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Geng X, Dong L, Zhu T, Yang C, Zhang J, Guo B, Chen H, Zhang Q, Song L. Genome-wide analysis of soybean hypoxia inducible gene domain containing genes: a functional investigation of GmHIGD3. FRONTIERS IN PLANT SCIENCE 2024; 15:1403841. [PMID: 39011304 PMCID: PMC11246964 DOI: 10.3389/fpls.2024.1403841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 06/12/2024] [Indexed: 07/17/2024]
Abstract
The response of Hypoxia Inducible Gene Domain (HIGD) proteins to hypoxia plays a crucial role in plant development. However, the research on this gene family in soybean has been lacking. In this study, we aimed to identify and comprehensively analyze soybean HIGD genes using the Glycine max genome database. As a result, six GmHIGD genes were successfully identified, and their phylogeny, gene structures, and putative conserved motifs were analyzed in comparison to Arabidopsis and rice. Collinearity analysis indicated that the HIGD gene family in soybean has expanded to some extent when compared to Arabidopsis. Additionally, the cis-elements in the promoter regions of GmHIGD and the transcription factors potentially binding to these regions were identified. All GmHIGD genes showed specific responsiveness to submergence and hypoxic stresses. Expression profiling through quantitative real-time PCR revealed that these genes were significantly induced by PEG treatment in root tissue. Co-expressed genes of GmHIGD were primarily associated with oxidoreductase and dioxygenase activities, as well as peroxisome function. Notably, one of GmHIGD genes, GmHIGD3 was found to be predominantly localized in mitochondria, and its overexpression in Arabidopsis led to a significantly reduction in catalase activity compared to wild-type plants. These results bring new insights into the functional role of GmHIGD in terms of subcellular localization and the regulation of oxidoreductase activity.
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Affiliation(s)
- Xiaoyan Geng
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu, China
| | - Lu Dong
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu, China
| | - Tiantian Zhu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu, China
| | - Chunhong Yang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jianhua Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu, China
| | - Binhui Guo
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu, China
| | - Huatao Chen
- Zhongshan Biological Breeding Laboratory, Nanjing, China
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Qun Zhang
- College of Life Sciences, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Li Song
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, Nanjing, China
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Jeffery HR, Mudukuti N, Buell CR, Childs KL, Cichy K. Gene expression profiling of soaked dry beans (Phaseolus vulgaris L.) reveals cell wall modification plays a role in cooking time. THE PLANT GENOME 2023; 16:e20364. [PMID: 37415293 DOI: 10.1002/tpg2.20364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/20/2023] [Accepted: 05/26/2023] [Indexed: 07/08/2023]
Abstract
Dry beans (Phaseolus vulgaris L.) are a nutritious food, but their lengthy cooking requirements are barriers to consumption. Presoaking is one strategy to reduce cooking time. Soaking allows hydration to occur prior to cooking, and enzymatic changes to pectic polysaccharides also occur during soaking that shorten the cooking time of beans. Little is known about how gene expression during soaking influences cooking times. The objectives of this study were to (1) identify gene expression patterns that are altered by soaking and (2) compare gene expression in fast-cooking and slow-cooking bean genotypes. RNA was extracted from four bean genotypes at five soaking time points (0, 3, 6, 12, and 18 h) and expression abundances were detected using Quant-seq. Differential gene expression analysis and weighted gene coexpression network analysis were used to identify candidate genes within quantitative trait loci for water uptake and cooking time. Genes related to cell wall growth and development as well as hypoxic stress were differentially expressed between the fast- and slow-cooking beans due to soaking. Candidate genes identified in the slow-cooking beans included enzymes that increase intracellular calcium concentrations and cell wall modification enzymes. The expression of cell wall-strengthening enzymes in the slow-cooking beans may increase their cooking time and ability to resist osmotic stress by preventing cell separation and water uptake in the cotyledon.
