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Pinto VB, Vidigal PMP, Dal-Bianco M, Almeida-Silva F, Venancio TM, Viana JMS. Transcriptome-based strategies for identifying aluminum tolerance genes in popcorn (Zea mays L. var. everta). Sci Rep 2023; 13:19400. [PMID: 37938583 PMCID: PMC10632369 DOI: 10.1038/s41598-023-46810-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/06/2023] [Indexed: 11/09/2023] Open
Abstract
Aluminum (Al) toxicity limits crop production worldwide. Although studies have identified genes associated with Al tolerance in crops, a large amount of data remains unexplored using other strategies. Here, we searched for single substitutions and InDels across differentially expressed genes (DEGs), linked DEGs to Al-tolerance QTLs reported in the literature for common maize, and investigated the alternative splicing regulated by Al3+ toxicity. We found 929 substitutions between DEGs in Al-tolerant and 464 in Al-sensitive inbred lines, of which 165 and 80 were non-synonymous, respectively. Only 12 NS variants had deleterious predicted effect on protein function in Al-tolerant and 13 in Al-sensitive. Moreover, 378 DEGs were mapped in Al-QTL regions for the Al-tolerant and 213 for the Al-sensitive. Furthermore, Al stress is primarily regulated at the transcriptional level in popcorn. Important genes identified, such as HDT1, SWEET4a, GSTs, SAD9, PIP2-2, CASP-like 5, and AGP, may benefit molecular assisted popcorn breeding or be useful in biotechnological approaches. These findings offer insights into the mechanisms of Al tolerance in popcorn and provide a 'hypothesis-free' strategy for identifying and prioritizing candidate genes that could be used to develop molecular markers or cultivars resilient to acidic soils.
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Affiliation(s)
- Vitor Batista Pinto
- Departamento de Biologia Geral, Universidade Federal de Viçosa (UFV), Viçosa, MG, 36570-000, Brazil.
- Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, 28013-602, Brazil.
| | | | - Maximiller Dal-Bianco
- Laboratório de Bioquímica Genética de Plantas/BIOAGRO. UFV, Viçosa, MG, 36570-000, Brazil
| | - Fabricio Almeida-Silva
- Laboratório de Química e Função de Proteínas e Peptídeos, CBB. UENF, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Thiago Motta Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, CBB. UENF, Campos dos Goytacazes, RJ, 28013-602, Brazil
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Ofoe R, Thomas RH, Asiedu SK, Wang-Pruski G, Fofana B, Abbey L. Aluminum in plant: Benefits, toxicity and tolerance mechanisms. FRONTIERS IN PLANT SCIENCE 2023; 13:1085998. [PMID: 36714730 PMCID: PMC9880555 DOI: 10.3389/fpls.2022.1085998] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Aluminum (Al) is the third most ubiquitous metal in the earth's crust. A decrease in soil pH below 5 increases its solubility and availability. However, its impact on plants depends largely on concentration, exposure time, plant species, developmental age, and growing conditions. Although Al can be beneficial to plants by stimulating growth and mitigating biotic and abiotic stresses, it remains unknown how Al mediates these effects since its biological significance in cellular systems is still unidentified. Al is considered a major limiting factor restricting plant growth and productivity in acidic soils. It instigates a series of phytotoxic symptoms in several Al-sensitive crops with inhibition of root growth and restriction of water and nutrient uptake as the obvious symptoms. This review explores advances in Al benefits, toxicity and tolerance mechanisms employed by plants on acidic soils. These insights will provide directions and future prospects for potential crop improvement.
