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Khodaeiaminjan M, Knoch D, Ndella Thiaw MR, Marchetti CF, Kořínková N, Techer A, Nguyen TD, Chu J, Bertholomey V, Doridant I, Gantet P, Graner A, Neumann K, Bergougnoux V. Genome-wide association study in two-row spring barley landraces identifies QTL associated with plantlets root system architecture traits in well-watered and osmotic stress conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1125672. [PMID: 37077626 PMCID: PMC10106628 DOI: 10.3389/fpls.2023.1125672] [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: 12/16/2022] [Accepted: 03/15/2023] [Indexed: 05/03/2023]
Abstract
Water availability is undoubtedly one of the most important environmental factors affecting crop production. Drought causes a gradual deprivation of water in the soil from top to deep layers and can occur at diverse stages of plant development. Roots are the first organs that perceive water deficit in soil and their adaptive development contributes to drought adaptation. Domestication has contributed to a bottleneck in genetic diversity. Wild species or landraces represent a pool of genetic diversity that has not been exploited yet in breeding program. In this study, we used a collection of 230 two-row spring barley landraces to detect phenotypic variation in root system plasticity in response to drought and to identify new quantitative trait loci (QTL) involved in root system architecture under diverse growth conditions. For this purpose, young seedlings grown for 21 days in pouches under control and osmotic-stress conditions were phenotyped and genotyped using the barley 50k iSelect SNP array, and genome-wide association studies (GWAS) were conducted using three different GWAS methods (MLM GAPIT, FarmCPU, and BLINK) to detect genotype/phenotype associations. In total, 276 significant marker-trait associations (MTAs; p-value (FDR)< 0.05) were identified for root (14 and 12 traits under osmotic-stress and control conditions, respectively) and for three shoot traits under both conditions. In total, 52 QTL (multi-trait or identified by at least two different GWAS approaches) were investigated to identify genes representing promising candidates with a role in root development and adaptation to drought stress.
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Affiliation(s)
- Mortaza Khodaeiaminjan
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
| | - Dominic Knoch
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | - Cintia F. Marchetti
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
| | - Nikola Kořínková
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
| | - Alexie Techer
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
| | - Thu D. Nguyen
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
| | - Jianting Chu
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Valentin Bertholomey
- Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain Centre de Recherche, Chappes, France
| | - Ingrid Doridant
- Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain Centre de Recherche, Chappes, France
| | - Pascal Gantet
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
- Unité Mixte de Recherche DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Andreas Graner
- Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Kerstin Neumann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Véronique Bergougnoux
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
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Kausar R, Wang X, Komatsu S. Crop Proteomics under Abiotic Stress: From Data to Insights. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11212877. [PMID: 36365330 PMCID: PMC9657731 DOI: 10.3390/plants11212877] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/09/2022] [Accepted: 10/22/2022] [Indexed: 06/09/2023]
Abstract
Food security is a major challenge in the present world due to erratic weather and climatic changes. Environmental stress negatively affects plant growth and development which leads to reduced crop yields. Technological advancements have caused remarkable improvements in crop-breeding programs. Proteins have an indispensable role in developing stress resilience and tolerance in crops. Genomic and biotechnological advancements have made the process of crop improvement more accurate and targeted. Proteomic studies provide the information required for such targeted approaches. The crosstalk among cellular components is being analyzed by subcellular proteomics. Additionally, the functional diversity of proteins is being unraveled by post-translational modifications during abiotic stress. The exploration of precise cellular responses and the networking among different cellular organelles help in the prediction of signaling pathways and protein-protein interactions. High-throughput mass-spectrometry-based protein studies are now possible due to incremental advancements in mass-spectrometry techniques, sample protocols, and bioinformatic tools as well as the increasing availability of plant genome sequence information for multiple species. In this review, the key role of proteomic analysis in identifying the abiotic-stress-responsive mechanisms in various crops was summarized. The development and availability of advanced computational tools were discussed in detail. The highly variable protein responses among different crops have provided a wide avenue for molecular-marker-assisted genetic buildup studies to develop smart, high-yielding, and stress-tolerant varieties to cope with food-security challenges.
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Affiliation(s)
- Rehana Kausar
- Department of Botany, University of Azad Jammu and Kashmir, Muzaffarabad 13100, Pakistan
| | - Xin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
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Xu Y, Wang H, Sahu SK, Li L, Liang H, Günther G, Wong GKS, Melkonian B, Melkonian M, Liu H, Wang S. Chromosome-level genome of Pedinomonas minor (Chlorophyta) unveils adaptations to abiotic stress in a rapidly fluctuating environment. THE NEW PHYTOLOGIST 2022; 235:1409-1425. [PMID: 35560066 DOI: 10.1111/nph.18220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
The Pedinophyceae (Viridiplantae) comprise a class of small uniflagellate algae with a pivotal position in the phylogeny of the Chlorophyta as the sister group of the 'core chlorophytes'. We present a chromosome-level genome assembly of the freshwater type species of the class, Pedinomonas minor. We sequenced the genome using Pacbio, Illumina and Hi-C technologies, performed comparative analyses of genome and gene family evolution, and analyzed the transcriptome under various abiotic stresses. Although the genome is relatively small (55 Mb), it shares many traits with core chlorophytes including number of introns and protein-coding genes, messenger RNA (mRNA) lengths, and abundance of transposable elements. Pedinomonas minor is only bounded by the plasma membrane, thriving in temporary habitats that frequently dry out. Gene family innovations and expansions and transcriptomic responses to abiotic stresses have shed light on adaptations of P. minor to its fluctuating environment. Horizontal gene transfers from bacteria and fungi have possibly contributed to the evolution of some of these traits. We identified a putative endogenization site of a nucleocytoplasmic large DNA virus and hypothesized that endogenous viral elements donated foreign genes to the host genome, their spread enhanced by transposable elements, located at gene boundaries in several of the expanded gene families.
