scholarly journals Deep expression scrutiny of juxtaposed wild and cultivated lentil furnishes new insight into aluminium tolerance mechanism

2020 ◽  
Author(s):  
Dharmendra Singh ◽  
Chandan Kumar Singh ◽  
Jyoti Taunk ◽  
Ram Sewak Singh Tomar ◽  
Madan Pal ◽  
...  
Keyword(s):  
Pathway Analysis ◽  
De Novo ◽  
Crop Improvement ◽  
Al Toxicity ◽  
Aluminium Tolerance ◽  
Regulation Of Transcription ◽  
Al Tolerance ◽  
Illumina Hiseq ◽  
Al Stress ◽  
Protein Ubiquitination

Abstract Background: Aluminium (Al) stress hinders crop productivity in acidic soils. Lentil contains rich source of protein and micronutrients and cultivated in different parts of world. To enhance knowledge about Al toxicity tolerance, present study emphasizes on mechanistic analysis of genes associated with Al stress through de novo transcriptomic analysis of tolerant (L-4602), wild (ILWL-15) and sensitive (BM-4) genotypes. Result: Illumina HiSeq 2500 platform evaluated contigs ranging from 15,305 to 18,861 for all the samples with N 50 values of 1795 bp. Four annotation softwares revealed differential regulation of several genes where 30,158 genes were specifically up-regulated for combinations under Al stress conditions alone. Top up-regulated Differentially Expressed Genes (DEGs) in tolerant cultivar when compared to the sensitive one were found to be involved in protein transport as well as degradation, defences, cell growth and development. Wild v/s cultivar comparison revealed upregulation of wild DEGs that are involved in regulation of transcription in differentiating cells, pre-mRNA splicing, catalysis and protein ubiquitination. Based on assembled Unigenes, 89,722 high-quality SNPs and 39,874 SSRs were detected. Twelve selected genes were validated using qRT-PCR. KEGG pathway analysis extracted 8,757 GO annotation terms within molecular, cellular and biological processes. Pathway analysis indicated that organic acid synthesis and their transportation along with detoxification of ROS, an alternate pathway involving metacaspase-1,4,9 for programmed cell death were also significantly induced due to Al stress. Conclusion: Present study unveils the characterization of differential transcripts generated under Al stress indicating Al tolerance as a multiplex phenomenon which will directly widen crop improvement programmes for Al toxicity utilizing molecular approaches.

scholarly journals Deep expression scrutiny provides genetic basis of aluminium tolerance in wild (Lens nigrican) and cultivated lentil (Lens culinaris Medik.)

2020 ◽  
Author(s):  
Dharmendra Singh ◽  
Chandan Kumar Singh ◽  
Jyoti Taunk ◽  
Shristi Sharma ◽  
RamSewak Singh Tomar ◽  
...  
Keyword(s):  
Pathway Analysis ◽  
De Novo ◽  
Crop Improvement ◽  
Al Toxicity ◽  
Aluminium Tolerance ◽  
Regulation Of Transcription ◽  
Al Tolerance ◽  
Illumina Hiseq ◽  
Al Stress ◽  
Protein Ubiquitination

Abstract Background: Aluminium (Al) stress hinders crop productivity in acidic soils. Lentil contains rich source of protein and micronutrients and cultivated in different parts of world. To enhance knowledge about Al toxicity tolerance, present study emphasizes on mechanistic analysis of genes associated with Al stress through de novo transcriptomic analysis of tolerant (L-4602), wild (ILWL-15) and sensitive (BM-4) genotypes. Result: Illumina HiSeq 2500 platform evaluated contigs ranging from 15,305 to 18,861 for all the samples with N50 values of 1795 bp. Four annotation softwares revealed differential regulation of several genes where 30,158 genes were specifically up-regulated for combinations under Al stress conditions alone. Top up-regulated Differentially Expressed Genes (DEGs) in tolerant cultivar when compared to the sensitive one were found to be involved in protein transport as well as degradation, defences, cell growth and development. Wild v/s cultivar comparison revealed upregulation of wild DEGs that are involved in regulation of transcription in differentiating cells, pre-mRNA splicing, catalysis and protein ubiquitination. Based on assembled Unigenes, 89,722 high-quality SNPs and 39,874 SSRs were detected. Twelve selected genes were validated using qRT-PCR. KEGG pathway analysis extracted 8,757 GO annotation terms within molecular, cellular and biological processes. Pathway analysis indicated that organic acid synthesis and their transportation along with detoxification of ROS, an alternate pathway involving metacaspase-1,4,9 for programmed cell death were also significantly induced due to Al stress.Conclusion: Present study unveils the characterization of differential transcripts generated under Al stress indicating Al tolerance as a multiplex phenomenon which will directly widen crop improvement programmes for Al toxicity utilizing molecular approaches.

