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Yin B, Jia J, Sun X, Hu X, Ao M, Liu W, Tian Z, Liu H, Li D, Tian W, Hao Y, Xia X, Sade N, Brotman Y, Fernie AR, Chen J, He Z, Chen W. Dynamic metabolite QTL analyses provide novel biochemical insights into kernel development and nutritional quality improvement in common wheat. Plant Commun 2024; 5:100792. [PMID: 38173227 DOI: 10.1016/j.xplc.2024.100792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 12/20/2023] [Accepted: 01/01/2024] [Indexed: 01/05/2024]
Abstract
Despite recent advances in crop metabolomics, the genetic control and molecular basis of the wheat kernel metabolome at different developmental stages remain largely unknown. Here, we performed widely targeted metabolite profiling of kernels from three developmental stages (grain-filling kernels [FKs], mature kernels [MKs], and germinating kernels [GKs]) using a population of 159 recombinant inbred lines. We detected 625 annotated metabolites and mapped 3173, 3143, and 2644 metabolite quantitative trait loci (mQTLs) in FKs, MKs, and GKs, respectively. Only 52 mQTLs were mapped at all three stages, indicating the high stage specificity of the wheat kernel metabolome. Four candidate genes were functionally validated by in vitro enzymatic reactions and/or transgenic approaches in wheat, three of which mediated the tricin metabolic pathway. Metabolite flux efficiencies within the tricin pathway were evaluated, and superior candidate haplotypes were identified, comprehensively delineating the tricin metabolism pathway in wheat. Finally, additional wheat metabolic pathways were re-constructed by updating them to incorporate the 177 candidate genes identified in this study. Our work provides new information on variations in the wheat kernel metabolome and important molecular resources for improvement of wheat nutritional quality.
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Affiliation(s)
- Bo Yin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jingqi Jia
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xu Sun
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Min Ao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wei Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhitao Tian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Wenfei Tian
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanfeng Hao
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nir Sade
- School of Plant Sciences and Food Security, The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yariv Brotman
- School of Plant Sciences and Food Security, The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv 69978, Israel
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Jie Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Yazhouwan National Laboratory, Sanya 572025, China.
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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2
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Lai D, Zhang K, He Y, Fan Y, Li W, Shi Y, Gao Y, Huang X, He J, Zhao H, Lu X, Xiao Y, Cheng J, Ruan J, Georgiev MI, Fernie AR, Zhou M. Multi-omics identification of a key glycosyl hydrolase gene FtGH1 involved in rutin hydrolysis in Tartary buckwheat (Fagopyrum tataricum). Plant Biotechnol J 2024; 22:1206-1223. [PMID: 38062934 PMCID: PMC11022807 DOI: 10.1111/pbi.14259] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/16/2023] [Accepted: 11/20/2023] [Indexed: 04/18/2024]
Abstract
Rutin, a flavonoid rich in buckwheat, is important for human health and plant resistance to external stresses. The hydrolysis of rutin to quercetin underlies the bitter taste of Tartary buckwheat. In order to identify rutin hydrolysis genes, a 200 genotypes mini-core Tartary buckwheat germplasm resource was re-sequenced with 30-fold coverage depth. By combining the content of the intermediate metabolites of rutin metabolism with genome resequencing data, metabolite genome-wide association analyses (GWAS) eventually identified a glycosyl hydrolase gene FtGH1, which could hydrolyse rutin to quercetin. This function was validated both in Tartary buckwheat overexpression hairy roots and in vitro enzyme activity assays. Mutation of the two key active sites, which were determined by molecular docking and experimentally verified via overexpression in hairy roots and transient expression in tobacco leaves, exhibited abnormal subcellular localization, suggesting functional changes. Sequence analysis revealed that mutation of the FtGH1 promoter in accessions of two haplotypes might be necessary for enzymatic activity. Co-expression analysis and GWAS revealed that FtbHLH165 not only repressed FtGH1 expression, but also increased seed length. This work reveals a potential mechanism behind rutin metabolism, which should provide both theoretical support in the study of flavonoid metabolism and in the molecular breeding of Tartary buckwheat.
