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Shen J, Wang X, Song H, Wang M, Niu T, Lei H, Qin C, Liu A. Physiology and transcriptomics highlight the underlying mechanism of sunflower responses to drought stress and rehydration. iScience 2023; 26:108112. [PMID: 37860690 PMCID: PMC10583116 DOI: 10.1016/j.isci.2023.108112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/15/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023] Open
Abstract
Drought can adversely influence the crop growth and production. Accordingly, sunflowers have strong adaptability to drought; hence, we conducted analyses for sunflower seedlings with drought stress and rehydration drought acclimation through physiological measurements and transcriptomics. It showed that drought can cause the accumulation of ROS and enhance the activity of antioxidant enzymes and the content of osmolytes. After rehydration, the contents of ROS and MDA were significantly reduced concomitant with increased antioxidant activity and osmotic adjustment. Totally, 2,589 DEGs were identified among treatments. Functional enrichment analysis showed that DEGs were mainly involved in plant hormone signal transduction, MAPK signaling, and biosynthesis of secondary metabolites. Comparison between differentially spliced genes and DEGs indicated that bHLH025, NAC53, and SINAT3 may be pivotal genes involved in sunflower drought resistance. Our results not only highlight the underlying mechanism of drought stress and rehydration in sunflower but also provide a theoretical basis for crop genetic breeding.
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Affiliation(s)
- Jie Shen
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Xi Wang
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Huifang Song
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Mingyang Wang
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China
| | - Tianzeng Niu
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Haiying Lei
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Cheng Qin
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Ake Liu
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
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Dwivedi SL, Quiroz LF, Reddy ASN, Spillane C, Ortiz R. Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs. Int J Mol Sci 2023; 24:15205. [PMID: 37894886 PMCID: PMC10607462 DOI: 10.3390/ijms242015205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Alternative splicing (AS) is a gene regulatory mechanism modulating gene expression in multiple ways. AS is prevalent in all eukaryotes including plants. AS generates two or more mRNAs from the precursor mRNA (pre-mRNA) to regulate transcriptome complexity and proteome diversity. Advances in next-generation sequencing, omics technology, bioinformatics tools, and computational methods provide new opportunities to quantify and visualize AS-based quantitative trait variation associated with plant growth, development, reproduction, and stress tolerance. Domestication, polyploidization, and environmental perturbation may evolve novel splicing variants associated with agronomically beneficial traits. To date, pre-mRNAs from many genes are spliced into multiple transcripts that cause phenotypic variation for complex traits, both in model plant Arabidopsis and field crops. Cataloguing and exploiting such variation may provide new paths to enhance climate resilience, resource-use efficiency, productivity, and nutritional quality of staple food crops. This review provides insights into AS variation alongside a gene expression analysis to select for novel phenotypic diversity for use in breeding programs. AS contributes to heterosis, enhances plant symbiosis (mycorrhiza and rhizobium), and provides a mechanistic link between the core clock genes and diverse environmental clues.
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Affiliation(s)
| | - Luis Felipe Quiroz
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 23053 Alnarp, SE, Sweden
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3
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Gao L, Kantar MB, Moxley D, Ortiz-Barrientos D, Rieseberg LH. Crop adaptation to climate change: An evolutionary perspective. MOLECULAR PLANT 2023; 16:1518-1546. [PMID: 37515323 DOI: 10.1016/j.molp.2023.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023]
Abstract
The disciplines of evolutionary biology and plant and animal breeding have been intertwined throughout their development, with responses to artificial selection yielding insights into the action of natural selection and evolutionary biology providing statistical and conceptual guidance for modern breeding. Here we offer an evolutionary perspective on a grand challenge of the 21st century: feeding humanity in the face of climate change. We first highlight promising strategies currently under way to adapt crops to current and future climate change. These include methods to match crop varieties with current and predicted environments and to optimize breeding goals, management practices, and crop microbiomes to enhance yield and sustainable production. We also describe the promise of crop wild relatives and recent technological innovations such as speed breeding, genomic selection, and genome editing for improving environmental resilience of existing crop varieties or for developing new crops. Next, we discuss how methods and theory from evolutionary biology can enhance these existing strategies and suggest novel approaches. We focus initially on methods for reconstructing the evolutionary history of crops and their pests and symbionts, because such historical information provides an overall framework for crop-improvement efforts. We then describe how evolutionary approaches can be used to detect and mitigate the accumulation of deleterious mutations in crop genomes, identify alleles and mutations that underlie adaptation (and maladaptation) to agricultural environments, mitigate evolutionary trade-offs, and improve critical proteins. Continuing feedback between the evolution and crop biology communities will ensure optimal design of strategies for adapting crops to climate change.
