1
|
Olmos E, Jimenez-Perez B, Roman-Garcia I, Fernandez-Garcia N. Salt-tolerance mechanisms in quinoa: Is glycinebetaine the missing piece of the puzzle? PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108276. [PMID: 38118328 DOI: 10.1016/j.plaphy.2023.108276] [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: 09/06/2023] [Revised: 11/15/2023] [Accepted: 12/08/2023] [Indexed: 12/22/2023]
Abstract
Salinization of arable land has been progressively increasing, which, along with the effects of climate change, poses a serious risk to food production. Quinoa is a halophyte species that grows and is productive in highly saline soils. This study addresses the mechanisms of response and adaptation to high salinity. We show that the differential distribution of sodium in plants depends on the variety, observing that varieties such as Pandela Rosada limit the passage transit of sodium to the aerial part of the plant, a mechanism that seems to be regulated by sodium transporters such as HKT1s or SOS1. Like other halophytes of the Amaranthaceae family, quinoa plants have salt glands (bladder cells), which have been reported to play an important role in salt tolerance. However, our study shows that the contribution of bladder glands to salt accumulation is rather low. The 1H-NMR metabolome study of quinoa subjected to salt stress showed important modifications in the contents of amino acids, sugars, organic acids, and quaternary ammonium compounds (glycinebetaine). The compound with a higher presence was glycinebetaine, which makes up 6% of the leaf dry matter under saline conditions. Our findings suggest that glycinebetaine can act as an osmolyte and/or osmoprotectant, facilitating plant development under high saline ambient.
Collapse
Affiliation(s)
- E Olmos
- Departamento de Biología del Estrés y Patología Vegetal. CEBAS-CSIC Campus Universitario de Espinardo, Edificio 25, 30100 Murcia Spain.
| | - B Jimenez-Perez
- Departamento de Biología del Estrés y Patología Vegetal. CEBAS-CSIC Campus Universitario de Espinardo, Edificio 25, 30100 Murcia Spain.
| | - I Roman-Garcia
- Departamento de Biología del Estrés y Patología Vegetal. CEBAS-CSIC Campus Universitario de Espinardo, Edificio 25, 30100 Murcia Spain.
| | - N Fernandez-Garcia
- Departamento de Biología del Estrés y Patología Vegetal. CEBAS-CSIC Campus Universitario de Espinardo, Edificio 25, 30100 Murcia Spain.
| |
Collapse
|
2
|
Rey E, Maughan PJ, Maumus F, Lewis D, Wilson L, Fuller J, Schmöckel SM, Jellen EN, Tester M, Jarvis DE. A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes. Commun Biol 2023; 6:1263. [PMID: 38092895 PMCID: PMC10719370 DOI: 10.1038/s42003-023-05613-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023] Open
Abstract
Quinoa (Chenopodium quinoa Willd.) is an allotetraploid seed crop with the potential to help address global food security concerns. Genomes have been assembled for four accessions of quinoa; however, all assemblies are fragmented and do not reflect known chromosome biology. Here, we use in vitro and in vivo Hi-C data to produce a chromosome-scale assembly of the Chilean accession PI 614886 (QQ74). The final assembly spans 1.326 Gb, of which 90.5% is assembled into 18 chromosome-scale scaffolds. The genome is annotated with 54,499 protein-coding genes, 96.9% of which are located on the 18 largest scaffolds. We also report an updated genome assembly for the B-genome diploid C. suecicum and use it, together with the A-genome diploid C. pallidicaule, to identify genomic rearrangements within the quinoa genome, including a large pericentromeric inversion representing 71.7% of chromosome Cq3B. Repetitive sequences comprise 65.2%, 48.6%, and 57.9% of the quinoa, C. pallidicaule, and C. suecicum genomes, respectively. Evidence suggests that the B subgenome is more dynamic and has expanded more than the A subgenome. These genomic resources will enable more accurate assessments of genome evolution within the Amaranthaceae and will facilitate future efforts to identify variation in genes underlying important agronomic traits in quinoa.
Collapse
Affiliation(s)
- Elodie Rey
- 1King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Peter J Maughan
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Daniel Lewis
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA
| | - Leanne Wilson
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA
| | - Juliana Fuller
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA
| | - Sandra M Schmöckel
- University of Hohenheim, Institute of Crop Science, Department Physiology of Yield Stability, 70599, Stuttgart, Germany
| | - Eric N Jellen
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA
| | - Mark Tester
- 1King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - David E Jarvis
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA.
| |
Collapse
|
3
|
Contreras E, Martín-Fernández L, Manaa A, Vicente-Carbajosa J, Iglesias-Fernández R. Identification of Reference Genes for Precise Expression Analysis during Germination in Chenopodium quinoa Seeds under Salt Stress. Int J Mol Sci 2023; 24:15878. [PMID: 37958860 PMCID: PMC10650251 DOI: 10.3390/ijms242115878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Chenopodium quinoa Willd. (quinoa), a member of the Amaranthaceae family, is an allotetraploid annual plant, endemic to South America. The plant of C. quinoa presents significant ecological plasticity with exceptional adaptability to several environmental stresses, including salinity. The resilience of quinoa to several abiotic stresses, as well as its nutritional attributes, have led to significant shifts in quinoa cultivation worldwide over the past century. This work first defines germination sensu stricto in quinoa where the breakage of the pericarp and the testa is followed by endosperm rupture (ER). Transcriptomic changes in early seed germination stages lead to unstable expression levels in commonly used reference genes that are typically stable in vegetative tissues. Noteworthy, no suitable reference genes have been previously identified specifically for quinoa seed germination under salt stress conditions. This work aims to identify these genes as a prerequisite step for normalizing qPCR data. To this end, germinating seeds from UDEC2 and UDEC4 accessions, with different tolerance to salt, have been analyzed under conditions of absence (0 mM NaCl) and in the presence (250 mM NaCl) of sodium chloride. Based on the relevant literature, six candidate reference genes, Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Monensin sensitivity1 (MON1), Polypyrimidine tract-binding protein (PTB), Actin-7 (ACT7), Ubiquitin-conjugating enzyme (UBC), and 18S ribosomal RNA (18S), were selected and assessed for stability using the RefFinder Tool encompassing the statistical algorithms geNorm, NormFinder, BestKeeper, and ΔCt in the evaluation. The data presented support the suitability of CqACT7 and CqUBC as reference genes for normalizing gene expression during seed germination under salinity stress. These recommended reference genes can be valuable tools for consistent qPCR studies on quinoa seeds.
Collapse
Affiliation(s)
- Estefanía Contreras
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (E.C.); (J.V.-C.)
| | - Lucía Martín-Fernández
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (E.C.); (J.V.-C.)
| | - Arafet Manaa
- Laboratory of Extremophile Plants, Centre of Biotechnology de Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia;
| | - Jesús Vicente-Carbajosa
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (E.C.); (J.V.-C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas (UPM), 28040 Madrid, Spain
| | - Raquel Iglesias-Fernández
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (E.C.); (J.V.-C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas (UPM), 28040 Madrid, Spain
| |
Collapse
|
4
|
Bhardwaj R, Yadav R, Vishwakarma H, Sharma K, Chandora R, Rana JC, Riar A. Agro-morphological and nutritional assessment of chenopod and quinoa germplasm-Highly adaptable potential crops. Food Sci Nutr 2023; 11:5446-5459. [PMID: 37701188 PMCID: PMC10494622 DOI: 10.1002/fsn3.3502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 05/12/2023] [Accepted: 05/24/2023] [Indexed: 09/14/2023] Open
Abstract
Quinoa belongs to the family Chenopodiaceae, a pseudo-grain having high nutritional value and is considered an underexploited vegetable crop with the potential to improve the nutritional security of millions. Therefore, assessing genetic diversity in Chenopodium germplasm to untap nutritional and site-specific adaptation potential would be of prime importance for breeders/researchers. The present study used 10 accessions of two Chenopodium species, that is, C. quinoa and C. album. Quantitative and qualitative phenotypic traits, proximate composition, minerals, and amino acids profiles were studied to compare the differences in nutritional value and extent of genetic diversity between these two species. Our results showed significant variation existed in yield attributing agro-morphological traits. All the traits were considered for hierarchical clustering and principal components analysis. Large genetic variability was observed in traits of Chenopodium accessions. The protein, dietary fiber, oil, and sugar content ranged from 16.6% to 19.7%, 16.8% to 26%, 3.54% to 8.46%, and 3.74% to 5.64%, respectively. The results showed that C. album and C. quinoa seeds had good nutritional value and health-promoting benefits. The C. quinoa was slightly ahead of than C. album in terms of nutritional value, but C. album accession IC415477 was at par for higher test weight, seed yield (117.02 g/plant), and other nutritional parameters with C. quinoa accessions. IC415477 and other potential accessions observed in this study may be taken up by breeders/researchers in the near future to dissect nutritional value of Chenopodium and related species for dietary diversity, which is imperative for the nutritional security of the ever-growing world's population.