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Affiliation(s)
- Hannah R Jeffery
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Nyasha Mudukuti
- Keough School of Global Affairs, University of Notre Dame, Notre Dame, IN, USA
| | - Carol Robin Buell
- Department of Crop & Soil Sciences, Center for Applied Genetic Technologies, and Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, Athens, GA, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Karen Cichy
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
- Sugarbeet and Bean Research Unit, USDA-ARS, East Lansing, MI, USA
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3
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Basso MF, Lourenço-Tessutti IT, Moreira-Pinto CE, Mendes RAG, Paes-de-Melo B, das Neves MR, Macedo AF, Figueiredo V, Grandis A, Macedo LLP, Arraes FBM, do Carmo Costa MM, Togawa RC, Enrich-Prast A, Marcelino-Guimaraes FC, Gomes ACMM, Silva MCM, Floh EIS, Buckeridge MS, de Almeida Engler J, Grossi-de-Sa MF. Overexpression of a soybean Globin (GmGlb1-1) gene reduces plant susceptibility to Meloidogyne incognita. PLANTA 2022; 256:83. [PMID: 36112244 DOI: 10.1007/s00425-022-03992-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
The overexpression of the GmGlb1-1 gene reduces plant susceptibility to Meloidogyne incognita. Non-symbiotic globin class #1 (Glb1) genes are expressed in different plant organs, have a high affinity for oxygen, and are related to nitric oxide (NO) turnover. Previous studies showed that soybean Glb1 genes are upregulated in soybean plants under flooding conditions. Herein, the GmGlb1-1 gene was identified in soybean as being upregulated in the nematode-resistant genotype PI595099 compared to the nematode-susceptible cultivar BRS133 during plant parasitism by Meloidogyne incognita. The Arabidopsis thaliana and Nicotiana tabacum transgenic lines overexpressing the GmGlb1-1 gene showed reduced susceptibility to M. incognita. Consistently, gall morphology data indicated that pJ2 nematodes that infected the transgenic lines showed developmental alterations and delayed parasitism progress. Although no significant changes in biomass and seed yield were detected, the transgenic lines showed an elongated, etiolation-like growth under well-irrigation, and also developed more axillary roots under flooding conditions. In addition, transgenic lines showed upregulation of some important genes involved in plant defense response to oxidative stress. In agreement, higher hydrogen peroxide accumulation and reduced activity of reactive oxygen species (ROS) detoxification enzymes were also observed in these transgenic lines. Thus, based on our data and previous studies, it was hypothesized that constitutive overexpression of the GmGlb1-1 gene can interfere in the dynamics of ROS production and NO scavenging, enhancing the acquired systemic acclimation to biotic and abiotic stresses, and improving the cellular homeostasis. Therefore, these collective data suggest that ectopic or nematode-induced overexpression, or enhanced expression of the GmGlb1-1 gene using CRISPR/dCas9 offers great potential for application in commercial soybean cultivars aiming to reduce plant susceptibility to M. incognita.
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Affiliation(s)
- Marcos Fernando Basso
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-917, Brazil
- National Institute of Science and Technology, INCT Plant Stress Biotech, EMBRAPA, Brasília, DF, 70770-917, Brazil
| | - Isabela Tristan Lourenço-Tessutti
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-917, Brazil
- National Institute of Science and Technology, INCT Plant Stress Biotech, EMBRAPA, Brasília, DF, 70770-917, Brazil
| | - Clidia Eduarda Moreira-Pinto
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-917, Brazil
- National Institute of Science and Technology, INCT Plant Stress Biotech, EMBRAPA, Brasília, DF, 70770-917, Brazil
- Federal University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Reneida Aparecida Godinho Mendes
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-917, Brazil
- Federal University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Bruno Paes-de-Melo
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-917, Brazil
- National Institute of Science and Technology, INCT Plant Stress Biotech, EMBRAPA, Brasília, DF, 70770-917, Brazil
| | - Maysa Rosa das Neves
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-917, Brazil
| | - Amanda Ferreira Macedo
- Department of Botany, Biosciences Institute, University of São Paulo, São Paulo, SP, 05508-090, Brazil
| | - Viviane Figueiredo