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Affiliation(s)
- Dili Lai
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
- College of AgricultureGuizhou UniversityGuiyangChina
| | - Kaixuan Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yuqi He
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yu Fan
- School of Food and Biological EngineeringChengdu UniversityChengduChina
| | - Wei Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yaliang Shi
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yuanfen Gao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xu Huang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jiayue He
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Hui Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xiang Lu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yawen Xiao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | | | - Jingjun Ruan
- College of AgricultureGuizhou UniversityGuiyangChina
| | - Milen I. Georgiev
- Laboratory of Metabolomics, Institute of MicrobiologyBulgarian Academy of SciencesPlovdivBulgaria
- Center of Plant Systems Biology and BiotechnologyPlovdivBulgaria
| | - Alisdair R. Fernie
- Center of Plant Systems Biology and BiotechnologyPlovdivBulgaria
- Department of Molecular PhysiologyMax‐Planck‐Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Meiliang Zhou
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
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Vicente MH, MacLeod K, Zhu F, Rafael DD, Figueira A, Fernie AR, Mohareb F, Kevei Z, Thompson AJ, Zsögön A, Peres LEP. The ORGAN SIZE (ORG) locus modulates both vegetative and reproductive gigantism in domesticated tomato. Ann Bot 2023; 132:1233-1248. [PMID: 37818893 PMCID: PMC10902882 DOI: 10.1093/aob/mcad150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/29/2023] [Accepted: 10/02/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND AND AIMS Gigantism is a key component of the domestication syndrome, a suite of traits that differentiates crops from their wild relatives. Allometric gigantism is strongly marked in horticultural crops, causing disproportionate increases in the size of edible parts such as stems, leaves or fruits. Tomato (Solanum lycopersicum) has attracted attention as a model for fruit gigantism, and many genes have been described controlling this trait. However, the genetic basis of a corresponding increase in size of vegetative organs contributing to isometric gigantism has remained relatively unexplored. METHODS Here, we identified a 0.4-Mb region on chromosome 7 in introgression lines (ILs) from the wild species Solanum pennellii in two different tomato genetic backgrounds (cv. 'M82' and cv. 'Micro-Tom') that controls vegetative and reproductive organ size in tomato. The locus, named ORGAN SIZE (ORG), was fine-mapped using genotype-by-sequencing. A survey of the literature revealed that ORG overlaps with previously mapped quantitative trait loci controlling tomato fruit weight during domestication. KEY RESULTS Alleles from the wild species led to lower cell number in different organs, which was partially compensated by greater cell expansion in leaves, but not in fruits. The result was a proportional reduction in leaf, flower and fruit size in the ILs harbouring the alleles from the wild species. CONCLUSIONS Our findings suggest that selection for large fruit during domestication also tends to select for increases in leaf size by influencing cell division. Since leaf size is relevant for both source-sink balance and crop adaptation to different environments, the discovery of ORG could allow fine-tuning of these parameters.
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Affiliation(s)
- Mateus Henrique Vicente
- Laboratory of Plant Developmental Genetics, Departamento de Ciências Biológicas, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São Paulo, CP 09, 13418-900, Piracicaba, SP, Brazil
| | - Kyle MacLeod
- Cranfield Soil and AgriFood Institute, Cranfield University, Cranfield, MK43 0AL, UK
| | - Feng Zhu
- Max-Planck-Institute for Molecular Plant Physiology, 14476 Potsdam, Germany
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070 Wuhan, China
| | - Diego D Rafael
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Antonio Figueira
- Laboratory of Plant Breeding, Centro de Energia Nuclear na Agricultura (CENA), USP, Av. Centenário, 303, 13400-970, Piracicaba, SP, Brazil
| | - Alisdair R Fernie
- Max-Planck-Institute for Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Fady Mohareb
- Cranfield Soil and AgriFood Institute, Cranfield University, Cranfield, MK43 0AL, UK
| | - Zoltan Kevei
- Cranfield Soil and AgriFood Institute, Cranfield University, Cranfield, MK43 0AL, UK
| | - Andrew J Thompson
- Cranfield Soil and AgriFood Institute, Cranfield University, Cranfield, MK43 0AL, UK
| | - Agustin Zsögön
- Max-Planck-Institute for Molecular Plant Physiology, 14476 Potsdam, Germany
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Lázaro Eustáquio Pereira Peres
- Laboratory of Plant Developmental Genetics, Departamento de Ciências Biológicas, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São Paulo, CP 09, 13418-900, Piracicaba, SP, Brazil