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Affiliation(s)
- Yan Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongli Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Linzhou Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Hongping Liang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Gerd Günther
- Private Laboratory, Knittkuhler Str. 61, Düsseldorf, 40629, Germany
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Barbara Melkonian
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Michael Melkonian
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Huan Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sibo Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
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Zafar TA, Allafi AR, Alkandari D, Al-Othman A. Rheological characteristics of wheat-chickpea composite flour doughs and effect of Amla powder ( Phyllanthus emblica L.) addition on the functional properties of bread. FOOD SCI TECHNOL INT 2020; 27:264-275. [PMID: 32847395 DOI: 10.1177/1082013220950068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Bread is a staple food for majority of the people worldwide, but it has a high glycemic effect. Substituting wheat flour partly with chickpea flour and the presence of bran is suggested to improve the glycemic effect of bread; however, the non-gluten substances in wheat flour adversely affect dough rheology. The addition of amla powder was tested on the rheological properties of wheat-chickpea flour composite doughs; also, the physical and sensory qualities of bread made thereof. The results showed that when the level of replacement of refined white flour (WF) or whole wheat flour (WWF) with chickpea flour was increased from 0 to 40%, it significantly affected the rheological properties and functionality of dough. A decreased farinograph water absorption, higher mixing tolerance index (i.e., weakening of dough), decreased resistance to extension, and lower ratio numbers were obtained with some differences between WF and WWF at the higher level of chickpea flour substitution. The addition of amla powder to WF: chickpea flour (60:40) blends reduced the angle of ascending (from 7.0 ± 0.7 to 6.0 ± 0.7) and angel of descending (from 3.2 ± 0.21 to 2.4 ± 0.2), indicating the slight tightening of gluten leading to dough breakdown. The addition of amla powder improved the mixing characteristics of the composite flour doughs, as well as the physical and sensory qualities of the bread. In conclusion, amla powder can help overcome the deleterious impact of adding chickpea flour to WF or WWF for producing good quality pan bread for people with type-2 diabetes.
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Affiliation(s)
- Tasleem A Zafar
- Department of Food Science and Nutrition, College of Life Sciences, Kuwait University, Safat, Kuwait
| | - Ahmad R Allafi
- Department of Food Science and Nutrition, College of Life Sciences, Kuwait University, Safat, Kuwait
| | - Dina Alkandari
- Department of Food Science and Nutrition, College of Life Sciences, Kuwait University, Safat, Kuwait
| | - Amani Al-Othman
- Department of Computer Science, Kuwait Institute for Scientific Research, Safat, Kuwait
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Hashimoto T, Mustafa G, Nishiuchi T, Komatsu S. Comparative Analysis of the Effect of Inorganic and Organic Chemicals with Silver Nanoparticles on Soybean under Flooding Stress. Int J Mol Sci 2020; 21:E1300. [PMID: 32075105 PMCID: PMC7072913 DOI: 10.3390/ijms21041300] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/03/2020] [Accepted: 02/11/2020] [Indexed: 12/13/2022] Open
Abstract
Extensive utilization of silver nanoparticles (NPs) in agricultural products results in their interaction with other chemicals in the environment. To study the combined effects of silver NPs with nicotinic acid and potassium nitrate (KNO3), a gel-free/label-free proteomic technique was used. Root length/weight and hypocotyl length/weight of soybean were enhanced by silver NPs mixed with nicotinic acid and KNO3. Out of a total 6340 identified proteins, 351 proteins were significantly changed, out of which 247 and 104 proteins increased and decreased, respectively. Differentially changed proteins were predominantly associated with protein degradation and synthesis according to the functional categorization. Protein-degradation-related proteins mainly consisted of the proteasome degradation pathway. The cell death was significantly higher in the root tips of soybean under the combined treatment compared to flooding stress. Accumulation of calnexin/calreticulin and glycoproteins was significantly increased under flooding with silver NPs, nicotinic acid, and KNO3. Growth of soybean seedlings with silver NPs, nicotinic acid, and KNO3 was improved under flooding stress. These results suggest that the combined mixture of silver NPs, nicotinic acid, and KNO3 causes positive effects on soybean seedling by regulating the protein quality control for the mis-folded proteins in the endoplasmic reticulum. Therefore, it might improve the growth of soybean under flooding stress.