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Affiliation(s)
- Lexuan Gao
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Michael B Kantar
- Department of Tropical Plant & Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Dylan Moxley
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences and Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, Australia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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Duruflé H, Balliau T, Blanchet N, Chaubet A, Duhnen A, Pouilly N, Blein-Nicolas M, Mangin B, Maury P, Langlade NB, Zivy M. Sunflower Hybrids and Inbred Lines Adopt Different Physiological Strategies and Proteome Responses to Cope with Water Deficit. Biomolecules 2023; 13:1110. [PMID: 37509146 PMCID: PMC10377273 DOI: 10.3390/biom13071110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Sunflower is a hybrid crop that is considered moderately drought-tolerant and adapted to new cropping systems required for the agro-ecological transition. Here, we studied the impact of hybridity status (hybrids vs. inbred lines) on the responses to drought at the molecular and eco-physiological level exploiting publicly available datasets. Eco-physiological traits and leaf proteomes were measured in eight inbred lines and their sixteen hybrids grown in the high-throughput phenotyping platform Phenotoul-Heliaphen. Hybrids and parental lines showed different growth strategies: hybrids grew faster in the absence of water constraint and arrested their growth more abruptly than inbred lines when subjected to water deficit. We identified 471 differentially accumulated proteins, of which 256 were regulated by drought. The amplitude of up- and downregulations was greater in hybrids than in inbred lines. Our results show that hybrids respond more strongly to water deficit at the molecular and eco-physiological levels. Because of presence/absence polymorphism, hybrids potentially contain more genes than their parental inbred lines. We propose that detrimental homozygous mutations and the lower number of genes in inbred lines lead to a constitutive defense mechanism that may explain the lower growth of inbred lines under well-watered conditions and their lower reactivity to water deficit.
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Affiliation(s)
- Harold Duruflé
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
- INRAE, ONF, BioForA, 45075 Orleans, France
| | - Thierry Balliau
- AgroParisTech, GQE-Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, 91190 Gif-sur-Yvette, France
| | - Nicolas Blanchet
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Adeline Chaubet
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Alexandra Duhnen
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Nicolas Pouilly
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Mélisande Blein-Nicolas
- AgroParisTech, GQE-Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, 91190 Gif-sur-Yvette, France
| | - Brigitte Mangin
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Pierre Maury
- INRAE, INP-ENSAT Toulouse, UMR AGIR, Université de Toulouse, 31000 Toulouse, France
| | | | - Michel Zivy
- AgroParisTech, GQE-Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, 91190 Gif-sur-Yvette, France
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Padalino G, Celatka CA, Rienhoff Jr. HY, Kalin JH, Cole PA, Lassalle D, Forde-Thomas J, Chalmers IW, Brancale A, Grunau C, Hoffmann KF. Chemical modulation of Schistosoma mansoni lysine specific demethylase 1 (SmLSD1) induces wide-scale biological and epigenomic changes. Wellcome Open Res 2023; 8:146. [PMID: 37520936 PMCID: PMC10375057 DOI: 10.12688/wellcomeopenres.18826.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2023] [Indexed: 08/01/2023] Open
Abstract
Background: Schistosoma mansoni, a parasitic worm species responsible for the neglected tropical disease schistosomiasis, undergoes strict developmental regulation of gene expression that is carefully controlled by both genetic and epigenetic processes. As inhibition of S. mansoni epigenetic machinery components impairs key transitions throughout the parasite's digenetic lifecycle, a greater understanding of how epi-drugs affect molecular processes in schistosomes could lead to the development of new anthelmintics. Methods: In vitro whole organism assays were used to assess the anti-schistosomal activity of 39 Homo sapiens Lysine Specific Demethylase 1 (HsLSD1) inhibitors on different parasite life cycle stages. Moreover, tissue-specific stains and genomic analysis shed light on the effect of these small molecules on the parasite biology. Results: Amongst this collection of small molecules, compound 33 was the most potent in reducing ex vivo viabilities of schistosomula, juveniles, miracidia and adults. At its sub-lethal concentration to adults (3.13 µM), compound 33 also significantly impacted oviposition, ovarian as well as vitellarian architecture and gonadal/neoblast stem cell proliferation. ATAC-seq analysis of adults demonstrated that compound 33 significantly affected chromatin structure (intragenic regions > intergenic regions), especially in genes differentially expressed in cell populations (e.g., germinal stem cells, hes2 + stem cell progeny, S1 cells and late female germinal cells) associated with these ex vivo phenotypes. KEGG analyses further highlighted that chromatin structure of genes associated with sugar metabolism as well as TGF-beta and Wnt signalling were also significantly perturbed by compound 33 treatment. Conclusions: This work confirms the importance of histone methylation in S. mansoni lifecycle transitions, suggesting that evaluation of LSD1 - targeting epi-drugs may facilitate the search for next-generation anti-schistosomal drugs. The ability of compound 33 to modulate chromatin structure as well as inhibit parasite survival, oviposition and stem cell proliferation warrants further investigations of this compound and its epigenetic target SmLSD1.