- Multiuser Unit of Environmental Analysis and Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-971, Brazil
| | - Adriana Grandis
- Department of Botany, Biosciences Institute, University of São Paulo, São Paulo, SP, 05508-090, Brazil
| | - Leonardo Lima Pepino Macedo
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-917, Brazil
- National Institute of Science and Technology, INCT Plant Stress Biotech, EMBRAPA, Brasília, DF, 70770-917, Brazil
| | - Fabrício Barbosa Monteiro Arraes
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-917, Brazil
- National Institute of Science and Technology, INCT Plant Stress Biotech, EMBRAPA, Brasília, DF, 70770-917, Brazil
| | - Marcos Mota do Carmo Costa
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-917, Brazil
| | - Roberto Coiti Togawa
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-917, Brazil
- National Institute of Science and Technology, INCT Plant Stress Biotech, EMBRAPA, Brasília, DF, 70770-917, Brazil
| | - Alex Enrich-Prast
- Multiuser Unit of Environmental Analysis and Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-971, Brazil
- Biogas Research Center and Department of Thematic Studies, Environmental Change, Linköping University, Linköping, Sweden
| | - Francismar Corrêa Marcelino-Guimaraes
- National Institute of Science and Technology, INCT Plant Stress Biotech, EMBRAPA, Brasília, DF, 70770-917, Brazil
- Embrapa Soybean, Londrina, PR, 86001-970, Brazil
| | | | - Maria Cristina Mattar Silva
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-917, Brazil
- National Institute of Science and Technology, INCT Plant Stress Biotech, EMBRAPA, Brasília, DF, 70770-917, Brazil
| | - Eny Iochevet Segal Floh
- Department of Botany, Biosciences Institute, University of São Paulo, São Paulo, SP, 05508-090, Brazil
| | | | - Janice de Almeida Engler
- National Institute of Science and Technology, INCT Plant Stress Biotech, EMBRAPA, Brasília, DF, 70770-917, Brazil
- INRAE, Université Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis, France
| | - Maria Fatima Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-917, Brazil.
- National Institute of Science and Technology, INCT Plant Stress Biotech, EMBRAPA, Brasília, DF, 70770-917, Brazil.
- Catholic University of Brasília, Brasília, DF, 71966-700, Brazil.
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Identification of Functional Genetic Variations Underlying Flooding Tolerance in Brazilian Soybean Genotypes. Int J Mol Sci 2022; 23:ijms231810611. [PMID: 36142529 PMCID: PMC9502317 DOI: 10.3390/ijms231810611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/23/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022] Open
Abstract
Flooding is a frequent environmental stress that reduces soybean (Glycine max) growth and grain yield in many producing areas in the world, such as, e.g., in the United States, Southeast Asia and Southern Brazil. In these regions, soybean is frequently cultivated in lowland areas by rotating with rice (Oryza sativa), which provides numerous technical, economic and environmental benefits. Given these realities, this work aimed to characterize physiological responses, identify genes differentially expressed under flooding stress in Brazilian soybean genotypes with contrasting flooding tolerance, and select SNPs with potential use for marker-assisted selection. Soybean cultivars TECIRGA 6070 (flooding tolerant) and FUNDACEP 62 (flooding sensitive) were grown up to the V6 growth stage and then flooding stress was imposed. Total RNA was extracted from leaves 24 h after the stress was imposed and sequenced. In total, 421 induced and 291 repressed genes were identified in both genotypes. TECIRGA 6070 presented 284 and 460 genes up- and down-regulated, respectively, under flooding conditions. Of those, 100 and 148 genes were exclusively up- and down-regulated, respectively, in the tolerant genotype. Based on the RNA sequencing data, SNPs in differentially expressed genes in response to flooding stress were identified. Finally, 38 SNPs, located in genes with functional annotation for response to abiotic stresses, were found in TECIRGA 6070 and absent in FUNDACEP 62. To validate them, 22 SNPs were selected for designing KASP assays that were used to genotype a panel of 11 contrasting genotypes with known phenotypes. In addition, the phenotypic and grain yield impacts were analyzed in four field experiments using a panel of 166 Brazilian soybean genotypes. Five SNPs possibly related to flooding tolerance in Brazilian soybean genotypes were identified. The information generated from this research will be useful to develop soybean genotypes adapted to poorly drained soils or areas subject to flooding.