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Aarabi F, Ghigi A, Ahchige MW, Bulut M, Geigenberger P, Neuhaus HE, Sampathkumar A, Alseekh S, Fernie AR. Genome-wide association study unveils ascorbate regulation by PAS/LOV PROTEIN during high light acclimation. Plant Physiol 2023; 193:2037-2054. [PMID: 37265123 PMCID: PMC10602610 DOI: 10.1093/plphys/kiad323] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 06/03/2023]
Abstract
Varying light conditions elicit metabolic responses as part of acclimation with changes in ascorbate levels being an important component. Here, we adopted a genome-wide association-based approach to characterize the response in ascorbate levels on high light (HL) acclimation in a panel of 315 Arabidopsis (Arabidopsis thaliana) accessions. These studies revealed statistically significant SNPs for total and reduced ascorbate under HL conditions at a locus in chromosome 2. Ascorbate levels under HL and the region upstream and within PAS/LOV PROTEIN (PLP) were strongly associated. Intriguingly, subcellular localization analyses revealed that the PLPA and PLPB splice variants co-localized with VITAMIN C DEFECTIVE2 (VTC2) and VTC5 in both the cytosol and nucleus. Yeast 2-hybrid and bimolecular fluorescence complementation analyses revealed that PLPA and PLPB interact with VTC2 and that blue light diminishes this interaction. Furthermore, PLPB knockout mutants were characterized by 1.5- to 1.7-fold elevations in their ascorbate levels, whereas knockout mutants of the cry2 cryptochromes displayed 1.2- to 1.3-fold elevations compared to WT. Our results collectively indicate that PLP plays a critical role in the elevation of ascorbate levels, which is a signature response of HL acclimation. The results strongly suggest that this is achieved via the release of the inhibitory effect of PLP on VTC2 upon blue light illumination, as the VTC2-PLPB interaction is stronger under darkness. The conditional importance of the cryptochrome receptors under different environmental conditions suggests a complex hierarchy underpinning the environmental control of ascorbate levels. However, the data we present here clearly demonstrate that PLP dominates during HL acclimation.
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Affiliation(s)
- Fayezeh Aarabi
- Central Metabolism, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Andrea Ghigi
- Central Metabolism, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Micha Wijesingha Ahchige
- Central Metabolism, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Mustafa Bulut
- Central Metabolism, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Peter Geigenberger
- Department Biology I, Ludwig-Maximilians-University Munich, Planegg-Martinsried 82152, Germany
| | - H Ekkehard Neuhaus
- Plant Physiology, University of Kaiserslautern, Kaiserslautern D-67653, Germany
| | - Arun Sampathkumar
- Central Metabolism, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Saleh Alseekh
- Central Metabolism, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
- Crop Quantitative Genetics, Centre of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Alisdair R Fernie
- Central Metabolism, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
- Crop Quantitative Genetics, Centre of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
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5
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Meyer RC, Weigelt-Fischer K, Tschiersch H, Topali G, Altschmied L, Heuermann MC, Knoch D, Kuhlmann M, Zhao Y, Altmann T. Dynamic growth QTL action in diverse light environments: characterization of light regime-specific and stable QTL in Arabidopsis. J Exp Bot 2023; 74:5341-5362. [PMID: 37306093 DOI: 10.1093/jxb/erad222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 06/10/2023] [Indexed: 06/13/2023]
Abstract
Plant growth is a complex process affected by a multitude of genetic and environmental factors and their interactions. To identify genetic factors influencing plant performance under different environmental conditions, vegetative growth was assessed in Arabidopsis thaliana cultivated under constant or fluctuating light intensities, using high-throughput phenotyping and genome-wide association studies. Daily automated non-invasive phenotyping of a collection of 382 Arabidopsis accessions provided growth data during developmental progression under different light regimes at high temporal resolution. Quantitative trait loci (QTL) for projected leaf area, relative growth rate, and PSII operating efficiency detected under the two light regimes were predominantly condition-specific and displayed distinct temporal activity patterns, with active phases ranging from 2 d to 9 d. Eighteen protein-coding genes and one miRNA gene were identified as potential candidate genes at 10 QTL regions consistently found under both light regimes. Expression patterns of three candidate genes affecting projected leaf area were analysed in time-series experiments in accessions with contrasting vegetative leaf growth. These observations highlight the importance of considering both environmental and temporal patterns of QTL/allele actions and emphasize the need for detailed time-resolved analyses under diverse well-defined environmental conditions to effectively unravel the complex and stage-specific contributions of genes affecting plant growth processes.