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Affiliation(s)
- Raphael Ofoe
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Bible Hill, NS, Canada
| | - Raymond H. Thomas
- School of Science and the Environment, Memorial University of Newfoundland, Grenfell Campus, Corner Brook, NL, Canada
| | - Samuel K. Asiedu
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Bible Hill, NS, Canada
| | - Gefu Wang-Pruski
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Bible Hill, NS, Canada
| | - Bourlaye Fofana
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Bible Hill, NS, Canada
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PE, Canada
| | - Lord Abbey
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Bible Hill, NS, Canada
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3
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Siqueira JA, Wakin T, Batista-Silva W, Silva JCF, Vicente MH, Silva JC, Clarindo WR, Zsögön A, Peres LEP, De Veylder L, Fernie AR, Nunes-Nesi A, Araújo WL. A long and stressful day: Photoperiod shapes aluminium tolerance in plants. JOURNAL OF HAZARDOUS MATERIALS 2022; 432:128704. [PMID: 35313159 DOI: 10.1016/j.jhazmat.2022.128704] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/06/2022] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
Aluminium (Al), a limiting factor for crop productivity in acidic soils (pH ≤ 5.5), imposes drastic constraints for food safety in developing countries. The major mechanisms that allow plants to cope with Al involve manipulations of organic acids metabolism and DNA-checkpoints. When assumed individually both approaches have been insufficient to overcome Al toxicity. On analysing the centre of origin of most cultivated plants, we hypothesised that day-length seems to be a pivotal agent modulating Al tolerance across distinct plant species. We observed that with increasing distance from the Equator, Al tolerance decreases, suggesting a relationship with the photoperiod. We verified that long-day (LD) species are generally more Al-sensitive than short-day (SD) species, whereas genetic conversion of tomato for SD growth habit boosts Al tolerance. Reduced Al tolerance correlates with DNA-checkpoint activation under LD. Furthermore, DNA-checkpoint-related genes are under positive selection in Arabidopsis accessions from regions with shorter days, suggesting that photoperiod act as a selective barrier for Al tolerance. A diel regulation and genetic diversity affect Al tolerance, suggesting that day-length orchestrates Al tolerance. Altogether, photoperiodic control of Al tolerance might contribute to solving the historical obstacle that imposes barriers for developing countries to reach a sustainable agriculture.
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Affiliation(s)
- João Antonio Siqueira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Thiago Wakin
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Willian Batista-Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - José Cleydson F Silva
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Matheus H Vicente
- Laboratory of Hormonal Control of Plant Development. Departamento de Ciências Biológicas (LCB), Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP 13418-900, Brazil
| | - Jéssica C Silva
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Wellington R Clarindo
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Agustin Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Lazaro E P Peres
- Laboratory of Hormonal Control of Plant Development. Departamento de Ciências Biológicas (LCB), Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP 13418-900, Brazil
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.
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Pinto VB, Almeida VC, Pereira-Lima ÍA, Vale EM, Araújo WL, Silveira V, Viana JMS. Deciphering the major metabolic pathways associated with aluminum tolerance in popcorn roots using label-free quantitative proteomics. PLANTA 2021; 254:132. [PMID: 34821986 DOI: 10.1007/s00425-021-03786-y] [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: 08/21/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
Al responsive proteins are associated with starch, sucrose, and other carbohydrate metabolic pathways. Sucrose synthase is a candidate to Al tolerance. Al responses are regulated at transcriptional and post-transcriptional levels. Aluminum toxicity is one of the important abiotic stresses that affects worldwide crop production. The soluble form of aluminum (Al3+) inhibits root growth by altering water and nutrient uptake, a process that also reduces plant growth and development. Under long-term Al3+ exposure, plants can activate several tolerance mechanisms. To date, no reports of large-scale proteomic data concerning maize responses to this ion have been published. To investigate the post-transcriptional regulation in response to Al toxicity, we performed label-free quantitative proteomics for comparative analysis of two Al-contrasting popcorn inbred lines and an Al-tolerant commercial hybrid during 72 h under Al-stress conditions. A total of 489 differentially accumulated proteins (DAPs) were identified in the Al-sensitive inbred line, 491 in the Al-tolerant inbred line, and 277 in the commercial hybrid. Among them, 120 DAPs were co-expressed in both Al tolerant genotypes. Bioinformatics analysis indicated that starch, sucrose, and other components of carbohydrate metabolism and glycolysis/gluconeogenesis are the biochemical processes regulated in response to Al toxicity. Sucrose synthase accumulation and an increase in sucrose content and starch degradation suggest that these components may enhance popcorn tolerance to Al stress. The accumulation of citrate synthase suggests a key role for this enzyme in the detoxification process in the Al-tolerant inbred line. The integration of transcriptomic and proteomic data indicates that the Al tolerance response presents a complex regulatory network into the transcription and translation dynamics of popcorn root development.
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Affiliation(s)
- Vitor Batista Pinto
- Departamento de Biologia Geral, Universidade Federal de Viçosa (UFV), Viçosa, MG, 36570-900, Brazil.
