University Wuhan China
- Shanghai Agrobiological Gene Center Shanghai China
| |
Collapse
|
10
|
Bhandari A, Sandhu N, Bartholome J, Cao-Hamadoun TV, Ahmadi N, Kumari N, Kumar A. Genome-Wide Association Study for Yield and Yield Related Traits under Reproductive Stage Drought in a Diverse indica-aus Rice Panel. RICE (NEW YORK, N.Y.) 2020; 13:53. [PMID: 32761553 PMCID: PMC7410978 DOI: 10.1186/s12284-020-00406-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/02/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Reproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. RESULTS The study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200 kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought. CONCLUSION These results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.
Collapse
Affiliation(s)
- Aditi Bhandari
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- Banasthali Vidyapith, Banasthali, 304022, India
| | - Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- Punjab Agricultural University, Ludhiana, 141004, India
| | - Jérôme Bartholome
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | - Tuong-Vi Cao-Hamadoun
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | - Nourollah Ahmadi
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | | | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines.
- IRRI South Asia Regional Centre, Varanasi, 221006, India.
| |
Collapse
|
11
|
Komivi D, Marie AM, Rong Z, Qi Z, Mei Y, Ndiaga C, Diaga D, Linhai W, Xiurong Z. The contrasting response to drought and waterlogging is underpinned by divergent DNA methylation programs associated with transcript accumulation in sesame. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:207-217. [PMID: 30466587 DOI: 10.1016/j.plantsci.2018.09.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 05/07/2023]
Abstract
DNA methylation is a heritable epigenetic mechanism that participates in gene regulation under abiotic stresses in plants. Sesame (Sesamum indicum) is typically considered a drought-tolerant crop but highly susceptible to waterlogging, probably because of its origin in Africa or India. Understanding DNA methylation patterns under drought and waterlogging conditions can provide insights into the regulatory mechanisms underlying sesame contrasting responses to these abiotic stresses. We combined Methylation-Sensitive Amplified Polymorphism and transcriptome analyses to profile cytosine methylation patterns, transcript accumulation, and their interplay in drought-tolerant and waterlogging-tolerant sesame genotypes. Drought stress strongly induced de novo methylation (DNM) whereas most of the loci were demethylated (DM) during the recovery phase. In contrast, waterlogging stress decreased the level of methylation but during the recovery phase, both DM and DNM were concomitantly deployed. In both stresses, the levels of the differentially accumulated transcripts (DATs) highly correlated with the methylation patterns. We observed that DM was associated with an increase of DAT levels while DNM was correlated with a decrease of DAT levels. Altogether, sesame has divergent epigenetic programs that respond to drought and waterlogging stresses and an interplay among DNA methylation and transcript accumulation may partly modulate the contrasting responses to these stresses.
Collapse
Affiliation(s)
- Dossa Komivi
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China; Centre d'Etude Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), Route de Khombole, Thiès, BP, 3320, Senegal; Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Code postal 10700, Dakar, Senegal.
| | - Ali Mmadi Marie
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China; Centre d'Etude Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), Route de Khombole, Thiès, BP, 3320, Senegal; Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Code postal 10700, Dakar, Senegal
| | - Zhou Rong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China
| | - Zhou Qi
- College of Life Science, Hubei University, Wuhan, China
| | - Yang Mei
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China
| | - Cisse Ndiaga
- Centre d'Etude Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), Route de Khombole, Thiès, BP, 3320, Senegal
| | - Diouf Diaga
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Code postal 10700, Dakar, Senegal
| | - Wang Linhai
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China
| | - Zhang Xiurong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, 430062, China.
| |
Collapse
|
12
|
Dwivedi SL, Siddique KHM, Farooq M, Thornton PK, Ortiz R. Using Biotechnology-Led Approaches to Uplift Cereal and Food Legume Yields in Dryland Environments. FRONTIERS IN PLANT SCIENCE 2018; 9:1249. [PMID: 30210519 PMCID: PMC6120061 DOI: 10.3389/fpls.2018.01249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/06/2018] [Indexed: 05/29/2023]
Abstract
Drought and heat in dryland agriculture challenge the enhancement of crop productivity and threaten global food security. This review is centered on harnessing genetic variation through biotechnology-led approaches to select for increased productivity and stress tolerance that will enhance crop adaptation in dryland environments. Peer-reviewed literature, mostly from the last decade and involving experiments with at least two seasons' data, form the basis of this review. It begins by highlighting the adverse impact of the increasing intensity and duration of drought and heat stress due to global warming on crop productivity and its impact on food and nutritional security in dryland environments. This is followed by (1) an overview of the physiological and molecular basis of plant adaptation to elevated CO2 (eCO2), drought, and heat stress; (2) the critical role of high-throughput phenotyping platforms to study phenomes and genomes to increase breeding efficiency; (3) opportunities to enhance stress tolerance and productivity in food crops (cereals and grain legumes) by deploying biotechnology-led approaches [pyramiding quantitative trait loci (QTL), genomic selection, marker-assisted recurrent selection, epigenetic variation, genome editing, and transgene) and inducing flowering independent of environmental clues to match the length of growing season; (4) opportunities to increase productivity in C3 crops by harnessing novel variations (genes and network) in crops' (C3, C4) germplasm pools associated with increased photosynthesis; and (5) the adoption, impact, risk assessment, and enabling policy environments to scale up the adoption of seed-technology to enhance food and nutritional security. This synthesis of technological innovations and insights in seed-based technology offers crop genetic enhancers further opportunities to increase crop productivity in dryland environments.