scholarly journals Comparative Transcriptome Analysis of Two Contrasting Soybean Varieties in Response to Aluminum Toxicity

2020 ◽  
Vol 21 (12) ◽  
pp. 4316
Author(s):  
Lijuan Zhao ◽  
Jingjing Cui ◽  
Yuanyuan Cai ◽  
Songnan Yang ◽  
Juge Liu ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Aluminum Toxicity ◽  
Metabolic Process ◽  
Al Toxicity ◽  
Regulation Of Transcription ◽  
Comparative Transcriptome ◽  
Al Tolerance ◽  
Comparative Transcriptome Analysis ◽  
Al Stress ◽  
Significant Difference

Aluminum (Al) toxicity is a major factor limiting crop productivity on acid soils. Soybean (Glycine max) is an important oil crop and there is great variation in Al tolerance in soybean germplasms. However, only a few Al-tolerance genes have been reported in soybean. Therefore, the purpose of this study was to identify candidate Al tolerance genes by comparative transcriptome analysis of two contrasting soybean varieties in response to Al stress. Two soybean varieties, M90-24 (M) and Pella (P), which showed significant difference in Al tolerance, were used for RNA-seq analysis. We identified a total of 354 Al-tolerance related genes, which showed up-regulated expression by Al in the Al-tolerant soybean variety M and higher transcript levels in M than P under Al stress. These genes were enriched in the Gene Ontology (GO) terms of cellular glucan metabolic process and regulation of transcription. Five out of 11 genes in the enriched GO term of cellular glucan metabolic process encode cellulose synthases, and one cellulose synthase gene (Glyma.02G205800) was identified as the key hub gene by co-expression network analysis. Furthermore, treatment of soybean roots with a cellulose biosynthesis inhibitor decreased the Al tolerance, indicating an important role of cellulose production in soybean tolerance to Al toxicity. This study provides a list of candidate genes for further investigation on Al tolerance mechanisms in soybean.

Combining ability for aluminium tolerance in triticale

1999 ◽  
Vol 133 (4) ◽  
pp. 371-377 ◽  
Author(s):  
X. G. ZHANG ◽  
R. S. JESSOP ◽  
F. ELLISON
Keyword(s):  
Genetic Variation ◽  
Stress Tolerance ◽  
Combining Ability ◽  
Additive Genetic Variance ◽  
Diallel Analysis ◽  
Aluminium Tolerance ◽  
Additive Effects ◽  
Al Tolerance ◽  
Al Stress ◽  
Polygenic System

Root re-growth, following aluminium (Al) stress, has been used as an indicator of Al stress tolerance. Genetic variation in root re-growth characteristics among eight triticale genotypes was investigated by a diallel analysis. Highly significant variation due to both general combining ability (GCA) effects and specific combining ability (SCA) effects indicated that both additive effects and non-additive effects were important in explaining the genetic variation for Al tolerance. The high estimates of heritability and the predictability ratio for root re-growth revealed the preponderance of additive genetic variance in the inheritance of Al tolerance. Differences in patterns of GCA effects and SCA effects among the parents provided strong evidence that the genetic control of variation for Al tolerance as assessed by root re-growth was a complex polygenic system. Three Al-tolerant genotypes, Tahara, Abacus, and 19th ITSN 70–4, were found to be the best general combiners for larger root re-growth, and they could be used in hybridization programmes to improve Al stress tolerance by following a simple pedigree method of selective breeding.

Recent molecular breeding advances for improving aluminium tolerance in maize and sorghum.