Collapse
Affiliation(s)
- Rakesh Bhardwaj
- ICAR– National Bureau of Plant Genetic ResourcesNew DelhiIndia
| | - Rashmi Yadav
- ICAR– National Bureau of Plant Genetic ResourcesNew DelhiIndia
| | | | - Kriti Sharma
- ICAR– National Bureau of Plant Genetic ResourcesNew DelhiIndia
| | - Rahul Chandora
- ICAR– National Bureau of Plant Genetic ResourcesNew DelhiIndia
| | - Jai Chand Rana
- Alliance of Bioversity International and CIATNew DelhiIndia
| | - Amritbir Riar
- Department of International CooperationResearch Institute of Organic Agriculture FiBLFrickSwitzerland
| |
Collapse
|
5
|
Liu Y, Wang M, Huang Y, Zhu P, Qian G, Zhang Y, Li L. Genome-Wide Identification and Analysis of R2R3-MYB Genes Response to Saline-Alkali Stress in Quinoa. Int J Mol Sci 2023; 24:ijms24119132. [PMID: 37298082 DOI: 10.3390/ijms24119132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
Soil saline-alkalization inhibits plant growth and development and seriously affects crop yields. Over their long-term evolution, plants have formed complex stress response systems to maintain species continuity. R2R3-MYB transcription factors are one of the largest transcription factor families in plants, widely involved in plant growth and development, metabolism, and stress response. Quinoa (Chenopodium quinoa Willd.), as a crop with high nutritional value, is tolerant to various biotic and abiotic stress. In this study, we identified 65 R2R3-MYB genes in quinoa, which are divided into 26 subfamilies. In addition, we analyzed the evolutionary relationships, protein physicochemical properties, conserved domains and motifs, gene structure, and cis-regulatory elements of CqR2R3-MYB family members. To investigate the roles of CqR2R3-MYB transcription factors in abiotic stress response, we performed transcriptome analysis to figure out the expression file of CqR2R3-MYB genes under saline-alkali stress. The results indicate that the expression of the six CqMYB2R genes was altered significantly in quinoa leaves that had undergone saline-alkali stress. Subcellular localization and transcriptional activation activity analysis revealed that CqMYB2R09, CqMYB2R16, CqMYB2R25, and CqMYB2R62, whose Arabidopsis homologues are involved in salt stress response, are localized in the nucleus and exhibit transcriptional activation activity. Our study provides basic information and effective clues for further functional investigation of CqR2R3-MYB transcription factors in quinoa.
Collapse
Affiliation(s)
- Yuqi Liu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Mingyu Wang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Yongshun Huang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Peng Zhu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Guangtao Qian
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Yiming Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Lixin Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| |
Collapse
|
6
|
Hosseini SS, Ramezanpour SS, Soltanloo H, Seifati SE. RNA-seq analysis and reconstruction of gene networks involved in response to salinity stress in quinoa (cv. Titicaca). Sci Rep 2023; 13:7308. [PMID: 37147414 PMCID: PMC10163252 DOI: 10.1038/s41598-023-34534-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/03/2023] [Indexed: 05/07/2023] Open
Abstract
To better understand the mechanisms involved in salinity stress, the adaptability of quinoa cv. Titicaca-a halophytic plant-was investigated at the transcriptome level under saline and non-saline conditions. RNA-sequencing analysis of leaf tissue at the four-leaf stage by Illumina paired-end method was used to compare salt stress treatment (four days after stress at 13.8 dsm-1) and control. Among the obtained 30,846,354 transcripts sequenced, 30,303 differentially expressed genes from the control and stress treatment samples were identified, with 3363 genes expressed ≥ 2 and false discovery rate (FDR) of < 0.001. Six differential expression genes were then selected and qRT-PCR was used to confirm the RNA-seq results. Some of the genes (Include; CML39, CBSX5, TRX1, GRXC9, SnRKγ1 and BAG6) and signaling pathways discussed in this paper not been previously studied in quinoa. Genes with ≥ 2 were used to design the gene interaction network using Cytoscape software, and AgriGO software and STRING database were used for gene ontology. The results led to the identification of 14 key genes involved in salt stress. The most effective hub genes involved in salt tolerance were the heat shock protein gene family. The transcription factors that showed a significant increase in expression under stress conditions mainly belonged to the WRKY, bZIP and MYB families. Ontology analysis of salt stress-responsive genes and hub genes revealed that metabolic pathways, binding, cellular processes and cellular anatomical entity are among the most effective processes involved in salt stress.
Collapse
Affiliation(s)
- Sahar Sadat Hosseini
- Department of Plant Breeding and Plant Biotechnology, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Golestan, Iran
| | - Seyedeh Sanaz Ramezanpour
- Department of Plant Breeding and Plant Biotechnology, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Golestan, Iran.
| | - Hassan Soltanloo
- Department of Arid Land and Desert Management, School of Natural Resources and Desert Studies, Yazd University, Yazd, Iran
| | - Seyed Ebrahim Seifati
- Department of Arid Land and Desert Management, School of Natural Resources and Desert Studies, Yazd University, Yazd, Iran
| |
Collapse
|
7
|
Ren Y, Ma R, Fan Y, Zhao B, Cheng P, Fan Y, Wang B. Genome-wide identification and expression analysis of the SPL transcription factor family and its response to abiotic stress in Quinoa (Chenopodium quinoa). BMC Genomics 2022; 23:773. [PMID: 36434504 PMCID: PMC9701020 DOI: 10.1186/s12864-022-08977-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/29/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Squamous promoter binding protein-like (SPL) proteins are a class of transcription factors that play essential roles in plant growth and development, signal transduction, and responses to biotic and abiotic stresses. The rapid development of whole genome sequencing has enabled the identification and characterization of SPL gene families in many plant species, but to date this has not been performed in quinoa (Chenopodium quinoa). RESULTS This study identified 23 SPL genes in quinoa, which were unevenly distributed on 18 quinoa chromosomes. Quinoa SPL genes were then classified into eight subfamilies based on homology to Arabidopsis thaliana SPL genes. We selected three dicotyledonous and monocotyledonous representative species, each associated with C. quinoa, for comparative sympatric mapping to better understand the evolution of the developmental mechanisms of the CqSPL family. Furthermore, we also used 15 representative genes from eight subfamilies to characterize CqSPLs gene expression in different tissues and at different fruit developmental stages under six different abiotic stress conditions. CONCLUSIONS This study, the first to identify and characterize SPL genes in quinoa, reported that CqSPL genes, especially CqSPL1, play a critical role in quinoa development and in its response to various abiotic stresses.
Collapse
Affiliation(s)
- Yanyan Ren
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi People’s Republic of China
| | - Rui Ma
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi People’s Republic of China
| | - Yue Fan
- College of Food Science and Engineering, Xinjiang Institute of Technology, 843100 Aksu, P.R. China
| | - Bingjie Zhao
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi People’s Republic of China
| | - Peng Cheng
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi People’s Republic of China
| | - Yu Fan
- grid.411292.d0000 0004 1798 8975School of Food and Biological Engineering, Chengdu University, Longquanyi District, 610106 Chengdu, P.R. China
| | - Baotong Wang
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi People’s Republic of China
| |
Collapse
|
8
|
Zahoor S, Naz R, Keyani R, Roberts TH, Hassan MN, Yasmin H, Nosheen A, Farman S. Rhizosphere bacteria associated with Chenopodium quinoa promote resistance to Alternaria alternata in tomato. Sci Rep 2022; 12:19027. [PMID: 36347914 PMCID: PMC9643462 DOI: 10.1038/s41598-022-21857-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 10/04/2022] [Indexed: 11/09/2022] Open
Abstract
Microorganisms can interact with plants to promote plant growth and act as biocontrol agents. Associations with plant growth-promoting rhizobacteria (PGPR) enhance agricultural productivity by improving plant nutrition and enhancing protection from pathogens. Microbial applications can be an ideal substitute for pesticides or fungicides, which can pollute the environment and reduce biological diversity. In this study, we isolated 68 bacterial strains from the root-adhering soil of quinoa (Chenopodium quinoa) seedlings. Bacterial strains exhibited several PGPR activities in vitro, including nutrient solubilization, production of lytic enzymes (cellulase, pectinase and amylase) and siderophore synthesis. These bacteria were further found to suppress the mycelial growth of the fungal pathogen Alternaria alternata. Nine bacterial strains were selected with substantial antagonistic activity and plant growth-promotion potential. These strains were identified based on their 16S rRNA gene sequences and selected for in planta experiments with tomato (Solanum lycopersicum) to estimate their growth-promotion and disease-suppression activity. Among the selected strains, B. licheniformis and B. pumilus most effectively promoted tomato plant growth, decreased disease severity caused by A. alternata infection by enhancing the activities of antioxidant defense enzymes and contributed to induced systemic resistance. This investigation provides evidence for the effectiveness and viability of PGPR application, particularly of B. licheniformis and B. pumilus in tomato, to promote plant growth and induce systemic resistance, making these bacteria promising candidates for biofertilizers and biocontrol agents.