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil.
- Setor de Genômica e Proteômica. CBB, Unidade de Biologia Integrativa, UENF, Campos dos Goytacazes, RJ, Brazil.
| | - Vinicius Costa Almeida
- Departamento de Biologia Geral, Universidade Federal de Viçosa (UFV), Viçosa, MG, 36570-900, Brazil
| | - Ítalo A Pereira-Lima
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa (UFV), Viçosa, MG, 36570-900, Brazil
| | - Ellen Moura Vale
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil
- Setor de Genômica e Proteômica. CBB, Unidade de Biologia Integrativa, UENF, Campos dos Goytacazes, RJ, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa (UFV), Viçosa, MG, 36570-900, Brazil
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil
- Setor de Genômica e Proteômica. CBB, Unidade de Biologia Integrativa, UENF, Campos dos Goytacazes, RJ, Brazil
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Singh CK, Singh D, Sharma S, Chandra S, Tomar RSS, Kumar A, Upadhyaya KC, Pal M. Mechanistic Association of Quantitative Trait Locus with Malate Secretion in Lentil ( Lens culinaris Medikus) Seedlings under Aluminium Stress. PLANTS 2021; 10:plants10081541. [PMID: 34451586 PMCID: PMC8400473 DOI: 10.3390/plants10081541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/12/2020] [Accepted: 10/20/2020] [Indexed: 12/04/2022]
Abstract
Aluminium (Al) toxicity acts as a major delimiting factor in the productivity of many crops including lentil. To alleviate its effect, plants have evolved with Al exclusion and inclusion mechanisms. The former involves the exudation of organic acid to restrict the entry of Al3+ to the root cells while latter involves detoxification of entered Al3+ by organic acids. Al-induced secretion of organic acids from roots is a well-documented mechanism that chelates and neutralizes Al3+ toxicity. In this study, F6 recombinant inbred lines (RILs) derived from a cross between L-7903 (Al-resistant) and BM-4 (Al-sensitive) were phenotyped to assess variation in secretion levels of malate and was combined with genotypic data obtained from 10 Al-resistance linked simple sequence repeat (SSRs) markers. A major quantitative trait loci (QTL) was mapped for malate (qAlt_ma) secretion with a logarithm of odd (LOD) value of 7.7 and phenotypic variation of 60.2%.Validated SSRs associated with this major QTL will be useful in marker assisted selection programmes for improving Al resistance in lentil.
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Affiliation(s)
- Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (C.K.S.); (S.S.)
- Amity Institute of Biotechnology, Amity University, Noida 201313, India;
| | - Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (C.K.S.); (S.S.)
- Correspondence: (D.S.); (M.P.); Tel.: +91-7011180774 (D.S.); +91-9868783354 (M.P.)
| | - Shristi Sharma
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (C.K.S.); (S.S.)
| | - Shivani Chandra
- Amity Institute of Biotechnology, Amity University, Noida 201313, India;
| | - Ram Sewak Singh Tomar
- ICAR-National Institute of Plant Biotechnology, Pusa Campus, New Delhi 110012, India;
| | - Arun Kumar
- National Phytotron Facility, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
| | - K. C. Upadhyaya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India;
| | - Madan Pal
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi 110012, India
- Correspondence: (D.S.); (M.P.); Tel.: +91-7011180774 (D.S.); +91-9868783354 (M.P.)
