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Brhane H, Haileselassie T, Tesfaye K, Ortiz R, Hammenhag C, Abreha KB, Vetukuri RR, Geleta M. Finger millet RNA-seq reveals differential gene expression associated with tolerance to aluminum toxicity and provides novel genomic resources. FRONTIERS IN PLANT SCIENCE 2022; 13:1068383. [PMID: 36570897 PMCID: PMC9780683 DOI: 10.3389/fpls.2022.1068383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/21/2022] [Indexed: 06/01/2023]
Abstract
Eleusine coracana, finger millet, is a multipurpose crop cultivated in arid and semi-arid regions of Africa and Asia. RNA sequencing (RNA-seq) was used in this study to obtain valuable genomic resources and identify genes differentially expressed between Al-tolerant and Al-susceptible genotypes. Two groups of finger millet genotypes were used: Al-tolerant (215836, 215845, and 229722) and Al-susceptible (212462, 215804 and 238323). The analysis of the RNA-seq data resulted in 198,546 unigenes, 56.5% of which were annotated with significant hits in one or more of the following six databases: NR (48.8%), GO (29.7%), KEGG (45%), PlantTFDB (19.0%), Uniprot (49.2%), and NT (46.2%). It is noteworthy that only 220 unigenes in the NR database had significant hits against finger millet sequences suggesting that finger millet's genomic resources are scarce. The gene expression analysis revealed that 322 genes were significantly differentially expressed between the Al-tolerant and Al-susceptible genotypes, of which 40.7% were upregulated while 59.3% were downregulated in Al-tolerant genotypes. Among the significant DEGs, 54.7% were annotated in the GO database with the top hits being ATP binding (GO:0005524) and DNA binding (GO:0003677) in the molecular function, DNA integration (GO:0015074) and cell redox homeostasis in the biological process, as well as cellular anatomical entity and intracellular component in the cellular component GO classes. Several of the annotated DEGs were significantly enriched for their corresponding GO terms. The KEGG pathway analysis resulted in 60 DEGs that were annotated with different pathway classes, of which carbohydrate metabolism and signal transduction were the most prominent. The homologs of a number of significant DEGs have been previously reported as being associated with Al or other abiotic stress responses in various crops, including carboxypeptidase SOL1, HMA3, AP2, bZIP, C3H, and WRKY TF genes. A more detailed investigation of these and other DEGs will enable genomic-led breeding for Al tolerance in finger millet. RNA-seq data analysis also yielded 119,073 SNP markers, the majority of which had PIC values above 0.3, indicating that they are highly informative. Additionally, 3,553 single-copy SSR markers were identified, of which trinucleotide SSRs were the most prevalent. These genomic resources contribute substantially to the enrichment of genomic databases for finger millet, and facilitate future research on this crop.
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Affiliation(s)
- Haftom Brhane
- Biology Department, Aksum University, Aksum, Ethiopia
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | | | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Ministry of Innovation and Technology, Addis Ababa, Ethiopia
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Kibrom B. Abreha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Ramesh R. Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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Vasconcelos CV, Costa AC, Müller C, Castoldi G, Costa AM, de Paula Barbosa K, Rodrigues AA, da Silva AA. Potential of calcium nitrate to mitigate the aluminum toxicity in Phaseolus vulgaris: effects on morphoanatomical traits, mineral nutrition and photosynthesis. ECOTOXICOLOGY (LONDON, ENGLAND) 2020; 29:203-216. [PMID: 32006192 DOI: 10.1007/s10646-020-02168-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/20/2020] [Indexed: 06/10/2023]
Abstract
Common bean (Phaseolus vulgaris) cultivation occurs mainly in regions with acidic soils, where high aluminum (Al) concentration is a major constraint to crop production. In this study, we evaluated tolerance and sensitivity traits to Al exposure and calcium (Ca) deficiency in bean plants, and determined the efficiency of Ca to mitigate the toxic Al effects. Two bean cultivars (BRS Estilo and Campos Gerais) were grown in three soil conditions: (I) soil liming with calcium hydroxide Ca(OH)2 and Al unavailable (-Al+Ca); (II) fertilized soil with calcium nitrate [Ca(NO3)2·4H2O] and Al available (+Al+Ca); and (III) soil without Ca addition and Al available (+Al-Ca). At the beginning of the reproductive stage, we evaluated the photosynthetic processes, mineral nutrition, and leaf anatomy and morphological traits of plants. The photosynthetic parameters were good tools for monitor Al sensitivity in bean. +Al+Ca soil treatment mitigated the deleterious effects of Al on growth and mineral nutrition of both bean cultivars. However, Ca did not prevent the toxic effects of Al on leaf anatomy. Al stress and Ca deficiency caused negative effects on nutrient content, photosynthetic activity and leaf anatomy of bean plants. Calcium mitigated Al toxicity, primarily in the Campos Gerais cultivar, showing the potential to improve bean crop productivity in acid soils.