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Affiliation(s)
- Takuya Hashimoto
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan; (T.H.); (G.M.)
| | - Ghazala Mustafa
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan; (T.H.); (G.M.)
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Takumi Nishiuchi
- Institute for Gene Research, Kanazawa University, Kanazawa 920-8640, Japan;
| | - Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan; (T.H.); (G.M.)
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Jia H, Zhang J, Li J, Sun P, Zhang Y, Xin X, Lu M, Hu J. Genome-wide transcriptomic analysis of a desert willow, Salix psammophila, reveals the function of hub genes SpMDP1 and SpWRKY33 in drought tolerance. BMC PLANT BIOLOGY 2019; 19:356. [PMID: 31416414 PMCID: PMC6694639 DOI: 10.1186/s12870-019-1900-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 06/20/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND Drought is a major environmental constraint to plant growth, development and productivity. Compared with most willows that are generally susceptible to drought, the desert willow Salix psammophila has extraordinary adaptation to drought stress. However, its molecular basis of drought tolerance is still largely unknown. RESULTS During polyethylene glycol 6000 (PEG 6000)-simulated drought stress, we found that the osmotic adjustment substances were accumulated and the antioxidant enzyme activities were enhanced in S. psammophila roots. A total of 8172 differentially expressed genes were identified in roots of S. psammophila through RNA-Sequencing. Based on K-means clustering, their expression patterns were classified into nine clusters, which were enriched in several stress-related processes including transcriptional regulation, response to various stresses, cell death, etc. Moreover, 672 transcription factors from 45 gene families were differentially expressed under drought stress. Furthermore, a weighted gene co-expression network was constructed, and eight genes were identified as hub genes. We demonstrated the function of two hub genes, magnesium-dependent phosphatase 1 (SpMDP1) and SpWRKY33, through overexpression in Arabidopsis thaliana. Overexpression of the two hub genes enhanced the drought tolerance in transgenic plants, suggesting that the identification of candidate drought tolerance genes in this study was highly efficient and credible. CONCLUSIONS Our study analyzed the physiological and molecular responses to drought stress in S. psammophila, and these results contribute to dissect the mechanism of drought tolerance of S. psammophila and facilitate identification of critical genes involved in drought tolerance for willow breeding.
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Affiliation(s)
- Huixia Jia
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Jin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Jianbo Li
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing, 102300 China
| | - Pei Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Yahong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Xuebing Xin
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing, 102300 China
| | - Mengzhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
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Neves DM, Santana-Vieira DDS, Dória MS, Freschi L, Ferreira CF, Soares Filho WDS, Costa MGC, Coelho Filho MA, Micheli F, Gesteira ADS. Recurrent water deficit causes alterations in the profile of redox proteins in citrus plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 132:497-507. [PMID: 30292982 DOI: 10.1016/j.plaphy.2018.09.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 06/08/2023]
Abstract
Plant acclimation to recurrent stress involves profound alterations in multiple genetic, metabolic and physiological processes. Stressful conditions usually implicate imbalance in reactive oxygen species (ROS) production and removal rates, which may lead to oxidative stress. However, the primary cellular targets of oxidative stress and their relevance in plant acclimation to abiotic stresses remains poorly characterized. By comparing redox proteomic and sugar profiles in citrus Valencia (VO) scions grafted onto two rootstocks with different soil water extraction capacities - Rangpur Lime (RL) and Sunki Maravilha (SM) - here we demonstrate that both ROS-mediated post-translational protein modification and changes in sugar composition are associated with acclimation to recurrent drought in citrus. The redox proteomic analysis of the distinct scion/rootstock combinations exposed to one (WD1), two (WD2) or three (WD3) water deficit episodes revealed a total of 32 and 55 redox protein spots present in VO/RL and VO/SM plants, respectively. Mass spectrometry analysis of these protein spots revealed essential targets of ROS-mediated posttranslational protein modification in citrus plants challenged by recurrent drought. The oxidation of cysteine thiol groups into glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was shown to increase in WD3 samples of the VO/RL combination, whereas the opposite was observed for the VO/SM combination. Similarly, recurrent drought promoted the oxidation of catalase thiol groups in VO/SM, but not in VO/RL. Carbohydrate profiling revealed that glucose, fructose and galactose may also contribute to the phenotypic differences observed between the citrus genotypes exposed to drought. These findings reveal for the first time that recurrent drought differentially affects the profile of redox proteomics of citrus, suggesting that this alteration may be part of the stress memory in perennial plants.
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Affiliation(s)
- Diana Matos Neves
- Departamento de Ciências Biológicas, Centro de Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | | | - Milena Santos Dória
- Departamento de Ciências Biológicas, Centro de Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Marcio Gilberto Cardoso Costa
- Departamento de Ciências Biológicas, Centro de Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | | | - Fabienne Micheli
- Departamento de Ciências Biológicas, Centro de Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil; CIRAD -UMR AGAP, Montpellier, France
| | - Abelmon da Silva Gesteira
- Departamento de Ciências Biológicas, Centro de Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil; Embrapa - Mandioca e Fruticultura, Cruz das Almas, Bahia, Brazil.
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