2021 ◽  
pp. 318-324
Author(s):  
Claudia Teixeira Guimaraes ◽  
Jurandir Vieira de Magalhaes
Keyword(s):  
Target Genes ◽  
Acid Soils ◽  
Genetic Effect ◽  
Al Toxicity ◽  
Aluminium Tolerance ◽  
Al Tolerance ◽  
Toxic Compound ◽  
The World ◽  
Breeding Programmes ◽  
Wide Adaptation

Abstract Citrate transporters belonging to the multidrug and toxic compound extrusion (MATE) family of membrane transporters in sorghum and maize, SbMATE and ZmMATE1, respectively, play a major role in aluminium (Al) tolerance. However, these MATE members show regulatory differences, as well as peculiarities in their genetic effect and mode of action. These aspects, which are discussed in this chapter, have to be considered to design successful breeding programmes in order to achieve maximum Al tolerance and, consequently, to improve grain and biomass production in regions of the world with Al toxicity. As shown in this chapter, target genes with major effects and molecular tools are available for marker-assisted breeding for improving Al tolerance both in sorghum and maize. However, wide adaptation to acid soils should be sought by pyramiding genes controlling different traits such as drought tolerance, P acquisition, resistance to diseases and other stresses commonly found in each agroecological environment.

scholarly journals In vitro rhizobia response and symbiosis process under aluminum stress

2018 ◽  
Vol 64 (8) ◽  
pp. 511-526 ◽  
Author(s):  
María D. Artigas Ramírez ◽  
Jéssica D. Silva ◽  
Naoko Ohkama-Ohtsu ◽  
Tadashi Yokoyama
Keyword(s):  
Metabolic Pathways ◽  
Al Toxicity ◽  
Plant Genotype ◽  
Al Tolerance ◽  
Aluminum Stress ◽  
Selective Force ◽  
Al Stress ◽  
Acidic Conditions ◽  
Ph Conditions

Aluminum (Al) toxicity is a major problem affecting soil fertility, microbial diversity, and nutrient uptake of plants. Rhizobia response and legume interaction under Al conditions are still unknown; it is important to understand how to develop and improve legume cultivation under Al stress. In this study, rhizobia response was recorded under different Al concentrations. Al effect on rhizobial cells was characterized by combination with different two pH conditions. Symbiosis process was compared between α- and β-rhizobia inoculated onto soybean varieties. Rhizobial cell numbers was decreased as Al concentration increased. However, induced Al tolerance considerably depended on rhizobia types and their origins. Accordingly, organic acid results were in correlation with growth rate and cell density which suggested that citric acid might be a positive selective force for Al tolerance and plant interaction on rhizobia. Al toxicity delayed and interrupted the plant–rhizobia interaction and the effect was more pronounced under acidic conditions. Burkholderia fungorum VTr35 significantly improved plant growth under acid–Al stress in combination with all soybean varieties. Moreover, plant genotype was an important factor to establish an effective nodulation and nitrogen fixation under Al stress. Additionally, tolerant rhizobia could be applied as an inoculant on stressful agroecosystems. Furthermore, metabolic pathways have still been unknown under Al stress.

Brachypodium distachyon: a model species for aluminium tolerance in Poaceae

2014 ◽  
Vol 41 (12) ◽  
pp. 1270 ◽  
Author(s):  
Roberto Contreras ◽  
Ana M. Figueiras ◽  
Francisco J. Gallego ◽  
Cesar Benito
Keyword(s):  
Promoter Region ◽  
Brachypodium Distachyon ◽  
Al Toxicity ◽  
Aluminium Tolerance ◽  
H2o2 Production ◽  
Al Tolerance ◽  
Model Species ◽  
Intense Staining ◽  
Qrt Pcr ◽  
Staining Methods

