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Integrated Transcriptome and Metabolome Analysis of Salinity Tolerance in Response to Foliar Application of β-Alanine in Cotton Seedlings - PubMed

  • ️Sun Jan 01 2023

Integrated Transcriptome and Metabolome Analysis of Salinity Tolerance in Response to Foliar Application of β-Alanine in Cotton Seedlings

Wei Ren et al. Genes (Basel). 2023.

Abstract

Salinity is amongst the serious abiotic stresses cotton plants face, impairing crop productivity. Foliar application of β-alanine is employed to improve salt tolerance in various crops, but the exact mechanism behind it is not yet completely understood. An advanced line SDS-01 of upland cotton Gossypium hirsutum L. was utilized to determine its salt tolerance. Foliar treatment with the β-alanine solution at different concentrations was applied to the seedlings stressed with 0.8% NaCl solution. On the 10th day of treatment, samples were collected for transcriptome and metabolome analyses. β-alanine solution at a concentration of 25 mM was found to be the best treatment with the lowest mortality rate and highest plant height and above-ground biomass under salt stress. Both differentially expressed genes and accumulated metabolites analyses showed improved tolerance of treated seedlings. The photosynthetic efficiency improved in seedlings due to higher expression of photosynthesis-antenna proteins and activation of hormones signal transduction after treatment with β-alanine. Highly expressed transcription factors observed were MYB, HD-ZIP, ARF, MYC, EREB, DELLA, ABF, H2A, H4, WRKY, and HK involved in the positive regulation of salinity tolerance in β-alanine-treated seedlings. Furthermore, compared to the control, the high accumulation of polyamines, coumarins, organic acids, and phenolic compounds in the β-alanine-treated seedlings helped regulate cellular antioxidant (glutathione and L-Cysteine) production. Hence, to improve salt tolerance and productivity in cotton, foliar application of β-alanine at the seedling stage can be a valuable management practice.

Keywords: conjoint analysis; differentially accumulated metabolites; differentially expressed genes; salt tolerance; upland cotton.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1

The chemical structure for β-alanine (a non-proteinogenic amino acid) [32].

Figure 2
Figure 2

Mean comparisons of morphological characteristics, i.e., (a) the mortality (%), (b) growth (cm), and (c) above-ground biomass (d), for cotton seedlings under salt stress pre-treated with the β-alanine solution at 25 days after planting. The bar graph showed significant statistical differences (p = 0.05) between the treatments (A2, A3, A4, and A5) and CK (A1). Bar plots with overlapping error bars are statistically insignificant, while the letters showed statistical significance if the samples did not share letters. (d) Phenotypes of the cotton seedlings exposed to 0.8% salt stress after exogenous treatment (foliar application) with 100 mL of β-alanine solution in concentrations as A1(CK) = 0 mM, A2 = 10 mM, A3 = 25 mM, A4 = 50 mM, and A5 = 100 mM.

Figure 3
Figure 3

(a) Heatmap was for depicting Pearson’s correlation coefficient of the sample gene expression. (b) Principal component analysis of the sample gene expression. Different colors represent different samples. (c) The overall fragment/kb of transcript/million mapped reads (FPKM) values for each replicate were represented as a graph of violin boxplots. The abscissa represented different samples; the ordinate illustrated each sample expression’s log2 values for FPKM, where β-alanine solution in different concentrations were used as A1(CK) = 0 mM, A2 = 10 mM, A3 = 25 mM, A4 = 50 mM, and A5 = 100 mM; 1, 2, and 3 with the treatments represent the replicates.

Figure 4
Figure 4

(a) A barplot exhibiting the number of differentially expressed genes (DEGs) with up and down regulations identified for the β-alanine-treated cotton seedling samples against salt stress. (b) Venn diagram illustrating the number of common and conserved DEGs between different comparison groups of treatments with CK(A1). β-alanine solution in different concentrations used were as follows: A1(CK) = 0 mM, A2 = 10 mM, A3 = 25 mM, A4 = 50 mM, and A5 = 100 mM; 1, 2, and 3 with the treatments represent the replicates.