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Affiliation(s)
- Camila Vilela Vasconcelos
- Laboratory of Ecophysiology and Plant Productivity, Goiano Federal Institute of Education Science and Technology, Campus Rio Verde, PO Box 66, Rio Verde, Goiás, 75901-970, Brazil
| | - Alan Carlos Costa
- Laboratory of Ecophysiology and Plant Productivity, Goiano Federal Institute of Education Science and Technology, Campus Rio Verde, PO Box 66, Rio Verde, Goiás, 75901-970, Brazil.
| | - Caroline Müller
- Laboratory of Ecophysiology and Plant Productivity, Goiano Federal Institute of Education Science and Technology, Campus Rio Verde, PO Box 66, Rio Verde, Goiás, 75901-970, Brazil
| | - Gustavo Castoldi
- Laboratory of Ecophysiology and Plant Productivity, Goiano Federal Institute of Education Science and Technology, Campus Rio Verde, PO Box 66, Rio Verde, Goiás, 75901-970, Brazil
| | - Andréia Mendes Costa
- Laboratory of Ecophysiology and Plant Productivity, Goiano Federal Institute of Education Science and Technology, Campus Rio Verde, PO Box 66, Rio Verde, Goiás, 75901-970, Brazil
| | - Kássia de Paula Barbosa
- Laboratory of Ecophysiology and Plant Productivity, Goiano Federal Institute of Education Science and Technology, Campus Rio Verde, PO Box 66, Rio Verde, Goiás, 75901-970, Brazil
| | - Arthur Almeida Rodrigues
- Laboratory of Plant Anatomy, Goiano Federal Institute of Education Science and Technology, Campus Rio Verde, PO Box 66, Rio Verde, Goiás, 75901-970, Brazil
| | - Adinan Alves da Silva
- Laboratory of Ecophysiology and Plant Productivity, Goiano Federal Institute of Education Science and Technology, Campus Rio Verde, PO Box 66, Rio Verde, Goiás, 75901-970, Brazil
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Krasnov GS, Dmitriev AA, Zyablitsin AV, Rozhmina TA, Zhuchenko AA, Kezimana P, Snezhkina AV, Fedorova MS, Novakovskiy RO, Pushkova EN, Povkhova LV, Bolsheva NL, Kudryavtseva AV, Melnikova NV. Aluminum Responsive Genes in Flax ( Linum usitatissimum L.). BIOMED RESEARCH INTERNATIONAL 2019; 2019:5023125. [PMID: 30941364 PMCID: PMC6421055 DOI: 10.1155/2019/5023125] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/22/2018] [Accepted: 12/12/2018] [Indexed: 01/08/2023]
Abstract
Flax (Linum usitatissimum L.) is a multipurpose crop which is used for the production of textile, oils, composite materials, pharmaceuticals, etc. Soil acidity results in a loss of seed and fiber production of flax, and aluminum toxicity is a major factor that depresses plant growth and development in acid conditions. In the present work, we evaluated gene expression alterations in four flax genotypes with diverse tolerance to aluminum exposure. Using RNA-Seq approach, we revealed genes that are differentially expressed under aluminum stress in resistant (Hermes, TMP1919) and sensitive (Lira, Orshanskiy) cultivars and selectively confirmed the identified alterations using qPCR. To search for differences in response to aluminum between resistant and sensitive genotypes, we developed the scoring that allowed us to suggest the involvement of MADS-box and NAC transcription factors regulating plant growth and development and enzymes participating in cell wall modifications in aluminum tolerance in flax. Using Gene Ontology (GO) enrichment analysis, we revealed that glutathione metabolism, oxidoreductase, and transmembrane transporter activities are the most affected by the studied stress in flax. Thus, we identified genes that are involved in aluminum response in resistant and sensitive genotypes and suggested genes that contribute to flax tolerance to the aluminum stress.