Aluminium (Al) toxicity is the main abiotic stress limiting plant productivity in acidic soils. Studies on Al tolerance have been conducted in Poaceae but their genomes are very complex. Fifty-nine diploid lines (2n = 10) of Brachypodium distachyon (L.) P. Beauv. and 37 allotetraploid samples (2n = 30) of Brachypodium hybridum Catalán, Joch. Müll., Hasterok & Jenkins sp. nov. were used to evaluate their tolerance to different Al concentrations. B. distachyon is Al-sensitive compared with oat, rice and rye. The diploid lines (except ABR8) were sensitive like barley and Arabidopsis; however, 10 allotetraploid samples were Al-tolerant. Four different root-staining methods were used to detect Al accumulation, cell death, lipid peroxidation and H2O2 production in diploid and allotetraploid plants. The roots treated with Al showed more intense staining in sensitive than tolerant lines. Also, without any staining, the Al treated roots of sensitive plants appear darker than roots from tolerant ones. The study concerning to the organic acids exudation shows that the exudation of citrate and malate was induced only in the roots from tolerant diploid line (ABR8) and tolerant allotetraploid samples. In contrast, the mRNA expression changes of several candidate genes for Al-activated transporters belonging to the ALMT and MATE families were analysed by quantitative PCR (qRT–PCR). The data obtained indicate that the transcripts from BdALMT1, BdMATE1 and BdMATE2 were present mainly in roots and, moreover, that the BdALMT1 transcript is present in higher amounts in the tolerant ABR8 than in the sensitive ABR1 plants indicating that this gene may be involved in Al tolerance. Finally, an insertion was detected in the promoter region of the BdALMT1 of tolerant diploid and allotetraploid plants.

scholarly journals Comparative Analyses Reveal Peroxidases Play Important Roles in Soybean Tolerance to Aluminum Toxicity

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 670
Author(s):  
Juge Liu ◽  
Xiangting Wang ◽  
Ning Wang ◽  
Yang Li ◽  
Ting Jin ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Aluminum Toxicity ◽  
Acid Soils ◽  
Al Toxicity ◽  
Al Tolerance ◽  
Al Stress ◽  
Important Barrier ◽  
Glycine Max L ◽  
Go Terms ◽  
H2o2 Pretreatment

Aluminum (Al) toxicity is an important barrier to soybean (Glycine max (L.) Merr.) production in acid soils. However, little is known about the genes underlying Al tolerance in soybean. We aim to find the key candidate genes and investigate their roles in soybean tolerance to Al toxicity in this study. Comparative transcriptome analyses of the Al-tolerant (KF) and Al-sensitive (GF) soybean varieties under control and Al stress at 6, 12, and 24 h were investigated. A total of 1411 genes showed specific up-regulation in KF or more up-regulation in KF than in GF by Al stress, which were significantly enriched in the GO terms of peroxidase (POD) activity, transporter activity (including the known Al tolerance-related ABC transporter, ALMT, and MATE), and four families of transcription factors (AP2, C3H4, MYB, WRKY). The expression levels of seven POD genes were up-regulated by Al stress for at least one time point in KF. The H2O2 pretreatment significantly improved Al tolerance of KF, which is likely due to increased POD activity induced by H2O2. Our results suggest that PODs play important roles in soybean tolerance to Al toxicity. We also propose a list of candidate genes for Al tolerance in KF, which would provide valuable insights into the Al tolerance mechanisms in soybean.

scholarly journals Overexpression of the Aldehyde Dehydrogenase Gene ZmALDH Confers Aluminum Tolerance in Arabidopsis thaliana

2022 ◽  
Vol 23 (1) ◽  
pp. 477
Author(s):  
Han-Mei Du ◽  
Chan Liu ◽  
Xin-Wu Jin ◽  
Cheng-Feng Du ◽  
Yan Yu ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Aldehyde Dehydrogenase ◽  
Aluminum Tolerance ◽  
Al Toxicity ◽  
Al Tolerance ◽  
Al Stress ◽  
Dehydrogenase Gene ◽  
Glutathione Cycle ◽  
Excessive Accumulation ◽  
Main Factor

Aluminum (Al) toxicity is the main factor limiting plant growth and the yield of cereal crops in acidic soils. Al-induced oxidative stress could lead to the excessive accumulation of reactive oxygen species (ROS) and aldehydes in plants. Aldehyde dehydrogenase (ALDH) genes, which play an important role in detoxification of aldehydes when exposed to abiotic stress, have been identified in most species. However, little is known about the function of this gene family in the response to Al stress. Here, we identified an ALDH gene in maize, ZmALDH, involved in protection against Al-induced oxidative stress. Al stress up-regulated ZmALDH expression in both the roots and leaves. The expression of ZmALDH only responded to Al toxicity but not to other stresses including low pH and other metals. The heterologous overexpression of ZmALDH in Arabidopsis increased Al tolerance by promoting the ascorbate-glutathione cycle, increasing the transcript levels of antioxidant enzyme genes as well as the activities of their products, reducing MDA, and increasing free proline synthesis. The overexpression of ZmALDH also reduced Al accumulation in roots. Taken together, these findings suggest that ZmALDH participates in Al-induced oxidative stress and Al accumulation in roots, conferring Al tolerance in transgenic Arabidopsis.