Collapse
Affiliation(s)
- Sidra Zahoor
- Department of Biosciences, COMSATS University Islamabad, Park Road, Chak Shahzad, Islamabad, Pakistan
| | - Rabia Naz
- Department of Biosciences, COMSATS University Islamabad, Park Road, Chak Shahzad, Islamabad, Pakistan.
| | - Rumana Keyani
- Department of Biosciences, COMSATS University Islamabad, Park Road, Chak Shahzad, Islamabad, Pakistan
| | - Thomas H Roberts
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Muhammad N Hassan
- Department of Biosciences, COMSATS University Islamabad, Park Road, Chak Shahzad, Islamabad, Pakistan
| | - Humaira Yasmin
- Department of Biosciences, COMSATS University Islamabad, Park Road, Chak Shahzad, Islamabad, Pakistan
| | - Asia Nosheen
- Department of Biosciences, COMSATS University Islamabad, Park Road, Chak Shahzad, Islamabad, Pakistan
| | - Saira Farman
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| |
Collapse
|
9
|
Shi P, Jiang R, Li B, Wang D, Fang D, Yin M, Yin M, Gu M. Genome-Wide Analysis and Expression Profiles of the VOZ Gene Family in Quinoa ( Chenopodium quinoa). Genes (Basel) 2022; 13:1695. [PMID: 36292580 PMCID: PMC9601790 DOI: 10.3390/genes13101695] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/19/2022] [Accepted: 09/19/2022] [Indexed: 11/26/2023] Open
Abstract
Vascular plant one zinc-finger (VOZ) proteins are a plant-specific transcription factor family and play important roles in plant development and stress responses. However, little is known about the VOZ genes in quinoa. In the present study, a genome-wide investigation of the VOZ gene family in quinoa was performed, including gene structures, conserved motifs, phylogeny, and expression profiles. A total of four quinoa VOZ genes distributed on three chromosomes were identified. Based on phylogenetic analysis, CqVOZ1 and CqVOZ3 belong to subfamily II, and CqVOZ2 and CqVOZ4 belong to subfamily III. Furthermore, the VOZ transcription factors of quinoa and sugarbeet were more closely related than other species. Except for CqVOZ3, all the other three CqVOZs have four exons and four introns. Analysis of conserved motifs indicated that each CqVOZ member contained seven common motifs. Multiple sequence alignment showed that the CqVOZ genes were highly conserved with consensus sequences, which might be plausibly significant for the preservation of structural integrity of the family proteins. Tissue expression analysis revealed that four CqVOZ genes were highly expressed in inflorescence and relatively low in leaves and stems, suggesting that these genes had obvious tissue expression specificity. The expression profiles of the quinoa CqVOZs under various abiotic stresses demonstrated that these genes were differentially induced by cold stress, salt stress, and drought stress. The transcript level of CqVOZ1 and CqVOZ4 were down-regulated by salt stress and drought stress, while CqVOZ2 and CqVOZ3 were up-regulated by cold, salt, and drought stress, which could be used as abiotic stress resistance candidate genes. This study systematically identifies the CqVOZ genes at the genome-wide level, contributing to a better understanding of the quinoa VOZ transcription factor family and laying a foundation for further exploring the molecular mechanism of development and stress resistance of quinoa.
Collapse
Affiliation(s)
- Pibiao Shi
- Xinyang Agricultural Experiment Station of Yancheng City, Jiangsu Academy of Agricultural Sciences, Yancheng 224049, China
| | - Runzhi Jiang
- Xinyang Agricultural Experiment Station of Yancheng City, Jiangsu Academy of Agricultural Sciences, Yancheng 224049, China
| | - Bin Li
- Xinyang Agricultural Experiment Station of Yancheng City, Jiangsu Academy of Agricultural Sciences, Yancheng 224049, China
| | - Deling Wang
- Xinyang Agricultural Experiment Station of Yancheng City, Jiangsu Academy of Agricultural Sciences, Yancheng 224049, China
| | - Di Fang
- Xinyang Agricultural Experiment Station of Yancheng City, Jiangsu Academy of Agricultural Sciences, Yancheng 224049, China
| | - Min Yin
- Xinyang Agricultural Experiment Station of Yancheng City, Jiangsu Academy of Agricultural Sciences, Yancheng 224049, China
| | - Mingming Yin
- Xinyang Agricultural Experiment Station of Yancheng City, Jiangsu Academy of Agricultural Sciences, Yancheng 224049, China
| | - Minfeng Gu
- Xinyang Agricultural Experiment Station of Yancheng City, Jiangsu Academy of Agricultural Sciences, Yancheng 224049, China
| |
Collapse
|
10
|
Luo C, He B, Shi P, Xi J, Gui H, Pang B, Cheng J, Hu F, Chen X, Lv Y. Transcriptome dynamics uncovers long non-coding RNAs response to salinity stress in Chenopodium quinoa. FRONTIERS IN PLANT SCIENCE 2022; 13:988845. [PMID: 36204077 PMCID: PMC9530330 DOI: 10.3389/fpls.2022.988845] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/24/2022] [Indexed: 06/01/2023]
Abstract
Chenopodium quinoa is a crop with outstanding tolerance to saline soil, but long non-coding RNAs (LncRNAs) expression profile driven by salt stress in quinoa has rarely been observed yet. Based on the high-quality quinoa reference genome and high-throughput RNA sequencing (RNA-seq), genome-wide identification of LncRNAs was performed, and their dynamic response under salt stress was then investigated. In total, 153,751 high-confidence LncRNAs were discovered and dispersed intensively in chromosomes. Expression profile analysis demonstrated significant differences between LncRNAs and coding RNAs. Under salt stress conditions, 4,460 differentially expressed LncRNAs were discovered, of which only 54 were differentially expressed at all the stress time points. Besides, strongly significantly correlation was observed between salt-responsive LncRNAs and their closest neighboring genes (r = 0.346, p-value < 2.2e-16). Furthermore, a weighted co-expression network was then constructed to infer the potential biological functions of LncRNAs. Seven modules were significantly correlated with salt treatments, resulting in 210 hub genes, including 22 transcription factors and 70 LncRNAs. These results indicated that LncRNAs might interact with transcription factors to respond to salinity stress. Gene ontology enrichment of the coding genes of these modules showed that they were highly related to regulating metabolic processes, biological regulation and response to stress. This study is the genome-wide analysis of the LncRNAs responding to salt stress in quinoa. The findings will provide a solid framework for further functional research of salt responsive LncRNAs, contributing to quinoa genetic improvement.
Collapse
Affiliation(s)
- Chuping Luo
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Bing He
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Pibiao Shi
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jinlong Xi
- Zhejiang Institute of Standardization, Hangzhou, China
| | - Hongbing Gui
- College of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, China
| | - Bingwen Pang
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, China
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junjie Cheng
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, China
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Fengqin Hu
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xi Chen
- School of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Jurong, China
| | - Yuanda Lv
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, China
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| |
Collapse
|
11
|
Full-Length Transcriptome Sequencing Reveals the Impact of Cold Stress on Alternative Splicing in Quinoa. Int J Mol Sci 2022; 23:ijms23105724. [PMID: 35628539 PMCID: PMC9144462 DOI: 10.3390/ijms23105724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/04/2023] Open
Abstract
Quinoa is a cold-resistant and nutrient-rich crop. To decipher the cold stress response of quinoa, the full-length transcriptomes of the cold-resistant quinoa variety CRQ64 and the cold-sensitive quinoa variety CSQ5 were compared. We identified 55,389 novel isoforms and 6432 novel genes in these transcriptomes. Under cold stress, CRQ64 had more differentially expressed genes (DEGs) and differentially alternative splicing events compared to non-stress conditions than CSQ5. DEGs that were specifically present only in CRQ64 were significantly enriched in processes which contribute to osmoregulation and ROS homeostasis in plants, such as sucrose metabolism and phenylpropanoid biosynthesis. More genes with differential alternative splicing under cold stress were enriched in peroxidase functions in CRQ64. In total, 5988 transcription factors and 2956 long non-coding RNAs (LncRNAs) were detected in this dataset. Many of these had altered expression patterns under cold stress compared to non-stress conditions. Our transcriptome results demonstrate that CRQ64 undergoes a wider stress response than CSQ5 under cold stress. Our results improved the annotation of the quinoa genome and provide new insight into the mechanisms of cold resistance in quinoa.
Collapse
|
12
|
Tovar JC, Berry JC, Quillatupa C, Castillo SE, Acosta‐Gamboa L, Fahlgren N, Gehan MA. Heat stress changes mineral nutrient concentrations in Chenopodium quinoa seed. PLANT DIRECT 2022; 6:e384. [PMID: 35146239 PMCID: PMC8818816 DOI: 10.1002/pld3.384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/04/2022] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Quinoa is a popular seed crop, often consumed for its high nutritional quality. We studied how heat stress in the roots or the shoots of quinoa plants affected the concentrations of 20 elements (aluminum, arsenic, boron, calcium, cadmium, cobalt, copper, iron, potassium, magnesium, manganese, molybdenum, sodium, nickel, phosphorous, rubidium, sulfur, selenium, strontium, and zinc) in quinoa seed. Elemental concentrations in quinoa seed were significantly changed after an 11-day heat treatment during anthesis. The type of panicle (main, secondary, and tertiary) sampled and the type of heat treatment (root only, shoot only, or whole plants) significantly affected elemental profiles in quinoa seed. Plants were also divided into five sections from top to bottom to assess the effect of panicle position on seed elemental profiles. Plant section had an effect on the concentrations of arsenic, iron, and sodium under control conditions and on copper with heat treatment. Overall, the time of panicle development in relation to the time of heat exposure had the largest effect on seed elemental concentrations. Interestingly, the quinoa plants were exposed to heat only during anthesis of the main panicle, but the elemental concentrations of seeds produced after heat treatment ended were still significantly changed, indicating that heat stress has long-lasting effects on quinoa plants. These findings demonstrate how the nutritional quality of quinoa seeds can be changed significantly even by relatively short heat spells.