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Affiliation(s)
- George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexander V. Zyablitsin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Tatiana A. Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Federal Research Center for Bast Fiber Crops, Torzhok 172002, Russia
| | - Alexander A. Zhuchenko
- Federal Research Center for Bast Fiber Crops, Torzhok 172002, Russia
- All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, Moscow 115598, Russia
| | - Parfait Kezimana
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Peoples' Friendship University of Russia (RUDN University), Moscow 117198, Russia
| | - Anastasiya V. Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Maria S. Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
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Wang N, Feng Z, Zhou Y, Zhu H, Yao Q. External hyphae of Rhizophagus irregularis DAOM 197198 are less sensitive to low pH than roots in arbuscular mycorrhizae: evidence from axenic culture system. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:649-657. [PMID: 28799726 DOI: 10.1111/1758-2229.12573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 05/10/2023]
Abstract
The growth of plant roots and arbuscular mycorrhizal fungi (AMF) can be inhibited by low pH; however, it is largely unknown which is more sensitive to low pH. This study aimed to compare the physiological and molecular responses of external hyphae (EH) and roots to low pH in terms of growth, development and functioning. We established AM symbiosis in a two-compartmented system (root compartment, RC; hyphal compartment, HC) using AMF and transformed hairy roots and exposed them to pH 6.5 and/or pH 4.5. The results showed that pH 4.5 significantly decreased root cell viability, while EH at pH 6.5 attenuated the effect. In either RC or HC, pH 4.5 reduced biomass, P content, colonization, ALP activity in roots, and ALP activity and polyphosphate accumulation in EH. GintPT expression in EH was inhibited by pH 4.5 in HC but not in RC. The expression of mycorrhiza-responsive LePTs was significantly reduced by the lower colonization due to decreased pH in either RC or HC, while the expression of non-mycorrhiza-responsive LePTs was not affected. Variation partitioning analysis indicated that EH was less sensitive to low pH than roots. The interactions between roots and EH under low pH stress merit further investigation.
