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

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.

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

10.21203/rs.2.21741/v1 ◽

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.

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

Agronomy ◽

10.3390/agronomy11040670 ◽

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.

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Comparative Transcriptome Analysis Provides New Insights into the Molecular Regulatory Mechanism of Adventitious Root Formation in Ramie (Boehmeria nivea L.)

Plants ◽

10.3390/plants10010160 ◽

2021 ◽

Vol 10 (1) ◽

pp. 160

Author(s):

Kunmei Chen ◽

Bing Guo ◽

Chunming Yu ◽

Ping Chen ◽

Jikang Chen ◽

...

Keyword(s):

Transcriptome Analysis ◽

Culture Condition ◽

Adventitious Root ◽

Regulatory Mechanism ◽

Adventitious Rooting ◽

Metabolic Process ◽

Comparative Transcriptome ◽

Water Culture ◽

Comparative Transcriptome Analysis ◽

Kegg Analysis

The occurrence of adventitious roots is necessary for the survival of cuttings. In this study, comparative transcriptome analysis between two ramie (Boehmeria nivea L.) varieties with different adventitious root (AR) patterns was performed by mRNA-Seq before rooting (control, CK) and 10 days water-induced adventitious rooting (treatment, T) to reveal the regulatory mechanism of rooting. Characterization of the two ramie cultivars, Zhongzhu No 2 (Z2) and Huazhu No 4 (H4), indicated that Z2 had a high adventitious rooting rate but H4 had a low rooting rate. Twelve cDNA libraries of the two varieties were constructed, and a total of 26,723 genes were expressed. In the non-water culture condition, the number of the distinctive genes in H4 was 2.7 times of that in Z2, while in the water culture condition, the number of the distinctive genes in Z2 was nearly 2 times of that in H4. A total of 4411 and 5195 differentially expressed genes (DEGs) were identified in the comparison of H4CK vs. H4T and Z2CK vs. Z2T, respectively. After the water culture, more DEGs were upregulated in Z2, but more DEGs were downregulated in H4. Gene ontology (GO) functional analysis of the DEGs indicated that the polysaccharide metabolic process, carbohydrate metabolic process, cellular carbohydrate metabolic process, cell wall macromolecule metabolic process, and photosystem GO terms were distinctively significantly enriched in H4. Simultaneously, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that photosynthesis, photosynthesis antenna proteins, and starch and sucrose metabolism pathways were distinctively significantly enriched in H4. Moreover, KEGG analysis showed that jasmonic acid (JA) could interact with ethylene to regulate the occurrence and number of AR in Z2. This study reveals the transcriptomic divergence of two ramie varieties with high and low adventitious rooting rates, and provides insights into the molecular regulatory mechanism of AR formation in ramie.

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

10.21203/rs.3.rs-17426/v1 ◽

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.

Download Full-text