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5
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Koltun A, Fuhrmann-Aoyagi MB, Cardoso Moraes LA, Lima Nepomuceno A, Simões Azeredo Gonçalves L, Mertz-Henning LM. Uncovering the roles of hemoglobins in soybean facing water stress. Gene 2022; 810:146055. [PMID: 34737003 DOI: 10.1016/j.gene.2021.146055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/14/2021] [Accepted: 10/28/2021] [Indexed: 11/22/2022]
Abstract
Water stress drastically hinders crop yield, including soybean - one of the world's most relevant feeding crops - threatening the food security of an ever-growing global population. Hemoglobins (GLBs) are involved in water stress tolerance; however, the role they effectively play in soybean remains underexplored. In this study, in silico and in vivo analyses were performed to identify soybean GLBs, capture their transcriptional profile under water stress, and overexpress promising members to assess how soybean cope with waterlogging. Seven GLBs were found, two GLB1 (non-symbiotic) and five GLB2 (symbiotic or leghemoglobins). Three out of the seven GLBs were differentially expressed in soybean RNA-seq libraries of water stress and were evaluated by real-time PCR. Consistently, GmGLB1-1 and GmGLB1-2 were moderately and highly expressed under waterlogging, respectively. Composite plants with roots overexpressing GmGLB1-1 or GmGLB1-2 (mostly) showed higher transcript abundance of stress-defensive genes involved in anaerobic, nitrogen, carbon, and antioxidant metabolism when subjected to waterlogging. In addition, soybean bearing p35S:GmGLB1-2 had lower H2O2 root content, a reactive oxygen species (ROS), under water excess compared with the control condition. Altogether these results suggest that GmGLB1-2 is a strong candidate for soybean genetic engineering to generate waterlogging-tolerant soybean cultivars.
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6
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Raul B, Bhattacharjee O, Ghosh A, Upadhyay P, Tembhare K, Singh A, Shaheen T, Ghosh AK, Torres-Jerez I, Krom N, Clevenger J, Udvardi M, Scheffler BE, Ozias-Akins P, Sharma RD, Bandyopadhyay K, Gaur V, Kumar S, Sinharoy S. Microscopic and Transcriptomic Analyses of Dalbergoid Legume Peanut Reveal a Divergent Evolution Leading to Nod-Factor-Dependent Epidermal Crack-Entry and Terminal Bacteroid Differentiation. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:131-145. [PMID: 34689599 DOI: 10.1094/mpmi-05-21-0122-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Root nodule symbiosis (RNS) is the pillar behind sustainable agriculture and plays a pivotal role in the environmental nitrogen cycle. Most of the genetic, molecular, and cell-biological knowledge on RNS comes from model legumes that exhibit a root-hair mode of bacterial infection, in contrast to the Dalbergoid legumes exhibiting crack-entry of rhizobia. As a step toward understanding this important group of legumes, we have combined microscopic analysis and temporal transcriptome to obtain a dynamic view of plant gene expression during Arachis hypogaea (peanut) nodule development. We generated comprehensive transcriptome data by mapping the reads to A. hypogaea, and two diploid progenitor genomes. Additionally, we performed BLAST searches to identify nodule-induced yet-to-be annotated peanut genes. Comparison between peanut, Medicago truncatula, Lotus japonicus, and Glycine max showed upregulation of 61 peanut orthologs among 111 tested known RNS-related genes, indicating conservation in mechanisms of nodule development among members of the Papilionoid family. Unlike model legumes, recruitment of class 1 phytoglobin-derived symbiotic hemoglobin (SymH) in peanut indicates diversification of oxygen-scavenging mechanisms in the Papilionoid family. Finally, the absence of cysteine-rich motif-1-containing nodule-specific cysteine-rich peptide (NCR) genes but the recruitment of defensin-like NCRs suggest a diverse molecular mechanism of terminal bacteroid differentiation. In summary, our work describes genetic conservation and diversification in legume-rhizobia symbiosis in the Papilionoid family, as well as among members of the Dalbergoid legumes.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Bikash Raul
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Oindrila Bhattacharjee
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
- Amity University Haryana, Amity Education Valley, Manesar, Panchgaon, Haryana 122412, India
| | - Amit Ghosh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Priya Upadhyay
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Kunal Tembhare
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ajeet Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Tarannum Shaheen
