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. 2020 May;47(5):3291-3303.
doi: 10.1007/s11033-020-05396-5. Epub 2020 Apr 17.

Transcriptome analysis of drought-tolerant sorghum genotype SC56 in response to water stress reveals an oxidative stress defense strategy

Farida Azzouz-Olden  1 , Arthur G Hunt  2 , Randy Dinkins  3
Affiliations

Transcriptome analysis of drought-tolerant sorghum genotype SC56 in response to water stress reveals an oxidative stress defense strategy

Farida Azzouz-Olden et al. Mol Biol Rep. 2020 May.

Abstract

Drought tolerance is a crucial trait for crops to curtail the yield loss inflicted by water stress, yet genetic improvement efforts are challenged by the complexity of this character. The adaptation of sorghum to abiotic stress, its genotypic variability, and relatively small genome make this species well-suited to dissect the molecular basis of drought tolerance. The use of differential transcriptome analysis provides a snapshot of the bioprocesses underlying drought response as well as genes that might be determinants of the drought tolerance trait. RNA sequencing data were analyzed via gene ontology enrichment to compare the transcriptome profiles of two sorghum lines, the drought-tolerant SC56 and the drought-sensitive Tx7000. SC56 outperformed Tx7000 in wet conditions by upregulating processes driving growth and guaranteeing homeostasis. The drought tolerance of SC56 seems to be an intrinsic trait occurring through overexpressing stress tolerance genes in wet conditions, notably genes acting in defense against oxidative stress (SOD1, SOD2, VTC1, MDAR1, MSRB2, and ABC1K1). Similarly to wet conditions, under drought, SC56 enhanced its transmembrane transport and maintained growth-promoting mechanisms. Under drought, SC56 also upregulated stress tolerance genes that heighten the antioxidant capacity (SOD1, RCI3, VTE1, UCP1, FD1, and FD2), regulatory factors (CIPK1 and CRK7), and repressors of premature senescence (SAUL1). The differential expression analysis uncovered biological processes which upregulation enables SC56 to be a better accumulator of biomass and connects the drought tolerance trait to key stress tolerance genes, making this genotype a judicious choice for isolation of tolerance genes.

Keywords: Drought; RNA-seq; Sorghum; Stay-green; Stress; Tolerance.

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Conflict of interest statement

All authors declare that they have no conflict of interest.

Figures

Fig. 1
Fig. 1
Pie chart of the number of differentially expressed genes. a Sections depict the experimental groups comparisons tagged with their respective total number of DEGs. b Sections represent group comparisons tagged with their corresponding number of upregulated DEGs. (Color figure online)
Fig. 2
Fig. 2
Genotype and water effects on gene regulation. a Genes differentially regulated in SC56 [SC56 (treat vs. cont)] and in Tx7000 [Tx7000 (treat vs. cont)] due to water regimen effect. b Genes differentially regulated due to genotype effect under drought [SC56 vs. TX7000 (treat)] and under irrigation [SC56 vs. TX7000 (cont)]. (Color figure online)
Fig. 3
Fig. 3
Numbers of upregulated DEGs by experimental group. a The Venn-diagram shows the number of non-overlapping DEGs (tags in non-common areas) as well as the number of overlapping transcripts between groups (intersecting areas). The depicted comparisons are the upregulation by SC56 versus Tx7000 under drought (S_t > Tx_t) and irrigation (S_c > Tx_c), and the upregulation by Tx7000 versus SC56 under drought (Tx_t > S_t) and irrigation (Tx_c > S_c). b Number of upregulated DEGs overlapping with the Arabidopsis list of drought responsive list from Phytozome. The considered comparisons are upregulation by drought treated SC56 compared to its control and treated Tx7000 (respectively, S_treat > S_cont and S_treat > Tx_treat), drought treated Tx7000 compared to its control and treated SC56 (respectively, Tx_ treat > Tx_cont and Tx_treat > S_treat), controls of both genotypes (S_cont > Tx_cont and Tx_cont > S_cont), and control versus treated (S_cont > S_treat and Tx_cont > S_treat). (Color figure online)
Fig. 4
Fig. 4
Hierarchical clustering of known drought-responsive genes identified in the differential expression analysis. Significant DEGs (p value < 0.05), at least in one comparison, are represented. Reported A. thaliana drought response orthologs were identified by mining the Phytozome database, and used to examine the DEG lists of the present study. Heatmap generated with parameters set to Euclidian distance and average linkage clustering method. (Color figure online)
Fig. 5
Fig. 5
Number of upregulated biological processes in SC56 and Tx7000. Considered comparisons: upregulation by drought treated SC56 compared to its control and treated Tx7000 (respectively, S_treat > S_cont and S_treat > Tx_treat), drought treated Tx7000 compared to its control and treated SC56 (respectively, Tx_ treat > Tx_cont and Tx_treat > S_treat), controls of both genotypes (S_cont > Tx_cont and Tx_cont > S_cont), and control versus treated (S_cont > S_treat and Tx_cont > S_treat
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