Collapse
|
13
|
Grimberg Å, Saripella GV, Repo-Carrasco Valencia RAM, Bengtsson T, Alandia G, Carlsson AS. Transcriptional Regulation of Quinoa Seed Quality: Identification of Novel Candidate Genetic Markers for Increased Protein Content. FRONTIERS IN PLANT SCIENCE 2022; 13:816425. [PMID: 35720573 PMCID: PMC9201758 DOI: 10.3389/fpls.2022.816425] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/12/2022] [Indexed: 05/11/2023]
Abstract
Quinoa (Chenopodium quinoa Willd.) is a crop that has great potential for increased cultivation in diverse climate regions. The seed protein quality obtained from this crop is high concerning the requirements to meet human nutritional needs, but the seed protein content is relatively low if compared to crops such as grain legumes. Increased seed protein content is desirable for increasing the economic viability of this crop in order for it to be used as a protein crop. In this study, we characterized three genotypes of quinoa with different levels of seed protein content. By performing RNA sequencing of developing seeds, we determined the genotype differences in gene expression and identified genetic polymorphisms that could be associated with increased protein content. Storage nutrient analyses of seeds of three quinoa genotypes (Titicaca, Pasankalla, and Regalona) from different ecoregions grown under controlled climate conditions showed that Pasankalla had the highest protein content (20%) and the lowest starch content (46%). Our seed transcriptome analyses revealed highly differentially expressed transcripts (DETs) in Pasankalla as compared to the other genotypes. These DETs encoded functions in sugar transport, starch and protein synthesis, genes regulating embryo size, and seed transcription factors. We selected 60 genes that encode functions in the central carbon metabolism and transcription factors as potential targets for the development of high-precision markers. Genetic polymorphisms, such as single nucleotide polymorphisms (SNPs) and base insertions and deletions (InDels), were found in 19 of the 60 selected genes, which can be further evaluated for the development of genetic markers for high seed protein content in quinoa. Increased cultivation of quinoa can contribute to a more diversified agriculture and support the plant protein diet shift. The identification of quinoa genotypes with contrasting seed quality can help establish a model system that can be used for the identification of precise breeding targets to improve the seed quality of quinoa. The data presented in this study based on nutrient and transcriptome analyses contribute to an enhanced understanding of the genetic regulation of seed quality traits in quinoa and suggest high-precision candidate markers for such traits.
Collapse
Affiliation(s)
- Åsa Grimberg
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
- *Correspondence: Åsa Grimberg,
| | | | | | - Therése Bengtsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Gabriela Alandia
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders S. Carlsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| |
Collapse
|
14
|
Abd El-Moneim D, ELsarag EIS, Aloufi S, El-Azraq AM, ALshamrani SM, Safhi FAA, Ibrahim AA. Quinoa ( Chenopodium quinoa Willd.): Genetic Diversity According to ISSR and SCoT Markers, Relative Gene Expression, and Morpho-Physiological Variation under Salinity Stress. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122802. [PMID: 34961273 PMCID: PMC8707205 DOI: 10.3390/plants10122802] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/08/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Quinoa (Chenopodium quinoa Willd.) is a halophytic crop that can withstand a variety of abiotic stresses, including salt. The present research examined the mechanisms of salt tolerance in five different quinoa genotypes at four different salinity levels (control (60), 80, 120, and 160 mM NaCl). ISSR and SCoT analysis revealed high polymorphism percentages of 90.91% and 85.26%, respectively. Furthermore, ISSR 1 and SCoT 7 attained the greatest number of polymorphic amplicons (27 and 26), respectively. Notably, LINE-6 and M-28 genotypes demonstrated the greatest number of unique positive and negative amplicons (50 and 42) generated from ISSR and SCoT, respectively. Protein pattern analysis detected 11 bands with a polymorphism percentage 27.27% among the quinoa genotypes, with three unique bands distinguishable for the M-28 genotype. Similarity correlation indicated that the highest similarity was between S-10 and Regeolone-3 (0.657), while the lowest similarity was between M-28 and LINE-6 (0.44). Significant variations existed among the studied salinity treatments, genotypes, and the interactions between them. The highest and lowest values for all the studied morpho-physiological and biochemical traits were recorded at 60 and 160 mM NaCl concentrations, respectively, except for the Na and proline contents, which exhibited the opposite relationship. The M-28 genotype demonstrated the highest values for all studied characteristics, while the LINE-6 genotype represented the lowest in both seasons. On the other hand, mRNA transcript levels for CqSOS1 did not exhibit differential expression in roots and leaf tissues, while the expression of CqNHX1 was upregulated more in both tissues for the M-28 genotype than for the LINE-6 genotype, and its maximum induction was seen in the leaves. Overall, the genotypes M-28 and LINE-6 were identified as the most and least salinity-tolerant, respectively.
Collapse
Affiliation(s)
- Diaa Abd El-Moneim
- Department of Plant Production (Genetic Branch), Faculty of Environmental and Agricultural Sciences, Arish University, El-Arish 45511, Egypt
| | - Eman I. S. ELsarag
- Department of Plant Production (Agronomy Branch), Faculty of Environmental and Agricultural Sciences, Arish University, El-Arish 45511, Egypt; (E.I.S.E.); (A.M.E.-A.)
| | - Salman Aloufi
- Department of Biotechnology, Faculty of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Asmaa M. El-Azraq
- Department of Plant Production (Agronomy Branch), Faculty of Environmental and Agricultural Sciences, Arish University, El-Arish 45511, Egypt; (E.I.S.E.); (A.M.E.-A.)
| | - Salha Mesfer ALshamrani
- Department of Biology, College of Science, University of Jeddah, Jeddah 21959, Saudi Arabia;
| | - Fatmah Ahmed Ahmed Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia;
| | - Amira A. Ibrahim
- Plant Protection and Biomolecular Diagnosis Department, Arid Lands Cultivation Research Institute, City of Scientific Research and Technological Applications, New Borg El-Arab, Alexandria 21934, Egypt
| |
Collapse
|
15
|
Vita F, Ghignone S, Bazihizina N, Rasouli F, Sabbatini L, Kiani-Pouya A, Kiferle C, Shabala S, Balestrini R, Mancuso S. Early responses to salt stress in quinoa genotypes with opposite behavior. PHYSIOLOGIA PLANTARUM 2021; 173:1392-1420. [PMID: 33847396 DOI: 10.1111/ppl.13425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/17/2021] [Accepted: 04/10/2021] [Indexed: 06/12/2023]
Abstract
Soil salinity is among the major abiotic stresses that plants must cope with, mainly in arid and semiarid regions. The tolerance to high salinity is an important agronomic trait to sustain food production. Quinoa is a halophytic annual pseudo-cereal species with high nutritional value that can secrete salt out of young leaves in external non-glandular cells called epidermal bladder cells (EBC). Previous work showed high salt tolerance, but low EBC density was associated with an improved response in the early phases of salinity stress, mediated by tissue-tolerance traits mainly in roots. We compared the transcript profiling of two quinoa genotypes with contrasting salt tolerance patterning to identify the candidate genes involved in the differentially early response among genotypes. The transcriptome profiling, supported by in vitro physiological analyses, provided insights into the early-stage molecular mechanisms, both at the shoot and root level, based on the sensitive/tolerance traits. Results showed the presence of numerous differentially expressed genes among genotypes, tissues, and treatments, with genes involved in hormonal and stress response upregulated mainly in the sensitive genotype, suggesting that tolerance may be correlated to restricted changes in gene expression, at least after a short salt stress. These data, showing constitutive differences between the two genotypes, represent a solid basis for further studies to characterize the salt tolerance traits. Additionally, new information provided by this work might be useful for the development of plant breeding or genome engineering programs in quinoa.