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Affiliation(s)
- Rhonda C Meyer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Kathleen Weigelt-Fischer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Henning Tschiersch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Georgia Topali
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Marc C Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Dominic Knoch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Markus Kuhlmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Breeding Research, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Thomas Altmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
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6
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Ahn E, Botkin J, Curtin SJ, Zsögön A. Ideotype breeding and genome engineering for legume crop improvement. Curr Opin Biotechnol 2023; 82:102961. [PMID: 37331239 DOI: 10.1016/j.copbio.2023.102961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/20/2022] [Accepted: 05/22/2023] [Indexed: 06/20/2023]
Abstract
Ideotype breeding is a strategy whereby traits are modeled a priori and then introduced into a model or crop species to assess their impact on yield. Thus, knowledge about the connection between genotype and phenotype is required for ideotype breeding to be deployed successfully. The growing understanding of the genetic basis of yield-related traits, combined with increasingly efficient genome engineering tools, improved transformation efficiency, and high-throughput genotyping of regenerants paves the way for the widespread adoption of ideotype breeding as a complement to conventional breeding. We briefly discuss how ideotype breeding, coupled with such state-of-the-art biotechnological tools, could contribute to knowledge-based legume breeding and accelerate yield gains to ensure food security in the coming decades.
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Affiliation(s)
- Ezekiel Ahn
- United States Department of Agriculture, Plant Science Research Unit, St Paul, MN 55108, USA
| | - Jacob Botkin
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | - Shaun J Curtin
- United States Department of Agriculture, Plant Science Research Unit, St Paul, MN 55108, USA; Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA; Center for Plant Precision Genomics, University of Minnesota, St. Paul, MN 55108, USA; Center for Genome Engineering, University of Minnesota, St. Paul, MN 55108, USA
| | - Agustin Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil.
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Roychowdhury R, Das SP, Gupta A, Parihar P, Chandrasekhar K, Sarker U, Kumar A, Ramrao DP, Sudhakar C. Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant's Abiotic Stress Tolerance Responses. Genes (Basel) 2023; 14:1281. [PMID: 37372461 DOI: 10.3390/genes14061281] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/03/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
The present day's ongoing global warming and climate change adversely affect plants through imposing environmental (abiotic) stresses and disease pressure. The major abiotic factors such as drought, heat, cold, salinity, etc., hamper a plant's innate growth and development, resulting in reduced yield and quality, with the possibility of undesired traits. In the 21st century, the advent of high-throughput sequencing tools, state-of-the-art biotechnological techniques and bioinformatic analyzing pipelines led to the easy characterization of plant traits for abiotic stress response and tolerance mechanisms by applying the 'omics' toolbox. Panomics pipeline including genomics, transcriptomics, proteomics, metabolomics, epigenomics, proteogenomics, interactomics, ionomics, phenomics, etc., have become very handy nowadays. This is important to produce climate-smart future crops with a proper understanding of the molecular mechanisms of abiotic stress responses by the plant's genes, transcripts, proteins, epigenome, cellular metabolic circuits and resultant phenotype. Instead of mono-omics, two or more (hence 'multi-omics') integrated-omics approaches can decipher the plant's abiotic stress tolerance response very well. Multi-omics-characterized plants can be used as potent genetic resources to incorporate into the future breeding program. For the practical utility of crop improvement, multi-omics approaches for particular abiotic stress tolerance can be combined with genome-assisted breeding (GAB) by being pyramided with improved crop yield, food quality and associated agronomic traits and can open a new era of omics-assisted breeding. Thus, multi-omics pipelines together are able to decipher molecular processes, biomarkers, targets for genetic engineering, regulatory networks and precision agriculture solutions for a crop's variable abiotic stress tolerance to ensure food security under changing environmental circumstances.