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Szurman-Zubrzycka M, Chwiałkowska K, Niemira M, Kwaśniewski M, Nawrot M, Gajecka M, Larsen PB, Szarejko I. Aluminum or Low pH - Which Is the Bigger Enemy of Barley? Transcriptome Analysis of Barley Root Meristem Under Al and Low pH Stress. Front Genet 2021; 12:675260. [PMID: 34220949 PMCID: PMC8244595 DOI: 10.3389/fgene.2021.675260] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/13/2021] [Indexed: 11/13/2022] Open
Abstract
Aluminum (Al) toxicity is considered to be the most harmful abiotic stress in acidic soils that today comprise more than 50% of the world’s arable lands. Barley belongs to a group of crops that are most sensitive to Al in low pH soils. We present the RNA-seq analysis of root meristems of barley seedlings grown in hydroponics at optimal pH (6.0), low pH (4.0), and low pH with Al (10 μM of bioavailable Al3+ ions). Two independent experiments were conducted: with short-term (24 h) and long-term (7 days) Al treatment. In the short-term experiment, more genes were differentially expressed (DEGs) between root meristems grown at pH = 6.0 and pH = 4.0, than between those grown at pH = 4.0 with and without Al treatment. The genes upregulated by low pH were associated mainly with response to oxidative stress, cell wall organization, and iron ion binding. Among genes upregulated by Al, overrepresented were those related to response to stress condition and calcium ion binding. In the long-term experiment, the number of DEGs between hydroponics at pH = 4.0 and 6.0 were lower than in the short-term experiment, which suggests that plants partially adapted to the low pH. Interestingly, 7 days Al treatment caused massive changes in the transcriptome profile. Over 4,000 genes were upregulated and almost 2,000 genes were downregulated by long-term Al stress. These DEGs were related to stress response, cell wall development and metal ion transport. Based on our results we can assume that both, Al3+ ions and low pH are harmful to barley plants. Additionally, we phenotyped the root system of barley seedlings grown in the same hydroponic conditions for 7 days at pH = 6.0, pH = 4.0, and pH = 4.0 with Al. The results correspond to transcriptomic data and show that low pH itself is a stress factor that causes a significant reduction of root growth and the addition of aluminum further increases this reduction. It should be noted that in acidic arable lands, plants are exposed simultaneously to both of these stresses. The presented transcriptome analysis may help to find potential targets for breeding barley plants that are more tolerant to such conditions.
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Affiliation(s)
- Miriam Szurman-Zubrzycka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Karolina Chwiałkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Magdalena Niemira
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Mirosław Kwaśniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Małgorzata Nawrot
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Monika Gajecka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Paul B Larsen
- Department of Biochemistry, University of California, Riverside, Riverside, CA, United States
| | - Iwona Szarejko
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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Worthington M, Perez JG, Mussurova S, Silva-Cordoba A, Castiblanco V, Cardoso Arango JA, Jones C, Fernandez-Fuentes N, Skot L, Dyer S, Tohme J, Di Palma F, Arango J, Armstead I, De Vega JJ. A new genome allows the identification of genes associated with natural variation in aluminium tolerance in Brachiaria grasses. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:302-319. [PMID: 33064149 PMCID: PMC7853602 DOI: 10.1093/jxb/eraa469] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 10/12/2020] [Indexed: 05/08/2023]
Abstract
Toxic concentrations of aluminium cations and low phosphorus availability are the main yield-limiting factors in acidic soils, which represent half of the potentially available arable land. Brachiaria grasses, which are commonly sown as forage in the tropics because of their resilience and low demand for nutrients, show greater tolerance to high concentrations of aluminium cations (Al3+) than most other grass crops. In this work, we explored the natural variation in tolerance to Al3+ between high and low tolerant Brachiaria species and characterized their transcriptional differences during stress. We identified three QTLs (quantitative trait loci) associated with root vigour during Al3+ stress in their hybrid progeny. By integrating these results with a new Brachiaria reference genome, we identified 30 genes putatively responsible for Al3+ tolerance in Brachiaria. We observed differential expression during stress of genes involved in RNA translation, response signalling, cell wall composition, and vesicle location homologous to aluminium-induced proteins involved in limiting uptake or localizing the toxin. However, there was limited regulation of malate transporters in Brachiaria, which suggests that exudation of organic acids and other external tolerance mechanisms, common in other grasses, might not be relevant in Brachiaria. The contrasting regulation of RNA translation and response signalling suggests that response timing is critical in high Al3+-tolerant Brachiaria.