Collapse
Affiliation(s)
- Federico Vita
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Stefano Ghignone
- National Research Council of Italy, Institute for Sustainable Plant Protection (CNR-IPSP), Torino, Italy
| | - Nadia Bazihizina
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Fatemeh Rasouli
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Australia
| | - Leonardo Sabbatini
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Ali Kiani-Pouya
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Australia
| | - Claudia Kiferle
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Raffaella Balestrini
- National Research Council of Italy, Institute for Sustainable Plant Protection (CNR-IPSP), Torino, Italy
| | - Stefano Mancuso
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| |
Collapse
|
16
|
Otterbach SL, Khoury H, Rupasinghe T, Mendis H, Kwan KH, Lui V, Natera SHA, Klaiber I, Allen NM, Jarvis DE, Tester M, Roessner U, Schmöckel SM. Characterization of epidermal bladder cells in Chenopodium quinoa. PLANT, CELL & ENVIRONMENT 2021; 44:3606-3622. [PMID: 34510479 DOI: 10.1111/pce.14181] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/01/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Chenopodium quinoa (quinoa) is considered a superfood with its favourable nutrient composition and being gluten free. Quinoa has high tolerance to abiotic stresses, such as salinity, water deficit (drought) and cold. The tolerance mechanisms are yet to be elucidated. Quinoa has epidermal bladder cells (EBCs) that densely cover the shoot surface, particularly the younger parts of the plant. Here, we report on the EBC's primary and secondary metabolomes, as well as the lipidome in control conditions and in response to abiotic stresses. EBCs were isolated from plants after cold, heat, high-light, water deficit and salt treatments. We used untargeted gas chromatography-mass spectrometry (GC-MS) to analyse metabolites and untargeted and targeted liquid chromatography-MS (LC-MS) for lipids and secondary metabolite analyses. We identified 64 primary metabolites, including sugars, organic acids and amino acids, 19 secondary metabolites, including phenolic compounds, betanin and saponins and 240 lipids categorized in five groups including glycerolipids and phospholipids. We found only few changes in the metabolic composition of EBCs in response to abiotic stresses; these were metabolites related with heat, cold and high-light treatments but not salt stress. Na+ concentrations were low in EBCs with all treatments and approximately two orders of magnitude lower than K+ concentrations.
Collapse
Affiliation(s)
- Sophie L Otterbach
- Department Physiology of Yield Stability, Institute Crop Science, Faculty of Agriculture, University of Hohenheim, Stuttgart, Germany
| | - Holly Khoury
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Thusitha Rupasinghe
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Himasha Mendis
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Kim H Kwan
- Metabolomics Australia, The University of Melbourne, Parkville, Victoria, Australia
| | - Veronica Lui
- Metabolomics Australia, The University of Melbourne, Parkville, Victoria, Australia
| | - Siria H A Natera
- Metabolomics Australia, The University of Melbourne, Parkville, Victoria, Australia
| | - Iris Klaiber
- Core Facility Hohenheim (640). Mass Spectrometry Unit, University of Hohenheim, Stuttgart, Germany
| | - Nathaniel M Allen
- Department Physiology of Yield Stability, Institute Crop Science, Faculty of Agriculture, University of Hohenheim, Stuttgart, Germany
| | - David E Jarvis
- Department of Plant and Wildlife Sciences, College of Life Sciences, Brigham Young University, Provo, Utah, USA
| | - Mark Tester
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ute Roessner
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Sandra M Schmöckel
- Department Physiology of Yield Stability, Institute Crop Science, Faculty of Agriculture, University of Hohenheim, Stuttgart, Germany
| |
Collapse
|
17
|
Ma Q, Su C, Dong CH. Genome-Wide Transcriptomic and Proteomic Exploration of Molecular Regulations in Quinoa Responses to Ethylene and Salt Stress. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112281. [PMID: 34834644 PMCID: PMC8625574 DOI: 10.3390/plants10112281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 06/02/2023]
Abstract
Quinoa (Chenopodiumquinoa Willd.), originated from the Andean region of South America, shows more significant salt tolerance than other crops. To reveal how the plant hormone ethylene is involved in the quinoa responses to salt stress, 4-week-old quinoa seedlings of 'NL-6' treated with water, sodium chloride (NaCl), and NaCl with ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) were collected and analyzed by transcriptional sequencing and tandem mass tag-based (TMT) quantitative proteomics. A total of 9672 proteins and 60,602 genes was identified. Among them, the genes encoding glutathione S-transferase (GST), peroxidase (POD), phosphate transporter (PT), glucan endonuclease (GLU), beta-galactosidase (BGAL), cellulose synthase (CES), trichome birefringence-like protein (TBL), glycine-rich cell wall structural protein (GRP), glucosyltransferase (GT), GDSL esterase/lipase (GELP), cytochrome P450 (CYP), and jasmonate-induced protein (JIP) were significantly differentially expressed. Further analysis suggested that the genes may mediate through osmotic adjustment, cell wall organization, reactive oxygen species (ROS) scavenging, and plant hormone signaling to take a part in the regulation of quinoa responses to ethylene and salt stress. Our results provide a strong foundation for exploration of the molecular mechanisms of quinoa responses to ethylene and salt stress.
Collapse
Affiliation(s)
- Qian Ma
- Correspondence: (Q.M.); (C.-H.D.); Tel.: +86-53258957640 (Q.M.); +86-53258957640 (C.-H.D.)
| | | | - Chun-Hai Dong
- Correspondence: (Q.M.); (C.-H.D.); Tel.: +86-53258957640 (Q.M.); +86-53258957640 (C.-H.D.)
| |
Collapse
|
18
|
Mizuno N, Toyoshima M, Fujita M, Fukuda S, Kobayashi Y, Ueno M, Tanaka K, Tanaka T, Nishihara E, Mizukoshi H, Yasui Y, Fujita Y. The genotype-dependent phenotypic landscape of quinoa in salt tolerance and key growth traits. DNA Res 2021; 27:5920640. [PMID: 33051662 PMCID: PMC7566363 DOI: 10.1093/dnares/dsaa022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/15/2020] [Indexed: 12/30/2022] Open
Abstract
Cultivation of quinoa (Chenopodium quinoa), an annual pseudocereal crop that originated in the Andes, is spreading globally. Because quinoa is highly nutritious and resistant to multiple abiotic stresses, it is emerging as a valuable crop to provide food and nutrition security worldwide. However, molecular analyses have been hindered by the genetic heterogeneity resulting from partial outcrossing. In this study, we generated 136 inbred quinoa lines as a basis for the molecular identification and characterization of gene functions in quinoa through genotyping and phenotyping. Following genotyping-by-sequencing analysis of the inbred lines, we selected 5,753 single-nucleotide polymorphisms (SNPs) in the quinoa genome. Based on these SNPs, we show that our quinoa inbred lines fall into three genetic sub-populations. Moreover, we measured phenotypes, such as salt tolerance and key growth traits in the inbred quinoa lines and generated a heatmap that provides a succinct overview of the genotype–phenotype relationship between inbred quinoa lines. We also demonstrate that, in contrast to northern highland lines, most lowland and southern highland lines can germinate even under high salinity conditions. These findings provide a basis for the molecular elucidation and genetic improvement of quinoa and improve our understanding of the evolutionary process underlying quinoa domestication.
Collapse
Affiliation(s)
- Nobuyuki Mizuno
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masami Toyoshima
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki 305-8686, Japan
| | - Miki Fujita
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki 305-0074, Japan
| | - Shota Fukuda
- Faculty of Agriculture, Tottori University, Tottori, Tottori 680-8550, Japan
| | - Yasufumi Kobayashi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki 305-8686, Japan
| | - Mariko Ueno
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kojiro Tanaka
- Technology Development Group, Actree Corporation, Hakusan, Ishikawa 924-0053, Japan
| | - Tsutomu Tanaka
- Technology Development Group, Actree Corporation, Hakusan, Ishikawa 924-0053, Japan
| | - Eiji Nishihara
- Faculty of Agriculture, Tottori University, Tottori, Tottori 680-8550, Japan
| | - Hiroharu Mizukoshi
- Technology Development Group, Actree Corporation, Hakusan, Ishikawa 924-0053, Japan
| | - Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yasunari Fujita
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki 305-8686, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| |
Collapse
|
19
|
Ogata T, Toyoshima M, Yamamizo-Oda C, Kobayashi Y, Fujii K, Tanaka K, Tanaka T, Mizukoshi H, Yasui Y, Nagatoshi Y, Yoshikawa N, Fujita Y. Virus-Mediated Transient Expression Techniques Enable Functional Genomics Studies and Modulations of Betalain Biosynthesis and Plant Height in Quinoa. FRONTIERS IN PLANT SCIENCE 2021; 12:643499. [PMID: 33815450 PMCID: PMC8014037 DOI: 10.3389/fpls.2021.643499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/11/2021] [Indexed: 05/24/2023]
Abstract
Quinoa (Chenopodium quinoa), native to the Andean region of South America, has been recognized as a potentially important crop in terms of global food and nutrition security since it can thrive in harsh environments and has an excellent nutritional profile. Even though challenges of analyzing the complex and heterogeneous allotetraploid genome of quinoa have recently been overcome, with the whole genome-sequencing of quinoa and the creation of genotyped inbred lines, the lack of technology to analyze gene function in planta is a major limiting factor in quinoa research. Here, we demonstrate that two virus-mediated transient expression techniques, virus-induced gene silencing (VIGS) and virus-mediated overexpression (VOX), can be used in quinoa. We show that apple latent spherical virus (ALSV) can induce gene silencing of quinoa phytoene desaturase (CqPDS1) in a broad range of quinoa inbred lines derived from the northern and southern highland and lowland sub-populations. In addition, we show that ALSV can be used as a VOX vector in roots. Our data also indicate that silencing a quinoa 3,4-dihydroxyphenylalanine 4,5-dioxygenase gene (CqDODA1) or a cytochrome P450 enzyme gene (CqCYP76AD1) inhibits betalain production and that knockdown of a reduced-height gene homolog (CqRHT1) causes an overgrowth phenotype in quinoa. Moreover, we show that ALSV can be transmitted to the progeny of quinoa plants. Thus, our findings enable functional genomics in quinoa, ushering in a new era of quinoa research.