scholarly journals Functional Characterization of Aluminum (Al)-Responsive Membrane-Bound NAC Transcription Factors in Soybean Roots

2021 ◽  
Vol 22 (23) ◽  
pp. 12854
Author(s):  
Yan Lin ◽  
Guoxuan Liu ◽  
Yingbing Xue ◽  
Xueqiong Guo ◽  
Jikai Luo ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Functional Characterization ◽  
Duplicate Gene ◽  
Al Toxicity ◽  
Al Tolerance ◽  
Cell Wall Modification ◽  
Nac Transcription Factors ◽  
Al Stress ◽  
Membrane Bound

The membrane-bound NAC transcription (NTL) factors have been demonstrated to participate in the regulation of plant development and the responses to multiple environmental stresses. This study is aimed to functionally characterize soybean NTL transcription factors in response to Al-toxicity, which is largely uncharacterized. The qRT-PCR assays in the present study found that thirteen out of fifteen GmNTL genes in the soybean genome were up-regulated by Al toxicity. However, among the Al-up-regulated GmNTLs selected from six duplicate gene pairs, only overexpressing GmNTL1, GmNTL4, and GmNTL10 could confer Arabidopsis Al resistance. Further comprehensive functional characterization of GmNTL4 showed that the expression of this gene in response to Al stress depended on root tissues, as well as the Al concentration and period of Al treatment. Overexpression of GmNTL4 conferred Al tolerance of transgenic Arabidopsis in long-term (48 and 72 h) Al treatments. Moreover, RNA-seq assay identified 517 DEGs regulated by GmNTL4 in Arabidopsis responsive to Al stress, which included MATEs, ALMTs, PMEs, and XTHs. These results suggest that the function of GmNTLs in Al responses is divergent, and GmNTL4 might confer Al resistance partially by regulating the expression of genes involved in organic acid efflux and cell wall modification.

scholarly journals MED12-Related (Neuro)Developmental Disorders: A Question of Causality

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 663
Author(s):  
Stijn van de Plassche ◽  
Arjan PM de Brouwer
Keyword(s):  
Developmental Disorders ◽  
De Novo ◽  
Expression Patterns ◽  
Mediator Complex ◽  
Gene Expression Patterns ◽  
Facial Dysmorphism ◽  
Regulation Of Transcription ◽  
Feeding Difficulties ◽  
Missense Variants ◽  
Pathogenic Variants

MED12 is a member of the Mediator complex that is involved in the regulation of transcription. Missense variants in MED12 cause FG syndrome, Lujan-Fryns syndrome, and Ohdo syndrome, as well as non-syndromic intellectual disability (ID) in hemizygous males. Recently, female patients with de novo missense variants and de novo protein truncating variants in MED12 were described, resulting in a clinical spectrum centered around ID and Hardikar syndrome without ID. The missense variants are found throughout MED12, whether they are inherited in hemizygous males or de novo in females. They can result in syndromic or nonsyndromic ID. The de novo nonsense variants resulting in Hardikar syndrome that is characterized by facial clefting, pigmentary retinopathy, biliary anomalies, and intestinal malrotation, are found more N-terminally, whereas the more C-terminally positioned variants are de novo protein truncating variants that cause a severe, syndromic phenotype consisting of ID, facial dysmorphism, short stature, skeletal abnormalities, feeding difficulties, and variable other abnormalities. This broad range of distinct phenotypes calls for a method to distinguish between pathogenic and non-pathogenic variants in MED12. We propose an isogenic iNeuron model to establish the unique gene expression patterns that are associated with the specific MED12 variants. The discovery of these patterns would help in future diagnostics and determine the causality of the MED12 variants.

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