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Affiliation(s)
- Margaret Worthington
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
- Present address: Department of Horticulture, University of Arkansas, 306 Plant Sciences Bldg, Fayetteville, AR 72701, USA
| | | | | | | | | | | | - Charlotte Jones
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK
| | - Narcis Fernandez-Fuentes
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK
| | - Leif Skot
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK
| | - Sarah Dyer
- Earlham Institute, Norwich Research Park, Norwich, UK
- Present address: NIAB, Huntingdon Road, Cambridge CB3 0LE, UK
| | - Joe Tohme
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | | | - Jacobo Arango
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Ian Armstead
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK
| | - Jose J De Vega
- Earlham Institute, Norwich Research Park, Norwich, UK
- Correspondence:
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8
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Matonyei TK, Barros BA, Guimaraes RGN, Ouma EO, Cheprot RK, Apolinário LC, Ligeyo DO, Costa MBR, Were BA, Kisinyo PO, Onkware AO, Noda RW, Gudu SO, Magalhaes JV, Guimaraes CT. Aluminum tolerance mechanisms in Kenyan maize germplasm are independent from the citrate transporter ZmMATE1. Sci Rep 2020; 10:7320. [PMID: 32355284 PMCID: PMC7193623 DOI: 10.1038/s41598-020-64107-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 04/07/2020] [Indexed: 11/09/2022] Open
Abstract
Aluminum (Al) toxicity on acid soils adversely affects maize yields, which can be overcome by combining soil amendments with genetic tolerance. In maize, ZmMATE1 confers Al tolerance via Al-activated citrate release, whereby citrate forms non-toxic complexes with Al3+ in the rhizosphere. Here, we investigated Al tolerance mechanisms in maize germplasm originated from Kenya based on quantitative trait loci (QTL) mapping. Five QTLs and four epistatic interactions explained ~51% of the phenotypic variation for Al tolerance. The lack of Al tolerance QTL on chromosome 6 and the much lower expression of ZmMATE1 in both Kenyan lines than in Cateto Al237, which donates the superior allele of ZmMATE1, strongly indicate that this gene does not play a significant role in Al tolerance in neither parent. In turn, maize homologs to genes previously implicated in Al tolerance in other species, ZmNrat1, ZmMATE3, ZmWRKY and ZmART1, co-localized with Al tolerance QTL and were more highly expressed in the parent that donate favorable QTL alleles. However, these candidate genes will require further studies for functional validation on maize Al tolerance. The existence of Al tolerance mechanisms independent from ZmMATE1 suggests it is possible to develop highly Al tolerant cultivars by pyramiding complementary Al tolerance genes in maize.
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Affiliation(s)
- Thomas K Matonyei
- University of Kabianga, Agroforestry and Rural Development Department, P.O. Box 2030-20200, Kericho, Kenya
| | - Beatriz A Barros
- Embrapa Milho e Sorgo, Rodovia MG 424 km 65, Sete Lagoas, 35701-970, Brazil
| | - Roberta G N Guimaraes
- Universidade Federal de São João del Rei, Campus Sete Lagoas, Rodovia MG 424 km 47, Sete Lagoas, 35701-970, Brazil
| | - Evans O Ouma
- Rongo University, P.O. Box 103-40404, Rongo, Kenya
| | | | - Leandro C Apolinário
- Faculdade Ciências da Vida, Av. Prefeito Alberto Moura, 12632, Sete Lagoas, MG, Brazil
| | - Dickson O Ligeyo
- Kenya Agricultural Research Institute, P.O. Box 450-30200, Kitale, Kenya
| | - Marcella B R Costa
- Universidade Federal de Minas Gerais, Departamento de Biologia Geral, Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brazil
| | | | | | | | - Roberto W Noda
- Embrapa Milho e Sorgo, Rodovia MG 424 km 65, Sete Lagoas, 35701-970, Brazil
| | | | | | - Claudia T Guimaraes
- Embrapa Milho e Sorgo, Rodovia MG 424 km 65, Sete Lagoas, 35701-970, Brazil.