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Affiliation(s)
- Ning Wang
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, Guangdong Engineering Research Center for Grass Science, Guangzhou 510642, China
- Department of Municipal Engineering, Guangdong Polytechnic of Water Resources and Electric Engineering, Guangzhou 510635, China
| | - Zengwei Feng
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, Guangdong Engineering Research Center for Grass Science, Guangzhou 510642, China
| | - Yang Zhou
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, Guangdong Engineering Research Center for Grass Science, Guangzhou 510642, China
| | - Honghui Zhu
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou 510070, China
| | - Qing Yao
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, Guangdong Engineering Research Center for Grass Science, Guangzhou 510642, China
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Moreno-Alvarado M, García-Morales S, Trejo-Téllez LI, Hidalgo-Contreras JV, Gómez-Merino FC. Aluminum Enhances Growth and Sugar Concentration, Alters Macronutrient Status and Regulates the Expression of NAC Transcription Factors in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:73. [PMID: 28261224 PMCID: PMC5306397 DOI: 10.3389/fpls.2017.00073] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 01/12/2017] [Indexed: 05/18/2023]
Abstract
Aluminum (Al) is a beneficial element for some plant species, especially when used at low concentrations. Though some transcription factors are induced by exposure to this element, no data indicate that Al regulates the expression of NAC genes in rice. In this study we tested the effect of applying 200 μM Al on growth, chlorophyll, amino acids, sugars, macronutrient concentration and regulation of NAC transcription factors gene expression in 24-day-old plants of four rice (Oryza sativa ssp. indica) cultivars: Cotaxtla, Tres Ríos, Huimanguillo and Temporalero, grown hydroponically under greenhouse conditions. Twenty days after treatment, we observed that Al enhanced growth in the four cultivars studied. On average, plants grown in the presence of Al produced 140% more root dry biomass and were 30% taller than control plants. Cotaxtla and Temporalero showed double the root length, while Huimanguillo and Cotaxtla had three times more root fresh biomass and 2.5 times more root dry biomass. Huimanguillo plants showed 1.5 times more shoot height, while Cotaxtla had almost double the root dry biomass. With the exception of Tres Ríos, the rest of the cultivars had almost double the chlorophyll concentration when treated with Al, whereas amino acid and proline concentrations were not affected by Al. Sugar concentration was also increased in plants treated with Al, almost 11-fold in comparison to the control. Furthermore, we observed a synergic response of Al application on P and K concentration in roots, and on Mg concentration in shoots. Twenty-four hours after Al treatment, NAC transcription factors gene expression was measured in roots by quantitative RT-PCR. Of the 57 NAC transcription factors genes primer-pairs tested, we could distinguish that 44% (25 genes) showed different expression patterns among rice cultivars, with most of the genes induced in Cotaxtla and Temporalero plants. Of the 25 transcription factors up-regulated, those showing differential expression mostly belonged to the NAM subfamily (56%). We conclude that Al improves growth, increases sugar concentration, P and K concentrations in roots, and Mg concentration in shoots, and report, for the first time, that Al differentially regulates the expression of NAC transcription factors in rice.
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Affiliation(s)
| | - Soledad García-Morales
- Biotechnology, Colegio de Postgraduados Campus CórdobaAmatlán de los Reyes, Mexico
- Plant Biotechnology, CONACYT-CIATEJ, El Bajío del ArenalZapopan, Mexico
| | | | | | - Fernando Carlos Gómez-Merino
- Biotechnology, Colegio de Postgraduados Campus CórdobaAmatlán de los Reyes, Mexico
- *Correspondence: Fernando Carlos Gómez-Merino
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Bojórquez-Quintal E, Escalante-Magaña C, Echevarría-Machado I, Martínez-Estévez M. Aluminum, a Friend or Foe of Higher Plants in Acid Soils. FRONTIERS IN PLANT SCIENCE 2017; 8:1767. [PMID: 29075280 PMCID: PMC5643487 DOI: 10.3389/fpls.2017.01767] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 09/27/2017] [Indexed: 05/11/2023]
Abstract
Aluminum (Al) is the most abundant metal in the earth's crust, but its availability depends on soil pH. Despite this abundance, Al is not considered an essential element and so far no experimental evidence has been put forward for a biological role. In plants and other organisms, Al can have a beneficial or toxic effect, depending on factors such as, metal concentration, the chemical form of Al, growth conditions and plant species. Here we review recent advances in the study of Al in plants at physiological, biochemical and molecular levels, focusing mainly on the beneficial effect of Al in plants (stimulation of root growth, increased nutrient uptake, the increase in enzyme activity, and others). In addition, we discuss the possible mechanisms involved in improving the growth of plants cultivated in soils with acid pH, as well as mechanisms of tolerance to the toxic effect of Al.
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Affiliation(s)
- Emanuel Bojórquez-Quintal
- CONACYT-Laboratorio de Análisis y Diagnóstico del Patrimonio, El Colegio de Michoacán, La Piedad, Mexico
| | - Camilo Escalante-Magaña
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Ileana Echevarría-Machado
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Manuel Martínez-Estévez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
- *Correspondence: Manuel Martínez-Estévez,
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