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Asim Kumar Ghosh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | | | - Nick Krom
- Noble Research Institute, 2510 Sam Noble Pkwy, Ardmore, OK 73401, U.S.A
| | - Josh Clevenger
- University of Georgia, Institute of Plant Breeding, Genetics and Genomics and Department of Horticulture, Tifton, GA 31793, U.S.A
| | - Michael Udvardi
- Noble Research Institute, 2510 Sam Noble Pkwy, Ardmore, OK 73401, U.S.A
| | - Brian E Scheffler
- United States Department of Agriculture-Agricultural Research Service Jamie Whitten Delta States Research Center (JWDSRC) Stoneville, JWDSRC, Bldg.1, Room 229, Experiment Station Road, PO Box 36, Stoneville, MS 38776-0036, U.S.A
| | - Peggy Ozias-Akins
- University of Georgia, Institute of Plant Breeding, Genetics and Genomics and Department of Horticulture, Tifton, GA 31793, U.S.A
| | - Ravi Datta Sharma
- Amity University Haryana, Amity Education Valley, Manesar, Panchgaon, Haryana 122412, India
| | - Kaustav Bandyopadhyay
- Amity University Haryana, Amity Education Valley, Manesar, Panchgaon, Haryana 122412, India
| | - Vineet Gaur
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shailesh Kumar
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Senjuti Sinharoy
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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Fuhrmann-Aoyagi MB, de Fátima Ruas C, Barbosa EGG, Braga P, Moraes LAC, de Oliveira ACB, Kanamori N, Yamaguchi-Shinozaki K, Nakashima K, Nepomuceno AL, Mertz-Henning LM. Constitutive expression of Arabidopsis bZIP transcription factor AREB1 activates cross-signaling responses in soybean under drought and flooding stresses. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153338. [PMID: 33401097 DOI: 10.1016/j.jplph.2020.153338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/25/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Abiotic stress, such as drought and flooding, are responsible for considerable losses in grain production worldwide. Soybean, the main cultivated oilseed in the world, is sensitive to both stresses. Plant molecular mechanisms answer via crosstalk of several signaling pathways, in which particular genes can respond to different stresses. Previous studies confirmed that overexpression of transcription factor AtAREB1 confers drought tolerance in soybean. However, plants containing this gene have not yet been tested under flooding. Thus, the objective of this study was to characterize genetically modified (GM) soybean plants overexpressing AtAREB1 under drought and flooding conditions in comparison to its genetic background. Physiological and biochemical measurements were performed. In addition, the expression level of genes commonly activated under both stresses was evaluated. The results supported the role of the AtAREB1 gene in conferring tolerance to water deficit in soybeans. Furthermore, under flooding, the GM line was efficient in maintaining a higher photosynthetic rate, intrinsic efficiency in water use, and instantaneous carboxylation efficiency, resulting in higher grain yield under stress. The GM line also presented higher protein content, lower concentration of hydrogen peroxide, and lower expression levels of genes related to fermentative metabolism and alanine biosynthesis. These results indicate that in addition to drought stress, plants overexpressing AtAREB1 exhibited better performance under flooding when compared to the non-GM line, suggesting a cross-signaling response to both abiotic factors.
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Affiliation(s)
- Martina Bianca Fuhrmann-Aoyagi
- Department of General Biology, Londrina State University, Rodovia Celso Garcia Cid, Campus Universitário, 86.057-970, Londrina, PR, Brazil.
| | - Claudete de Fátima Ruas
- Department of General Biology, Londrina State University, Rodovia Celso Garcia Cid, Campus Universitário, 86.057-970, Londrina, PR, Brazil.
| | - Elton Gargioni Grisoste Barbosa
- Fundação de Apoio à Pesquisa e ao Desenvolvimento (FAPED), Rua Dr. Campos Júnior, 49 - Centro, 35700-039, Sete Lagoas, MG, Brazil.
| | - Patricia Braga
- Agronomy Department, Universidade Estadual de Londrina (UEL), Rodovia Celso Garcia Cid, Pr 445, Km 380, 86050-900, Londrina, PR, Brazil.
| | | | | | - Norihito Kanamori
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan.
| | - Kazuko Yamaguchi-Shinozaki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan; Research Institute for Agricultural and Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan.
| | - Kazuo Nakashima
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan.
| | - Alexandre Lima Nepomuceno
- Embrapa Soja, Rodovia Carlos João Strass, Acesso Orlando Amaral, Warta, PO. Box 231, 86001-970, Londrina, PR, Brazil.
| | - Liliane Marcia Mertz-Henning
- Embrapa Soja, Rodovia Carlos João Strass, Acesso Orlando Amaral, Warta, PO. Box 231, 86001-970, Londrina, PR, Brazil.