Collapse
Affiliation(s)
- Takuya Ogata
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | - Masami Toyoshima
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | - Chihiro Yamamizo-Oda
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | - Yasufumi Kobayashi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | - Kenichiro Fujii
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | - Kojiro Tanaka
- Technology Development Group, Actree Corporation, Hakusan, Japan
| | - Tsutomu Tanaka
- Technology Development Group, Actree Corporation, Hakusan, Japan
| | | | - Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yukari Nagatoshi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | | | - Yasunari Fujita
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| |
Collapse
|
20
|
Shi P, Gu M. Transcriptome analysis and differential gene expression profiling of two contrasting quinoa genotypes in response to salt stress. BMC PLANT BIOLOGY 2020; 20:568. [PMID: 33380327 PMCID: PMC7774241 DOI: 10.1186/s12870-020-02753-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/24/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND Soil salinity is one of the major abiotic stress factors that affect crop growth and yield, which seriously restricts the sustainable development of agriculture. Quinoa is considered as one of the most promising crops in the future for its high nutrition value and strong adaptability to extreme weather and soil conditions. However, the molecular mechanisms underlying the adaptive response to salinity stress of quinoa remain poorly understood. To identify candidate genes related to salt tolerance, we performed reference-guided assembly and compared the gene expression in roots treated with 300 mM NaCl for 0, 0.5, 2, and 24 h of two contrasting quinoa genotypes differing in salt tolerance. RESULTS The salt-tolerant (ST) genotype displayed higher seed germination rate and plant survival rate, and stronger seedling growth potential as well than the salt-sensitive (SS) genotype under salt stress. An average of 38,510,203 high-quality clean reads were generated. Significant Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified to deeper understand the differential response. Transcriptome analysis indicated that salt-responsive genes in quinoa were mainly related to biosynthesis of secondary metabolites, alpha-Linolenic acid metabolism, plant hormone signal transduction, and metabolic pathways. Moreover, several pathways were significantly enriched amongst the differentially expressed genes (DEGs) in ST genotypes, such as phenylpropanoid biosynthesis, plant-pathogen interaction, isoquinoline alkaloid biosynthesis, and tyrosine metabolism. One hundred seventeen DEGs were common to various stages of both genotypes, identified as core salt-responsive genes, including some transcription factor members, like MYB, WRKY and NAC, and some plant hormone signal transduction related genes, like PYL, PP2C and TIFY10A, which play an important role in the adaptation to salt conditions of this species. The expression patterns of 21 DEGs were detected by quantitative real-time PCR (qRT-PCR) and confirmed the reliability of the RNA-Seq results. CONCLUSIONS We identified candidate genes involved in salt tolerance in quinoa, as well as some DEGs exclusively expressed in ST genotype. The DEGs common to both genotypes under salt stress may be the key genes for quinoa to adapt to salinity environment. These candidate genes regulate salt tolerance primarily by participating in reactive oxygen species (ROS) scavenging system, protein kinases biosynthesis, plant hormone signal transduction and other important biological processes. These findings provide theoretical basis for further understanding the regulation mechanism underlying salt tolerance network of quinoa, as well establish foundation for improving its tolerance to salinity in future breeding programs.
Collapse
Affiliation(s)
- Pibiao Shi
- Xinyang Agricultural Experiment Station of Yancheng City, Yancheng, 224049, Jiangsu, China
| | - Minfeng Gu
- Xinyang Agricultural Experiment Station of Yancheng City, Yancheng, 224049, Jiangsu, China.
| |
Collapse
|
21
|
Agro-Morphological, Yield and Quality Traits and Interrelationship with Yield Stability in Quinoa ( Chenopodium quinoa Willd.) Genotypes under Saline Marginal Environment. PLANTS 2020; 9:plants9121763. [PMID: 33322139 PMCID: PMC7764209 DOI: 10.3390/plants9121763] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/05/2020] [Accepted: 12/11/2020] [Indexed: 12/27/2022]
Abstract
Quinoa (Chenopodium quinoa Willd.) is a halophytic crop that shows resistance to multiple abiotic stresses, including salinity. In this study we investigated the salinity tolerance mechanisms of six contrasting quinoa cultivars belonging to the coastal region of Chile using agro-physiological parameters (plant height (PH), number of branches/plant (BN), number of panicles/plant (PN), panicle length (PL), biochemical traits (leaf C%, leaf N%, grain protein contents); harvest index and yield (seed yield and plant dry biomass (PDM) under three salinity levels (0, 10, and 20 d Sm-1 NaCl). The yield stability was evaluated through comparision of seed yield characteristics [(static environmental variance (S2) and dynamic Wricke's ecovalence (W2)]. Results showed that significant variations existed in agro-morphological and yield attributes. With increasing salinity levels, yield contributing parameters (number of panicles and panicle length) decreased. Salt stress reduced the leaf carbon and nitrogen contents. Genotypes Q21, and AMES13761 showed higher seed yield (2.30 t ha-1), more productivity and stability at various salinities as compared to the other genotypes. Salinity reduced seed yield to 44.48% and 60% at lower (10 dS m-1) and higher salinity (20 dS m-1), respectively. Grain protein content was highest in NSL106398 and lowest in Q29 when treated with saline water. Seed yield was positively correlated with PH, TB, HI, and C%. Significant and negative correlations were observed between N%, protein contents and seed yield. PH showed significant positive correlation with APL, HI, C% and C:N ratio. HI displayed positive correlations with C%, N% and protein content., All measured plant traits, except for C:N ratio, responded to salt in a genotype-specific way. Our results indicate that the genotypes (Q21 and AMES13761) proved their suitability under sandy desert soils of Dubai, UAE as they exhibited higher seed yield while NSL106398 showed an higher seed protein content. The present research highlights the need to preserve quinoa biodiversity for a better seedling establishment, survival and stable yield in the sandy desertic UAE environment.
Collapse
|
22
|
Li F, Liu J, Guo X, Yin L, Zhang H, Wen R. Genome-wide survey, characterization, and expression analysis of bZIP transcription factors in Chenopodium quinoa. BMC PLANT BIOLOGY 2020; 20:405. [PMID: 32873228 PMCID: PMC7466520 DOI: 10.1186/s12870-020-02620-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 08/25/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Chenopodium quinoa Willd. (quinoa) is a pseudocereal crop of the Amaranthaceae family and represents a promising species with the nutritional content and high tolerance to stressful environments, such as soils affected by high salinity. The basic leucine zipper (bZIP) transcription factor represents exclusively in eukaryotes and can be related to many biological processes. So far, the genomes of quinoa and 3 other Amaranthaceae crops (Spinacia oleracea, Beta vulgaris, and Amaranthus hypochondriacus) have been fully sequenced. However, information about the bZIPs in these Amaranthaceae species is limited, and genome-wide analysis of the bZIP family is lacking in quinoa. RESULTS We identified 94 bZIPs in quinoa (named as CqbZIP1-CqbZIP94). All the CqbZIPs were phylogenetically splitted into 12 distinct subfamilies. The proportion of CqbZIPs was different in each subfamily, and members within the same subgroup shared conserved exon-intron structures and protein motifs. Besides, 32 duplicated CqbZIP gene pairs were investigated, and the duplicated CqbZIPs had mainly undergone purifying selection pressure, which suggested that the functions of the duplicated CqbZIPs might not diverge much. Moreover, we identified the bZIP members in 3 other Amaranthaceae species, and 41, 32, and 16 orthologous gene pairs were identified between quinoa and S. oleracea, B. vulgaris, and A. hypochondriacus, respectively. Among them, most were a single copy being present in S. oleracea, B. vulgaris, and A. hypochondriacus, and two copies being present in allotetraploid quinoa. The function divergence within the bZIP orthologous genes might be limited. Additionally, 11 selected CqbZIPs had specific spatial expression patterns, and 6 of 11 CqbZIPs were up-regulated in response to salt stress. Among the selected CqbZIPs, 3 of 4 duplicated gene pairs shared similar expression patterns, suggesting that these duplicated genes might retain some essential functions during subsequent evolution. CONCLUSIONS The present study provided the first systematic analysis for the phylogenetic classification, motif and gene structure, expansion pattern, and expression profile of the bZIP family in quinoa. Our results would lay an important foundation for functional and evolutionary analysis of CqbZIPs, and provide promising candidate genes for further investigation in tissue specificity and their functional involvement in quinoa's resistance to salt stress.