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Affiliation(s)
- Gilda Padalino
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, Wales, CF10 3NB, UK
| | | | | | - Jay H. Kalin
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Philip A. Cole
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Josephine Forde-Thomas
- Department of Life Sciences (DLS), Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
| | - Iain W. Chalmers
- Department of Life Sciences (DLS), Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, Wales, CF10 3NB, UK
| | | | - Karl F. Hoffmann
- Department of Life Sciences (DLS), Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
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Zhao X, Xiao L, Mi J, Kang L, Lin C, Chen W, Huang H, Yan J, Yi Z, Sang T, Liu W. Development of energy plants from hybrids between Miscanthus sacchariflorus and M. lutarioriparius grown on reclaimed mine land in the Loess Plateau of China. FRONTIERS IN PLANT SCIENCE 2023; 13:1017712. [PMID: 36726684 PMCID: PMC9885154 DOI: 10.3389/fpls.2022.1017712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/15/2022] [Indexed: 06/18/2023]
Abstract
Miscanthus, a promising bioenergy plant, has a high biomass yield with high cellulose content suitable for biofuel production. However, harsh climatic and poor soil conditions, such as barren lands or abandoned mines, pose a challenge to the survival and yield of Miscanthus feedstock on the marginal land. The selection from the interspecific hybrids of Miscanthus might combine high survival rates and high yield, which benefits energy crop development in multi-stressful environments. A total of 113 F1 hybrids between Miscanthus sacchariflorus and M. lutarioriparius together with the parents were planted and evaluated for multiple morphological and physiological traits on the mine land of the Loess Plateau of China. The majority of hybrids had higher establishment rates than M. sacchariflorus while M. lutarioriparius failed to survive for the first winter. Nearly all hybrid genotypes outperformed M. lutarioriparius for yield-related traits including plant height, tiller number, tiller diameter, and leaf area. The average biomass of the hybrids was 20 times higher than that of surviving parent, M. sacchariflorus. Furthermore, the photosynthetic rates and water use efficiency of the hybrids were both significantly higher than those of the parents, which might be partly responsible for their higher yield. A total of 29 hybrids with outstanding traits related to yield and stress tolerance were identified as candidates. The study investigated for the first time the hybrids between local individuals of M. sacchariflorus and high-biomass M. lutarioriparius, suggesting that this could be an effective approach for high-yield energy crop development on vast of marginal lands.
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Affiliation(s)
- Xuhong Zhao
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liang Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Jia Mi
- Shanxi Key Laboratory for Ecological Restoration of Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Lifang Kang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Cong Lin
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wenli Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hongmei Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Juan Yan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Zili Yi
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Tao Sang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wei Liu
- Key Laboratory of Dryland Agriculture, MOA, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
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Understanding Gene Action, Combining Ability, and Heterosis to Identify Superior Aromatic Rice Hybrids Using Artificial Neural Network. J FOOD QUALITY 2022. [DOI: 10.1155/2022/9282733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The aromatic rice represents a smaller but independent rice collection, the quality of which is considered to be highly acceptable. Farmers are interested in growing aromatic rice due to high premium market price. The prime objective of this study was to enhance genetic improvement of aromatic rice. Combining ability analysis (GCA and SCA) and gene action are studied in a set of 7 × 7 half-diallel crosses. Twenty-one hybrids along with their seven parents were assessed in randomized complete block design. Different quantitative characters were used to estimate the magnitude of heterosis. GCA and SCA significance for all traits revealed the importance of both additive and nonadditive genetic components. Several genes determine quantitative traits, with each gene having very little impacts and being easily influenced by environmental factors. Pusa Basmati-1 and Govindobhog were the best combiners among the seven parents. In terms of per se performance, heterosis, and SCA effects on seed yield per plant and important yield qualities, the crosses BM-24 Deharadun Pahari, Baskota × Tulaipanji, and Pusa Basmati-1 × Tulaipanji may be of interest. Because of its interconnected processing properties, ANN can play a critical role in this experiment. As a result, the current study was carried out to collect data and validate it using an artificial neural network (ANN) on the combining ability, gene action, and heterosis involved in the expression of diverse fragrant rice features. Using ANN, the validation of the result was done and it was found that the overall efficiency was approximately 99%.
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