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8
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Lai MC, Lai ZY, Jhan LH, Lai YS, Kao CF. Prioritization and Evaluation of Flooding Tolerance Genes in Soybean [ Glycine max (L.) Merr.]. Front Genet 2021; 11:612131. [PMID: 33584812 PMCID: PMC7873447 DOI: 10.3389/fgene.2020.612131] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/31/2020] [Indexed: 11/22/2022] Open
Abstract
Soybean [Glycine max (L.) Merr.] is one of the most important legume crops abundant in edible protein and oil in the world. In recent years there has been increasingly more drastic weather caused by climate change, with flooding, drought, and unevenly distributed rainfall gradually increasing in terms of the frequency and intensity worldwide. Severe flooding has caused extensive losses to soybean production and there is an urgent need to breed strong soybean seeds with high flooding tolerance. The present study demonstrates bioinformatics big data mining and integration, meta-analysis, gene mapping, gene prioritization, and systems biology for identifying prioritized genes of flooding tolerance in soybean. A total of 83 flooding tolerance genes (FTgenes), according to the appropriate cut-off point, were prioritized from 36,705 test genes collected from multidimensional genomic features linking to soybean flooding tolerance. Several validation results using independent samples from SoyNet, genome-wide association study, SoyBase, GO database, and transcriptome databases all exhibited excellent agreement, suggesting these 83 FTgenes were significantly superior to others. These results provide valuable information and contribution to research on the varieties selection of soybean.
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Affiliation(s)
- Mu-Chien Lai
- Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Zheng-Yuan Lai
- Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Li-Hsin Jhan
- Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Ya-Syuan Lai
- Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Feng Kao
- Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan.,Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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González-Guzmán M, Gómez-Cadenas A, Arbona V. Abscisic Acid as an Emerging Modulator of the Responses of Plants to Low Oxygen Conditions. FRONTIERS IN PLANT SCIENCE 2021; 12:661789. [PMID: 33981326 PMCID: PMC8107475 DOI: 10.3389/fpls.2021.661789] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/06/2021] [Indexed: 05/11/2023]
Abstract
Different environmental and developmental cues involve low oxygen conditions, particularly those associated to abiotic stress conditions. It is widely accepted that plant responses to low oxygen conditions are mainly regulated by ethylene (ET). However, interaction with other hormonal signaling pathways as gibberellins (GAs), auxin (IAA), or nitric oxide (NO) has been well-documented. In this network of interactions, abscisic acid (ABA) has always been present and regarded to as a negative regulator of the development of morphological adaptations to soil flooding: hyponastic growth, adventitious root emergence, or formation of secondary aerenchyma in different plant species. However, recent evidence points toward a positive role of this plant hormone on the modulation of plant responses to hypoxia and, more importantly, on the ability to recover during the post-hypoxic period. In this work, the involvement of ABA as an emerging regulator of plant responses to low oxygen conditions alone or in interaction with other hormones is reviewed and discussed.
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10
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Wang X, Komatsu S. Review: Proteomic Techniques for the Development of Flood-Tolerant Soybean. Int J Mol Sci 2020; 21:E7497. [PMID: 33053653 PMCID: PMC7589014 DOI: 10.3390/ijms21207497] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/04/2020] [Accepted: 10/08/2020] [Indexed: 12/16/2022] Open
Abstract
Soybean, which is rich in protein and oil as well as phytochemicals, is cultivated in several climatic zones. However, its growth is markedly decreased by flooding stress, which is caused by climate change. Proteomic techniques were used for understanding the flood-response and -tolerant mechanisms in soybean. Subcellular proteomics has potential to elucidate localized cellular responses and investigate communications among subcellular components during plant growth and under stress stimuli. Furthermore, post-translational modifications play important roles in stress response and tolerance to flooding stress. Although many flood-response mechanisms have been reported, flood-tolerant mechanisms have not been fully clarified for soybean because of limitations in germplasm with flooding tolerance. This review provides an update on current biochemical and molecular networks involved in soybean tolerance against flooding stress, as well as recent developments in the area of functional genomics in terms of developing flood-tolerant soybeans. This work will expedite marker-assisted genetic enhancement studies in crops for developing high-yielding stress-tolerant lines or varieties under abiotic stress.