Collapse
Affiliation(s)
- Feng Li
- College of Life Science, Shanxi Datong University, Datong, 037009, People's Republic of China
- Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Jianxia Liu
- College of Life Science, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Xuhu Guo
- College of Life Science, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Lili Yin
- College of Life Science, Shanxi Datong University, Datong, 037009, People's Republic of China
- Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Hongli Zhang
- College of Life Science, Shanxi Datong University, Datong, 037009, People's Republic of China
- Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Riyu Wen
- Maize Research Institute, Shanxi Academy of Agricultural Sciences, Xinzhou, 034000, People's Republic of China.
| |
Collapse
|
23
|
Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom ®CicerSNP Array in Chickpea. Int J Mol Sci 2020; 21:ijms21145058. [PMID: 32709160 PMCID: PMC7404205 DOI: 10.3390/ijms21145058] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/10/2020] [Accepted: 07/14/2020] [Indexed: 01/22/2023] Open
Abstract
Globally, chickpea production is severely affected by salinity stress. Understanding the genetic basis for salinity tolerance is important to develop salinity tolerant chickpeas. A recombinant inbred line (RIL) population developed using parental lines ICCV 10 (salt-tolerant) and DCP 92-3 (salt-sensitive) was screened under field conditions to collect information on agronomy, yield components, and stress tolerance indices. Genotyping data generated using Axiom®CicerSNP array was used to construct a linkage map comprising 1856 SNP markers spanning a distance of 1106.3 cM across eight chickpea chromosomes. Extensive analysis of the phenotyping and genotyping data identified 28 quantitative trait loci (QTLs) explaining up to 28.40% of the phenotypic variance in the population. We identified QTL clusters on CaLG03 and CaLG06, each harboring major QTLs for yield and yield component traits under salinity stress. The main-effect QTLs identified in these two clusters were associated with key genes such as calcium-dependent protein kinases, histidine kinases, cation proton antiporter, and WRKY and MYB transcription factors, which are known to impart salinity stress tolerance in crop plants. Molecular markers/genes associated with these major QTLs, after validation, will be useful to undertake marker-assisted breeding for developing better varieties with salinity tolerance.
Collapse
|
24
|
Guarino F, Ruiz KB, Castiglione S, Cicatelli A, Biondi S. The combined effect of Cr(III) and NaCl determines changes in metal uptake, nutrient content, and gene expression in quinoa (Chenopodium quinoa Willd.). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 193:110345. [PMID: 32092578 DOI: 10.1016/j.ecoenv.2020.110345] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/05/2020] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
Many areas of the world are affected simultaneously by salinity and heavy metal pollution. Halophytes are considered as useful candidates in remediation of such soils due to their ability to withstand both osmotic stress and ion toxicity deriving from high salt concentrations. Quinoa (Chenopodium quinoa Willd) is a halophyte with a high resistance to abiotic stresses (drought, salinity, frost), but its capacity to cope with heavy metals has not yet been fully investigated. In this pot experiment, we investigated phytoextraction capacity, effects on nutrient levels (P and Fe), and changes in gene expression in response to application of Cr(III) in quinoa plants grown on saline or non-saline soil. Plants were exposed for three weeks to 500 mg kg-1 soil of Cr(NO3)3·9H2O either in the presence or absence of 150 mM NaCl. Results show that plants were able tolerate this soil concentration of Cr(III); the metal was mainly accumulated in roots where it reached the highest concentration (ca. 2.6 mg g-1 DW) in the presence of NaCl. On saline soil, foliar Na concentration was significantly reduced by Cr(III). Phosphorus translocation to leaves was reduced in the presence of Cr(III), while Fe accumulation was enhanced by treatment with NaCl alone. A real-time RT-qPCR analysis was conducted on genes encoding for sulfate, iron, and phosphate transporters, a phytochelatin, a metallothionein, glutathione synthetase, a dehydrin, Hsp70, and enzymes responsible for the biosynthesis of proline (P5CS), glycine betaine (BADH), tocopherols (TAT), and phenolic compounds (PAL). Cr(III), and especially Cr(III)+NaCl, affected transcript levels of most of the investigated genes, indicating that tolerance to Cr is associated with changes in phosphorus and sulfur allocation, and activation of stress-protective molecules. Moderately saline conditions, in most cases, enhanced this response, suggesting that the halophytism of quinoa could contribute to prime the plants to respond to chromium stress.
Collapse
Affiliation(s)
- Francesco Guarino
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Fisciano, Salerno, Italy
| | - Karina B Ruiz
- Departamento Agricultura del Desierto, Universidad Arturo Prat (UNAP), Iquique, Chile; Dipartimento di Science Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Stefano Castiglione
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Fisciano, Salerno, Italy
| | - Angela Cicatelli
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Fisciano, Salerno, Italy.
| | - Stefania Biondi
- Dipartimento di Science Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| |
Collapse
|
25
|
RNA-seq Analysis of Salt-Stressed Versus Non Salt-Stressed Transcriptomes of Chenopodium quinoa Landrace R49. Genes (Basel) 2019; 10:genes10121042. [PMID: 31888133 PMCID: PMC6947843 DOI: 10.3390/genes10121042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/26/2019] [Accepted: 12/07/2019] [Indexed: 12/16/2022] Open
Abstract
Quinoa (Chenopodium quinoa Willd.), a model halophytic crop species, was used to shed light on salt tolerance mechanisms at the transcriptomic level. An RNA-sequencing analysis of genotype R49 at an early vegetative stage was performed by Illumina paired-ends method comparing high salinity and control conditions in a time-course pot experiment. Genome-wide transcriptional salt-induced changes and expression profiling of relevant salt-responsive genes in plants treated or not with 300 mM NaCl were analyzed after 1 h and 5 days. We obtained up to 49 million pairs of short reads with an average length of 101 bp, identifying a total of 2416 differentially expressed genes (DEGs) based on the treatment and time of sampling. In salt-treated vs. control plants, the total number of up-regulated and down-regulated genes was 945 and 1471, respectively. The number of DEGs was higher at 5 days than at 1 h after salt treatment, as reflected in the number of transcription factors, which increased with time. We report a strong transcriptional reprogramming of genes involved in biological processes like oxidation-reduction, response to stress and response to abscisic acid (ABA), and cell wall organization. Transcript analyses by real-time RT- qPCR supported the RNA-seq results and shed light on the contribution of roots and shoots to the overall transcriptional response. In addition, it revealed a time-dependent response in the expression of the analyzed DEGs, including a quick (within 1 h) response for some genes, suggesting a "stress-anticipatory preparedness" in this highly salt-tolerant genotype.
Collapse
|
26
|
Genome-Wide Identification, Characterization, and Expression Analysis of the NAC Transcription Factor in Chenopodium quinoa. Genes (Basel) 2019; 10:genes10070500. [PMID: 31262002 PMCID: PMC6678211 DOI: 10.3390/genes10070500] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/20/2019] [Accepted: 06/26/2019] [Indexed: 12/28/2022] Open
Abstract
The NAC (NAM, ATAF, and CUC) family is one of the largest families of plant-specific transcription factors. It is involved in many plant growth and development processes, as well as abiotic/biotic stress responses. So far, little is known about the NAC family in Chenopodium quinoa. In the present study, a total of 90 NACs were identified in quinoa (named as CqNAC1-CqNAC90) and phylogenetically divided into 14 distinct subfamilies. Different subfamilies showed diversities in gene proportions, exon-intron structures, and motif compositions. In addition, 28 CqNAC duplication events were investigated, and a strong subfamily preference was found during the NAC expansion in quinoa, indicating that the duplication event was not random across NAC subfamilies during quinoa evolution. Moreover, the analysis of Ka/Ks (non-synonymous substitution rate/synonymous substitution rate) ratios suggested that the duplicated CqNACs might have mainly experienced purifying selection pressure with limited functional divergence. Additionally, 11 selected CqNACs showed significant tissue-specific expression patterns, and all the CqNACs were positively regulated in response to salt stress. The result provided evidence for selecting candidate genes for further characterization in tissue/organ specificity and their functional involvement in quinoa's strong salinity tolerance.
Collapse
|
27
|
Yue H, Chang X, Zhi Y, Wang L, Xing G, Song W, Nie X. Evolution and Identification of the WRKY Gene Family in Quinoa ( Chenopodium quinoa). Genes (Basel) 2019; 10:genes10020131. [PMID: 30754717 PMCID: PMC6409747 DOI: 10.3390/genes10020131] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/26/2019] [Accepted: 01/28/2019] [Indexed: 12/02/2022] Open
Abstract
The WRKY gene family plays a unique role in plant stress tolerance. Quinoa is a cultivated crop worldwide that is known for its high stress tolerance. The WRKY gene family in quinoa has not yet been studied. Using a genome-wide search method, we identified 1226 WRKY genes in 15 plant species, seven animal species, and seven fungi species. WRKY proteins were not found in animal species and five fungi species, but were, however, widespread in land plants. A total of 92 CqWRKY genes were identified in quinoa. Based on the phylogenetic analysis, these CqWRKY genes were classified into three groups. The CqWRKY proteins have a highly conserved heptapeptide WRKYGQK with 15 conserved elements. Furthermore, a total of 25 CqWRKY genes were involved in the co-expression pathway of organ development and osmotic stress. The expression level of more than half of these CqWRKY genes showed significant variation under salt or drought stress. This study reports, for the first time, the findings of the CqWRKY gene family in quinoa at the genome-wide level. This information will be beneficial for our understanding of the molecular mechanisms of stress tolerance in crops, such as quinoa.