Collapse
Affiliation(s)
| | | | - Muhammad Farooq
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al Khoud, Oman
- University of Agriculture, Faisalabad, Pakistan
| | - Philip K. Thornton
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| |
Collapse
|
13
|
|
14
|
Abstract
Landraces are key elements of agricultural biodiversity that have long been considered a source of useful traits. Their importance goes beyond subsistence agriculture and the essential need to preserve genetic diversity, because landraces are farmer-developed populations that are often adapted to environmental conditions of significance to tackle environmental concerns. It is therefore increasingly important to identify adaptive traits in crop landraces and understand their molecular basis. This knowledge is potentially useful for promoting more sustainable agricultural techniques, reducing the environmental impact of high-input cropping systems, and diminishing the vulnerability of agriculture to global climate change. In this review, we present an overview of the opportunities and limitations offered by landraces’ genomics. We discuss how rapid advances in DNA sequencing techniques, plant phenotyping, and recombinant DNA-based biotechnology encourage both the identification and the validation of the genomic signature of local adaptation in crop landraces. The integration of ‘omics’ sciences, molecular population genetics, and field studies can provide information inaccessible with earlier technological tools. Although empirical knowledge on the genetic and genomic basis of local adaptation is still fragmented, it is predicted that genomic scans for adaptation will unlock an intraspecific molecular diversity that may be different from that of modern varieties.
Collapse
|
15
|
Xia H, Huang W, Xiong J, Yan S, Tao T, Li J, Wu J, Luo L. Differentially Methylated Epiloci Generated from Numerous Genotypes of Contrasting Tolerances Are Associated with Osmotic-Tolerance in Rice Seedlings. FRONTIERS IN PLANT SCIENCE 2017; 8:11. [PMID: 28154573 PMCID: PMC5243842 DOI: 10.3389/fpls.2017.00011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 01/03/2017] [Indexed: 05/20/2023]
Abstract
DNA methylation plays an essential role in plant responses to environmental stress. Since drought develops into a rising problem in rice cultivation, investigations on genome-wide DNA methylation in responses to drought stress and in-depth explorations of its association with drought-tolerance are required. For this study, 68 rice accessions were used for an evaluation of their osmotic-tolerance related to 20% PEG6000 simulated physiological traits. The tolerant group revealed significantly higher levels of total antioxidant capacity and higher contents of H2O2 in both normal and osmotic-stressed treatments, as well as higher survival ratios. We furthermore investigated the DNA methylation status in normal, osmotic-stressed, and re-watering treatments via the methylation-sensitive amplification polymorphism (MSAP). The averaged similarity between two rice accessions from tolerant and susceptible groups was approximately 50%, similar with that between two accessions within the tolerant/susceptible group. However, the proportion of overall tolerance-associated epiloci was only 5.2% of total epiloci. The drought-tolerant accessions revealed lower DNA methylation levels in the stressed condition and more de-methylation events when they encountered osmotic stress, compared to the susceptible group. During the recovery process, the drought-tolerant accessions possessed more re-methylation events. Fourteen differentially methylated epiloci (DME) were, respectively, generated in normal, osmotic-stressed, and re-watering treatments. Approximately, 35.7% DME were determined as tolerance-associated epiloci. Additionally, rice accessions with lower methylation degrees on DME in the stressed conditions had a higher survival ratio compared to these with higher methylation degrees. This result is consistent with the lower DNA methylation levels of tolerant accessions observed in the stressed treatment. Methylation degrees on a differentially methylated epilocus may further influence gene regulation in the rice seedling in response to the osmotic stress. All these results indicate that DME generated from a number of genotypes could have higher probabilityies for association with stress-tolerance, rather than DME generated from two genotypes of contrasting tolerance. The DME found in this study are suspected to be good epigenetic markers for the application in drought-tolerant rice breeding. They could also be a valuable tool to study the epigenetic differentiation in the drought-tolerance between upland and lowland rice ecotypes.
Collapse
Affiliation(s)
- Hui Xia
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Weixia Huang
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Jie Xiong
- Shanghai Agrobiological Gene CenterShanghai, China
- College of Plant Sciences and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Shuaigang Yan
- Shanghai Agrobiological Gene CenterShanghai, China
- College of Plant Sciences and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Tao Tao
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Jiajia Li
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Jinhong Wu
- Shanghai Agrobiological Gene CenterShanghai, China
| | - Lijun Luo
- Shanghai Agrobiological Gene CenterShanghai, China
- *Correspondence: Lijun Luo
| |
Collapse
|