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Affiliation(s)
- Xin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Setsuko Komatsu
- Faculty of Environmental and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
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Safavi-Rizi V, Herde M, Stöhr C. RNA-Seq reveals novel genes and pathways associated with hypoxia duration and tolerance in tomato root. Sci Rep 2020; 10:1692. [PMID: 32015352 PMCID: PMC6997459 DOI: 10.1038/s41598-020-57884-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/03/2020] [Indexed: 11/09/2022] Open
Abstract
Due to climate change, economically important crop plants will encounter flooding periods causing hypoxic stress more frequently. This may lead to reduced yields and endanger food security. As roots are the first organ to be affected by hypoxia, the ability to sense and respond to hypoxic stress is crucial. At the molecular level, therefore, fine-tuning the regulation of gene expression in the root is essential for hypoxia tolerance. Using an RNA-Seq approach, we investigated transcriptome modulation in tomato roots of the cultivar 'Moneymaker', in response to short- (6 h) and long-term (48 h) hypoxia. Hypoxia duration appeared to have a significant impact on gene expression such that the roots of five weeks old tomato plants showed a distinct time-dependent transcriptome response. We observed expression changes in 267 and 1421 genes under short- and long-term hypoxia, respectively. Among these, 243 genes experienced changed expression at both time points. We identified tomato genes with a potential role in aerenchyma formation which facilitates oxygen transport and may act as an escape mechanism enabling hypoxia tolerance. Moreover, we identified differentially regulated genes related to carbon and amino acid metabolism and redox homeostasis. Of particular interest were the differentially regulated transcription factors, which act as master regulators of downstream target genes involved in responses to short and/or long-term hypoxia. Our data suggest a temporal metabolic and anatomic adjustment to hypoxia in tomato root which requires further investigation. We propose that the regulated genes identified in this study are good candidates for further studies regarding hypoxia tolerance in tomato or other crops.
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Affiliation(s)
- Vajiheh Safavi-Rizi
- Department of Plant physiology, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Soldmannstrasse 15, D-17487, Greifswald, Germany.
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Institute of Plant Nutrition, Leibniz University Hannover, Herrenhäuser Strasse 2, 30419, Hannover, Germany
| | - Christine Stöhr
- Department of Plant physiology, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Soldmannstrasse 15, D-17487, Greifswald, Germany
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12
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Ma L, Shi Y, Siemianowski O, Yuan B, Egner TK, Mirnezami SV, Lind KR, Ganapathysubramanian B, Venditti V, Cademartiri L. Hydrogel-based transparent soils for root phenotyping in vivo. Proc Natl Acad Sci U S A 2019; 116:11063-11068. [PMID: 31088969 PMCID: PMC6561166 DOI: 10.1073/pnas.1820334116] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Root phenotypes are increasingly explored as predictors of crop performance but are still challenging to characterize. Media that mimic field conditions (e.g., soil, sand) are opaque to most forms of radiation, while transparent media do not provide field-relevant growing conditions and phenotypes. We describe here a "transparent soil" formed by the spherification of hydrogels of biopolymers. It is specifically designed to support root growth in the presence of air, water, and nutrients, and allows the time-resolved phenotyping of roots in vivo by both photography and microscopy. The roots developed by soybean plants in this medium are significantly more similar to those developed in real soil than those developed in hydroponic conditions and do not show signs of hypoxia. Lastly, we show that the granular nature and tunable properties of these hydrogel beads can be leveraged to investigate the response of roots to gradients in water availability and soil stiffness.