Collapse
Affiliation(s)
- Hong Yue
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
- College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Xi Chang
- Xizang Agriculture and Animal Husbandry College, Linzhi 860000, Xizang, China.
| | - Yongqiang Zhi
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Lan Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Guangwei Xing
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Weining Song
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| |
Collapse
|
28
|
Waqas M, Yaning C, Iqbal H, Shareef M, Ur Rehman H, Iqbal S, Mahmood S. Soil drenching of paclobutrazol: An efficient way to improve quinoa performance under salinity. PHYSIOLOGIA PLANTARUM 2019; 165:219-231. [PMID: 30133704 DOI: 10.1111/ppl.12820] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 08/08/2018] [Accepted: 08/16/2018] [Indexed: 06/08/2023]
Abstract
Salinity extent and severity is rising because of poor management practices on agricultural lands, possibility lies to grow salt-tolerant crops with better management techniques. Therefore, a highly nutritive salt-tolerant crop quinoa with immense potential to contribute for future food security was selected for this investigation. Soil drenching of paclobutrazol (PBZ; 20 mg l-1 ) was used to understand the ionic relations, gaseous exchange characteristics, oxidative defense system and yield under saline conditions (400 mM NaCl) including normal (0 mM NaCl) and no PBZ (0 mg l-1 ) as controls. The results revealed that salinity stress reduced the growth and yield of quinoa through perturbing ionic homeostasis with the consequences of overproduction of reactive oxygen species (ROS), oxidative damages and reduced photosynthesis. PBZ improved the quinoa performance through regulation of ionic homeostasis by decreasing Na+ , Cl- , while improving K+ , Mg2+ and Ca2+ concentration. It also enhanced the antioxidative system including ascorbic acid, phenylalanine ammonia-lyase, polyphenol oxidase and glutathione peroxidase, which scavenged the ROS (H2 O2 and O2 •- ) and lowered the oxidative damages (malondialdehyde level) under salinity in roots and more specifically in leaf tissues. The photosynthetic rate and stomatal conductance consequently improved (16 and 21%, respectively) in salt-stressed quinoa PBZ-treated compared to the non-treated ones and contributed to the improvement of panicle length (33%), 100-grain weight (8%) and grain yield (38%). Therefore, PBZ can be opted as a shotgun approach to improve quinoa performance and other crops under high saline conditions.
Collapse
Affiliation(s)
- Muhammad Waqas
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Institute of Ecology and Geography, University of Chinese Academy of Sciences, Beijing, China
| | - Chen Yaning
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Hassan Iqbal
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Institute of Ecology and Geography, University of Chinese Academy of Sciences, Beijing, China
| | - Muhammad Shareef
- Xinjiang Institute of Ecology and Geography, University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Biography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Hafeez Ur Rehman
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Shahid Iqbal
- Department of Agronomy, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Sajid Mahmood
- Rapid Soil Fertility Survey and Soil Testing Institute Punjab, Lahore, Pakistan
| |
Collapse
|
29
|
Hinojosa L, González JA, Barrios-Masias FH, Fuentes F, Murphy KM. Quinoa Abiotic Stress Responses: A Review. PLANTS (BASEL, SWITZERLAND) 2018; 7:E106. [PMID: 30501077 PMCID: PMC6313892 DOI: 10.3390/plants7040106] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 02/07/2023]
Abstract
Quinoa (Chenopodium quinoa Willd.) is a genetically diverse Andean crop that has earned special attention worldwide due to its nutritional and health benefits and its ability to adapt to contrasting environments, including nutrient-poor and saline soils and drought stressed marginal agroecosystems. Drought and salinity are the abiotic stresses most studied in quinoa; however, studies of other important stress factors, such as heat, cold, heavy metals, and UV-B light irradiance, are severely limited. In the last few decades, the incidence of abiotic stress has been accentuated by the increase in unpredictable weather patterns. Furthermore, stresses habitually occur as combinations of two or more. The goals of this review are to: (1) provide an in-depth description of the existing knowledge of quinoa's tolerance to different abiotic stressors; (2) summarize quinoa's physiological responses to these stressors; and (3) describe novel advances in molecular tools that can aid our understanding of the mechanisms underlying quinoa's abiotic stress tolerance.
Collapse
Affiliation(s)
- Leonardo Hinojosa
- Sustainable Seed Systems Lab, Department of Crop and Soil Sciences, College of Agricultural, Human, and Natural Resource Sciences, Washington State University, Pullman, WA 99164-6420, USA.
- Facultad de Recursos Naturales, Escuela de Agrnomía, Escuela Superior Politecnica del Chimborazo, Riobamba 060106, Ecuador.
| | - Juan A González
- Fundación Miguel Lillo, Instituto de Ecología, Miguel Lillo, San Miguel de Tucumán Post 4000, Argentina.
| | - Felipe H Barrios-Masias
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada-Reno, Reno, NV 89557, USA.
| | - Francisco Fuentes
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Vicuña Mackenna, Macul, Santiago 4860, Chile.
| | - Kevin M Murphy
- Sustainable Seed Systems Lab, Department of Crop and Soil Sciences, College of Agricultural, Human, and Natural Resource Sciences, Washington State University, Pullman, WA 99164-6420, USA.
| |
Collapse
|
30
|
Abstract
Food security for a growing world population remains one of the most challenging tasks. Rapid climate change accelerates the loss of arable land used for crop production, while it simultaneously imposes increasing biotic and abiotic stresses on crop plants. Analysis and molecular understanding of the factors governing stress tolerance is in the focus of scientific and applied research. One plant is often mentioned in the context with stress resistance—Chenopodium quinoa. Through improved breeding strategies and the use of next generation approaches to study and understand quinoa’s salinity tolerance, an important step towards securing food supply is taken.
Collapse
|
31
|
Witzel K, Matros A, Møller ALB, Ramireddy E, Finnie C, Peukert M, Rutten T, Herzog A, Kunze G, Melzer M, Kaspar-Schoenefeld S, Schmülling T, Svensson B, Mock HP. Plasma membrane proteome analysis identifies a role of barley membrane steroid binding protein in root architecture response to salinity. PLANT, CELL & ENVIRONMENT 2018; 41:1311-1330. [PMID: 29385242 DOI: 10.1111/pce.13154] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 05/19/2023]
Abstract
Although the physiological consequences of plant growth under saline conditions have been well described, understanding the core mechanisms conferring plant salt adaptation has only started. We target the root plasma membrane proteomes of two barley varieties, cvs. Steptoe and Morex, with contrasting salinity tolerance. In total, 588 plasma membrane proteins were identified by mass spectrometry, of which 182 were either cultivar or salinity stress responsive. Three candidate proteins with increased abundance in the tolerant cv. Morex were involved either in sterol binding (a GTPase-activating protein for the adenosine diphosphate ribosylation factor [ZIGA2], and a membrane steroid binding protein [MSBP]) or in phospholipid synthesis (phosphoethanolamine methyltransferase [PEAMT]). Overexpression of barley MSBP conferred salinity tolerance to yeast cells, whereas the knock-out of the heterologous AtMSBP1 increased salt sensitivity in Arabidopsis. Atmsbp1 plants showed a reduced number of lateral roots under salinity, and root-tip-specific expression of barley MSBP in Atmsbp1 complemented this phenotype. In barley, an increased abundance of MSBP correlates with reduced root length and lateral root formation as well as increased levels of auxin under salinity being stronger in the tolerant cv. Morex. Hence, we concluded the involvement of MSBP in phytohormone-directed adaptation of root architecture in response to salinity.
Collapse
Affiliation(s)
- Katja Witzel
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Stadt Seeland, Gatersleben, Germany
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979, Großbeeren, Germany
| | - Andrea Matros
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Stadt Seeland, Gatersleben, Germany
| | - Anders L B Møller
- Technical University of Denmark, Søltofts Plads, Building 224, 2800, Kongens Lyngby, Denmark
| | - Eswarayya Ramireddy
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Free University of Berlin, Albrecht-Thaer-Weg 6, 14195, Berlin, Germany
| | - Christine Finnie
- Technical University of Denmark, Søltofts Plads, Building 224, 2800, Kongens Lyngby, Denmark
| | - Manuela Peukert
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Stadt Seeland, Gatersleben, Germany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Stadt Seeland, Gatersleben, Germany
| | - Andreas Herzog
- Biosystems Engineering, Fraunhofer Institute for Factory Operation and Automation, Joseph-von-Fraunhofer-Straße 1, 39106, Magdeburg, Germany
| | - Gotthard Kunze
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Stadt Seeland, Gatersleben, Germany
| | - Michael Melzer
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Stadt Seeland, Gatersleben, Germany
| | - Stephanie Kaspar-Schoenefeld
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Stadt Seeland, Gatersleben, Germany
| | - Thomas Schmülling
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Free University of Berlin, Albrecht-Thaer-Weg 6, 14195, Berlin, Germany
| | - Birte Svensson
- Technical University of Denmark, Søltofts Plads, Building 224, 2800, Kongens Lyngby, Denmark
| | - Hans-Peter Mock
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Stadt Seeland, Gatersleben, Germany
| |
Collapse
|