Figure 5
Figure 5

(a) Two-way hierarchical clustering of DEGs enriched in photosynthesis pathways (Ko00195) based on log2FC values. KEGG pathway map of the DEGs enriched in photosynthesis-antenna proteins (Ko00195). The red boxes are for the representation of enriched DEGs in photosynthesis. (b) The pathway showed increased expression of DEGs for photosystem II, chlorophyll, antenna proteins, etc., in the β-alanine-treated seedlings from A1 vs. A3 treatment as compared to A1(CK). β-alanine solution in different concentrations used were as follows: A1(CK) = 0 mM, A2 = 10 mM, A3 = 25 mM, A4 = 50 mM, and A5 = 100 mM; 1, 2, and 3 with the treatments represent the replicates.

Figure 6
Figure 6

(a) Pearson’s correlation coefficient heatmap of the detected metabolites in β-alanine-treated and control cotton seedlings challenged with salt stress. (b) Principal component analyses of metabolites extracted from CK and treated cotton seedlings. (c) Heatmap of relative intensities of metabolites. Where A1(CK) = 0.8% salt stressed, A2, A3, A4, and A5, salt-stressed seedlings exogenously sprayed with β-alanine solution in different concentrations of A2 = 10 mM, A3 = 25 mM, A4 = 50 mM, and A5 = 100 mM; 1, 2, and 3 with the treatments represent the replicates.

Figure 7
Figure 7

(a) Venn diagram of the differentially accumulated metabolites between different treatment comparisons. (b) K-means diagram of the differentially accumulated metabolites among CK and treated cotton seedling samples (A1 vs. A2, A1 vs. A3, A1 vs. A4, and A1 vs. A5). The x-axis represents the sample groups, the y-axis represents the relative content of standardized metabolites, the sub-class represents the number of the metabolite category with the same changing trend, and the metabolite represents the number of metabolites in the category. Where A1(CK) = 0.8% salt stressed, A2, A3, A4, and A5, salt-stressed seedlings exogenously sprayed with β-alanine solution in different concentrations of A2 = 10 mM, A3 = 25 mM, A4 = 50 mM, and A5 = 100 mM; 1, 2, and 3 with the treatments represent the replicates.

Figure 8
Figure 8

Top 10 up-down accumulated metabolites in different treatment comparisons of the β-alanine-treated cotton seedlings exposed to salt stress. (a) A1vsA2, (b) A1vsA3, (c) A1vsA4, (d) A1vsA5. The bar graphs with log2 fold change values of the differentially accumulated metabolites, where red and green colors represent up and down regulations, respectively and the encircled metabolite compounds were found conserved in more than two comparison groups of treatments. A1(CK) = 0.8% salt stressed, A2, A3, A4, and A5 = 0.8% salt-stressed seedlings with foliar application of 100 mL of 50 µM, 100 µM, 200 µM, and 500 µM β-alanine solution, respectively.

Figure 9
Figure 9

Conjoint analyses of transcriptome and metabolome data from β-alanine-treated cotton seedling samples. PCA of (a) transcriptome and (b) metabolome data to visualize the differences between the sample groups and no differences between replicates. Pearson correlation coefficient analyses via nine quadrant plots of genes and metabolites illustrate different multiples of genes and metabolites with a correlation coefficient >0.8 in each differential group. (c) A1vsA2, (d) A1vsA3, (e) A1vsA4, (f) A1vsA5. The black dotted line, from left to right, from top to bottom, divides the chart into 9 quadrants. A1(CK) = 0.8% salt stressed, A2, A3, A4, and A5 = 0.8% salt-stressed seedlings with foliar application of 100 mL of 50 µM, 100 µM, 200 µM, and 500 µM β-alanine solution, respectively.

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This work was funded by the Department of Science and Technology of Xinjiang (Grant No. 2022E01070).

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