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Affiliation(s)
- Lin Ma
- Department of Materials Science & Engineering, Iowa State University of Science and Technology, Ames, IA 50011
| | - Yichao Shi
- Department of Materials Science & Engineering, Iowa State University of Science and Technology, Ames, IA 50011
| | - Oskar Siemianowski
- Department of Materials Science & Engineering, Iowa State University of Science and Technology, Ames, IA 50011
| | - Bin Yuan
- Department of Chemical & Biological Engineering, Iowa State University of Science and Technology, Ames, IA 50011
| | - Timothy K Egner
- Department of Chemistry, Iowa State University of Science and Technology, Ames, IA 50011
| | - Seyed Vahid Mirnezami
- Department of Mechanical Engineering, Iowa State University of Science and Technology, Ames, IA 50011
| | - Kara R Lind
- Department of Materials Science & Engineering, Iowa State University of Science and Technology, Ames, IA 50011
| | | | - Vincenzo Venditti
- Department of Chemistry, Iowa State University of Science and Technology, Ames, IA 50011
| | - Ludovico Cademartiri
- Department of Materials Science & Engineering, Iowa State University of Science and Technology, Ames, IA 50011;
- Department of Chemical & Biological Engineering, Iowa State University of Science and Technology, Ames, IA 50011
- Ames Laboratory, US Department of Energy, Ames, IA 50011
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Abstract
A major problem of climate change is the increasing duration and frequency of heavy rainfall events. This leads to soil flooding that negatively affects plant growth, eventually leading to death of plants if the flooding persists for several days. Most crop plants are very sensitive to flooding, and dramatic yield losses occur due to flooding each year. This review summarizes recent progress and approaches to enhance crop resistance to flooding. Most experiments have been done on maize, barley, and soybean. Work on other crops such as wheat and rape has only started. The most promising traits that might enhance crop flooding tolerance are anatomical adaptations such as aerenchyma formation, the formation of a barrier against radial oxygen loss, and the growth of adventitious roots. Metabolic adaptations might be able to improve waterlogging tolerance as well, but more studies are needed in this direction. Reasonable approaches for future studies are quantitative trait locus (QTL) analyses or genome-wide association (GWA) studies in combination with specific tolerance traits that can be easily assessed. The usage of flooding-tolerant relatives or ancestral cultivars of the crop of interest in these experiments might enhance the chances of finding useful tolerance traits to be used in breeding.
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Lancet D, Zidovetzki R, Markovitch O. Systems protobiology: origin of life in lipid catalytic networks. J R Soc Interface 2018; 15:20180159. [PMID: 30045888 PMCID: PMC6073634 DOI: 10.1098/rsif.2018.0159] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/29/2018] [Indexed: 12/17/2022] Open
Abstract
Life is that which replicates and evolves, but there is no consensus on how life emerged. We advocate a systems protobiology view, whereby the first replicators were assemblies of spontaneously accreting, heterogeneous and mostly non-canonical amphiphiles. This view is substantiated by rigorous chemical kinetics simulations of the graded autocatalysis replication domain (GARD) model, based on the notion that the replication or reproduction of compositional information predated that of sequence information. GARD reveals the emergence of privileged non-equilibrium assemblies (composomes), which portray catalysis-based homeostatic (concentration-preserving) growth. Such a process, along with occasional assembly fission, embodies cell-like reproduction. GARD pre-RNA evolution is evidenced in the selection of different composomes within a sparse fitness landscape, in response to environmental chemical changes. These observations refute claims that GARD assemblies (or other mutually catalytic networks in the metabolism first scenario) cannot evolve. Composomes represent both a genotype and a selectable phenotype, anteceding present-day biology in which the two are mostly separated. Detailed GARD analyses show attractor-like transitions from random assemblies to self-organized composomes, with negative entropy change, thus establishing composomes as dissipative systems-hallmarks of life. We show a preliminary new version of our model, metabolic GARD (M-GARD), in which lipid covalent modifications are orchestrated by non-enzymatic lipid catalysts, themselves compositionally reproduced. M-GARD fills the gap of the lack of true metabolism in basic GARD, and is rewardingly supported by a published experimental instance of a lipid-based mutually catalytic network. Anticipating near-future far-reaching progress of molecular dynamics, M-GARD is slated to quantitatively depict elaborate protocells, with orchestrated reproduction of both lipid bilayer and lumenal content. Finally, a GARD analysis in a whole-planet context offers the potential for estimating the probability of life's emergence. The invigorated GARD scrutiny presented in this review enhances the validity of autocatalytic sets as a bona fide early evolution scenario and provides essential infrastructure for a paradigm shift towards a systems protobiology view of life's origin.
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Affiliation(s)
- Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Raphael Zidovetzki
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA 92521, USA
| | - Omer Markovitch
- Origins Center, Center for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Groningen, the Netherlands
- Blue Marble Space Institute of Science, Seattle, WA, USA
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