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9
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Wang X, Cheng Y, Yang C, Yang C, Mu Y, Xia Q, Ma Q. QTL mapping for aluminum tolerance in RIL population of soybean (Glycine max L.) by RAD sequencing. PLoS One 2019; 14:e0223674. [PMID: 31661499 PMCID: PMC6818782 DOI: 10.1371/journal.pone.0223674] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 09/25/2019] [Indexed: 11/23/2022] Open
Abstract
Aluminum (Al3+) toxicity is a typical abiotic stress that severely limits crop production in acidic soils. In this study, an RIL (recombinant inbred line, F12) population derived from the cross of Zhonghuang 24 (ZH 24) and Huaxia 3 (HX 3) (160 lines) was tested using hydroponic cultivation. Relative root elongation (RRE) and apical Al3+ content (AAC) were evaluated for each line, and a significant negative correlation was detected between the two indicators. Based on a high-density genetic linkage map, the phenotypic data were used to identify quantitative trait loci (QTLs) associated with these traits. With composite interval mapping (CIM) of the linkage map, five QTLs that explained 39.65% of RRE and AAC variation were detected on chromosomes (Chrs) Gm04, Gm16, Gm17 and Gm19. Two new QTLs, qRRE_04 and qAAC_04, were located on the same region of bin93-bin94 on Chr Gm04, which explained 7.09% and 8.98% phenotypic variation, respectively. Furthermore, the results of the expression analysis of candidate genes in the five genetic regions of the QTLs showed that six genes (Glyma.04g218700, Glyma.04g212800, Glyma.04g213300, Glyma.04g217400, Glyma.04g216100 and Glyma.04g220600) exhibited significant differential expression between the Al3+ treatment and the control of two parents. The results of qRT-PCR analysis indicated that Glyma.04g218700 was upregulated by Al3+ treatment with the hundreds-fold increased expression level and may be a candidate gene with potential roles in the response to aluminum stress. Therefore, our efforts will enable future functional analysis of candidate genes and will contribute to the strategies for improvement of aluminum tolerance in soybean.
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Affiliation(s)
- Xinxin Wang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
- The National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yanbo Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
- The National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Ce Yang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
- The National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Cunyi Yang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
- The National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yinghui Mu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
- The National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Qiuju Xia
- The Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Qibin Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
- The National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, Guangdong, China
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10
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Singh CK, Singh D, Tomar RSS, Karwa S, Upadhyaya KC, Pal M. Molecular mapping of aluminium resistance loci based on root re-growth and Al-induced fluorescent signals (callose accumulation) in lentil (Lens culinaris Medikus). Mol Biol Rep 2018; 45:2103-2113. [PMID: 30218353 DOI: 10.1007/s11033-018-4368-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/06/2018] [Indexed: 11/30/2022]
Abstract
Development of aluminium (Al) resistant genotypes through molecular breeding is a major approach for increasing seed yield under acidic conditions. There are no available reports on mapping of Al resistance loci and molecular breeding for Al resistant varieties in lentil. The present study reports a major quantitative trait loci (QTL) for Al resistance using simple sequence repeat (SSR) markers in F2 and F3 mapping populations derived from contrasting parents. Phenotypic response to Al was measured on the bases of root re-growth (RRG), fluorescent signals (callose accumulation) and Al contents in hydroponic assay. After screening 495 SSR markers to search polymorphism between two contrasting parents, 73 polymorphic markers were used for bulk segregation analysis. Two major QTLs were identified using seven trait linked markers, one each for fluorescent signals and RRG mapped on linkage group (LG) 1 under Al stress conditions in F2 mapping population of cross BM-4 × L-4602. One major QTL (qAlt_fs) was localised between PLC_88 and PBA_LC_373, covering 25.9 cM with adjacent marker PLC_88 at a distance of 0.4 cM. Another major QTL (qAlt_rrg) for RRG was in the marker interval of PBA_LC_1247 and PLC_51, covering a distance of 45.7 cM with nearest marker PBA_LC_1247 at a distance of 21.2 cM. Similarly, in F3 families of BM-4 × L-4602 and BM-4 × L-7903, LG-1 was extended to 285.9 and 216.4 cM respectively, having four newly developed genic-SSR markers. These QTLs had a logarithm of odd (LOD) value of 140.5 and 28.8 along with phenotypic variation of 52% and 11% for fluorescent signals and RRG respectively, whereas, qAlt_rrg had LOD of 36 and phenotypic variance of 25% in F3 population of BM-4 × L-4602. Two major QTLs identified in the present study can be further dissected for candidate gene discovery and development of molecular markers for breeding improved varieties with high Al resistance.