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Affiliation(s)
- Rajib Roychowdhury
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO)-The Volcani Institute, Rishon Lezion 7505101, Israel
| | - Soumya Prakash Das
- School of Bioscience, Seacom Skills University, Bolpur 731236, West Bengal, India
| | - Amber Gupta
- Dr. Vikram Sarabhai Institute of Cell and Molecular Biology, Faculty of Science, Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
| | - Parul Parihar
- Department of Biotechnology and Bioscience, Banasthali Vidyapith, Banasthali 304022, Rajasthan, India
| | - Kottakota Chandrasekhar
- Department of Plant Biochemistry and Biotechnology, Sri Krishnadevaraya College of Agricultural Sciences (SKCAS), Affiliated to Acharya N.G. Ranga Agricultural University (ANGRAU), Guntur 522034, Andhra Pradesh, India
| | - Umakanta Sarker
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Ajay Kumar
- Department of Botany, Maharshi Vishwamitra (M.V.) College, Buxar 802102, Bihar, India
| | - Devade Pandurang Ramrao
- Department of Biotechnology, Mizoram University, Pachhunga University College Campus, Aizawl 796001, Mizoram, India
| | - Chinta Sudhakar
- Plant Molecular Biology Laboratory, Department of Botany, Sri Krishnadevaraya University, Anantapur 515003, Andhra Pradesh, India
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8
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Zhu F, Bulut M, Cheng Y, Alseekh S, Fernie AR. Metabolite-Based Genome-Wide Association Studies of Large-Scale Metabolome Analysis to Illustrate Alterations in the Metabolite Landscape of Plants upon Responses to Stresses. Methods Mol Biol 2023; 2642:241-255. [PMID: 36944883 DOI: 10.1007/978-1-0716-3044-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Given that anthropogenic activities are evoking a profound effect on the climate resulting in more extreme events such as severe drought and heat waves while global demand for food is ever-increasing, understanding plant responses to stresses is critical. As metabolites are fundamental for plant growth regulation and plant lifespan and an important component of yield, illustrating how the metabolite landscape of plant changes following stress will supply important clues as to how to improve the plant resistance to stress. Recently, billions of single-nucleotide polymorphisms (SNPs) have been obtained and used to identify the associations between genetic variants of genomes and relevant crop agronomic traits through different genetic methods such as genome-wide association studies (GWAS). Therefore, in this chapter, we provide comprehensive guidelines concerning the experimental design, metabolite profiling, and metabolite-based genome-wide association studies (mGWAS) of large-scale metabolome analysis to accelerate the future identification of the valuable stress-resistant genes and metabolites.
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Affiliation(s)
- Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Mustafa Bulut
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Yunjiang Cheng
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria.
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Sadhukhan A, Prasad SS, Mitra J, Siddiqui N, Sahoo L, Kobayashi Y, Koyama H. How do plants remember drought? Planta 2022; 256:7. [PMID: 35687165 DOI: 10.1007/s00425-022-03924-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
Plants develop both short-term and transgenerational memory of drought stress through epigenetic regulation of transcription for a better response to subsequent exposure. Recurrent spells of droughts are more common than a single drought, with intermittent moist recovery intervals. While the detrimental effects of the first drought on plant structure and physiology are unavoidable, if survived, plants can memorize the first drought to present a more robust response to the following droughts. This includes a partial stomatal opening in the watered recovery interval, higher levels of osmoprotectants and ABA, and attenuation of photosynthesis in the subsequent exposure. Short-term drought memory is regulated by ABA and other phytohormone signaling with transcriptional memory behavior in various genes. High levels of methylated histones are deposited at the drought-tolerance genes. During the recovery interval, the RNA polymerase is stalled to be activated by a pause-breaking factor in the subsequent drought. Drought leads to DNA demethylation near drought-response genes, with genetic control of the process. Progenies of the drought-exposed plants can better adapt to drought owing to the inheritance of particular methylation patterns. However, a prolonged watered recovery interval leads to loss of drought memory, mediated by certain demethylases and chromatin accessibility factors. Small RNAs act as critical regulators of drought memory by altering transcript levels of drought-responsive target genes. Further studies in the future will throw more light on the genetic control of drought memory and the interplay of genetic and epigenetic factors in its inheritance. Plants from extreme environments can give queues to understanding robust memory responses at the ecosystem level.
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Affiliation(s)
- Ayan Sadhukhan
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Karwar, Jodhpur, 342037, India.
| | - Shiva Sai Prasad
- Department of Agriculture, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur, Andhra Pradesh, 522502, India
| | - Jayeeta Mitra
- Department of Botany, Arunachal University of Studies, Arunachal Pradesh, Namsai, 792103, India
| | - Nadeem Siddiqui
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur, Andhra Pradesh, 522502, India
| | - Lingaraj Sahoo
- Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India
| | - Yuriko Kobayashi
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
| | - Hiroyuki Koyama
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
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