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Affiliation(s)
- Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India.,Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | | | - Sourabh Karwa
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - K C Upadhyaya
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Madan Pal
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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11
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Plant Protection by Benzoxazinoids—Recent Insights into Biosynthesis and Function. AGRONOMY-BASEL 2018. [DOI: 10.3390/agronomy8080143] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Benzoxazinoids (BXs) are secondary metabolites present in many Poaceae including the major crops maize, wheat, and rye. In contrast to other potentially toxic secondary metabolites, BXs have not been targets of counter selection during breeding and the effect of BXs on insects, microbes, and neighbouring plants has been recognised. A broad knowledge about the mode of action and metabolisation in target organisms including herbivorous insects, aphids, and plants has been gathered in the last decades. BX biosynthesis has been elucidated on a molecular level in crop cereals. Recent advances, mainly made by investigations in maize, uncovered a significant diversity in the composition of BXs within one species. The pattern can be specific for single plant lines and dynamic changes triggered by biotic and abiotic stresses were observed. Single BXs might be toxic, repelling, attractive, and even growth-promoting for insects, depending on the particular species. BXs delivered into the soil influence plant and microbial communities. Furthermore, BXs can possibly be used as signalling molecules within the plant. In this review we intend to give an overview of the current data on the biosynthesis, structure, and function of BXs, beyond their characterisation as mere phytotoxins.
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12
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Zhou S, Richter A, Jander G. Beyond Defense: Multiple Functions of Benzoxazinoids in Maize Metabolism. PLANT & CELL PHYSIOLOGY 2018; 59:1528-1537. [PMID: 29584935 DOI: 10.1093/pcp/pcy064] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Indexed: 05/21/2023]
Abstract
Benzoxazinoids are a class of indole-derived plant metabolites that function in defense against numerous pests and pathogens. Due to their abundance in maize (Zea mays) and other important cereal crops, benzoxazinoids have been the subject of extensive research for >50 years. Whereas benzoxazinoids can account for 1% or more of the dry weight in young seedlings constitutively, their accumulation in older plants is induced locally by pest and pathogen attack. Although the biosynthetic pathways for most maize benzoxazinoids have been identified, unanswered questions remain about the developmental and defense-induced regulation of benzoxazinoid metabolism. Recent research shows that, in addition to their central role in the maize chemical defense repertoire, benzoxazinoids may have important functions in regulating other defense responses, flowering time, auxin metabolism, iron uptake and perhaps aluminum tolerance. Investigation of natural variation in maize benzoxazinoid accumulation, which is greatly facilitated by recent genomics advances, will have a major impact in this research area by leading to the discovery of previously unknown genes and functions of benzoxazinoid metabolism.
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Affiliation(s)
- Shaoqun Zhou
- Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY, USA
- Plant Biology Section, School of Integrated Plant Science, Cornell University, Ithaca, NY, USA
| | - Annett Richter
- Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY, USA
| | - Georg Jander
- Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY, USA
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13
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Zhang M, Lu X, Li C, Zhang B, Zhang C, Zhang XS, Ding Z. Auxin Efflux Carrier ZmPGP1 Mediates Root Growth Inhibition under Aluminum Stress. PLANT PHYSIOLOGY 2018; 177:819-832. [PMID: 29720555 PMCID: PMC6001327 DOI: 10.1104/pp.17.01379] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 04/15/2018] [Indexed: 05/25/2023]
Abstract
Auxin has been shown to enhance root growth inhibition under aluminum (Al) stress in Arabidopsis (Arabidopsis thaliana). However, in maize (Zea mays), auxin may play a negative role in the Al-induced inhibition of root growth. In this study, we identified mutants deficient in the maize auxin efflux carrier P-glycoprotein (ZmPGP1) after ethyl methanesulfonate mutagenesis and used them to elucidate the contribution of ZmPGP1 to Al-induced root growth inhibition. Root growth in the zmpgp1 mutant, which forms shortened roots and is hyposensitive to auxin, was less inhibited by Al stress than that in the inbred line B73. In the zmpgp1 mutants, the root tips displayed higher auxin accumulation and enhanced auxin signaling under Al stress, which was also consistent with the increased expression of auxin-responsive genes. Based on the behavior of the auxin-responsive marker transgene, DR5rev:RFP, we concluded that Al stress reduced the level of auxin in the root tip, which contrasts with the tendency of Al stress-induced Arabidopsis plants to accumulate more auxin in their root tips. In addition, Al stress induced the expression of ZmPGP1 Therefore, in maize, Al stress is associated with reduced auxin accumulation in root tips, a process that is regulated by ZmPGP1 and thus causes inhibition of root growth. This study provides further evidence about the role of auxin and auxin polar transport in Al-induced root growth regulation in maize.
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Affiliation(s)
- Maolin Zhang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, College of Life Sciences, Shandong University, Jinan 250100, Shandong, China
| | - Xiaoduo Lu
- Insititue of Molecular Breeding for Maize, Qilu Normal University, Jinan 250200, China
| | - Cuiling Li
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, College of Life Sciences, Shandong University, Jinan 250100, Shandong, China
| | - Bing Zhang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, College of Life Sciences, Shandong University, Jinan 250100, Shandong, China
| | - Chunyi Zhang
- Department of Crop Genomics and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xian-Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Zhaojun Ding
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, College of Life Sciences, Shandong University, Jinan 250100, Shandong, China
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14
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Lu M, Wang Z, Fu S, Yang G, Shi M, Lu Y, Wang X, Xia J. Functional characterization of the SbNrat1 gene in sorghum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 262:18-23. [PMID: 28716414 DOI: 10.1016/j.plantsci.2017.05.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/22/2017] [Accepted: 05/23/2017] [Indexed: 05/08/2023]
Abstract
The Natural Resistance Associated Macrophage Protein (Nramp) members play diverse roles in metal transport in plants. Recent studies have showed that OsNrat1 (OsNramp4) encodes an Al transporter, which is required for rice Al tolerance. In this study, we functionally characterized a Nramp member in sorghum, SbNrat1, which is homologous to OsNrat1 with 88% identity. SbNrat1 was expressed in both roots and shoots, and its expression was not induced by Al treatment. When expressed in yeast, SbNrat1 transports trivalent Al ion, but not Mn and Cd. Furthermore, introduction of SbNrat1 into the rice mutant osnrat1 can rescue its sensitivity to Al. However, no correlation between Al tolerance and the expression level of SbNrat1 was found in thirteen sorghum cultivars tested. These results indicate that SbNrat1 functions as an Al transporter that is possibly involved in basic Al tolerance in sorghum.
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Affiliation(s)
- Muxue Lu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Zhigang Wang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Shan Fu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Guangzhe Yang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Mingxing Shi
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Youshe Lu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Xiaohu Wang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Jixing Xia
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China.
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15
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Anami SE, Zhang L, Xia Y, Zhang Y, Liu Z, Jing H. Sweet sorghum ideotypes: genetic improvement of stress tolerance. Food Energy Secur 2015. [DOI: 10.1002/fes3.54] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Sylvester Elikana Anami
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
- Institute of Biotechnology Research Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya
| | - Li‐Min Zhang
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Yan Xia
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Yu‐Miao Zhang
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Zhi‐Quan Liu
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Hai‐Chun Jing
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
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16
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Poschenrieder C, Tolrà R, Hajiboland R, Arroyave C, Barceló J. Mechanisms of Hyper-resistance and Hyper-tolerance to Aluminum in Plants. ALUMINUM STRESS ADAPTATION IN PLANTS 2015. [DOI: 10.1007/978-3-319-19968-9_5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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17
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Kochian LV, Piñeros MA, Liu J, Magalhaes JV. Plant Adaptation to Acid Soils: The Molecular Basis for Crop Aluminum Resistance. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:571-98. [PMID: 25621514 DOI: 10.1146/annurev-arplant-043014-114822] [Citation(s) in RCA: 429] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Aluminum (Al) toxicity in acid soils is a significant limitation to crop production worldwide, as approximately 50% of the world's potentially arable soil is acidic. Because acid soils are such an important constraint to agriculture, understanding the mechanisms and genes conferring resistance to Al toxicity has been a focus of intense research interest in the decade since the last article on crop acid soil tolerance was published in this journal. An impressive amount of progress has been made during that time that has greatly increased our understanding of the diversity of Al resistance genes and mechanisms, how resistance gene expression is regulated and triggered by Al and Al-induced signals, and how the proteins encoded by these genes function and are regulated. This review examines the state of our understanding of the physiological, genetic, and molecular bases for crop Al tolerance, looking at the novel Al resistance genes and mechanisms that have been identified over the past ten years. Additionally, it examines how the integration of molecular and genetic analyses of crop Al resistance is starting to be exploited for the improvement of crop plants grown on acid soils via both molecular-assisted breeding and biotechnology approaches.
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Affiliation(s)
- Leon V Kochian
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, New York 14853; , ,
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