Transcriptome profiling shows a rapid variety-specific response in two Andigenum potato varieties under drought stress

Abstract

Potato is a drought-sensitive crop whose global sustainable production is threatened by alterations in water availability. Whilst ancestral Solanum tuberosum Andigenum landraces retain wild drought tolerance mechanisms, their molecular bases remain poorly understood. In this study, an aeroponic growth system was established to investigate stress responses in leaf and root of two Andigenum varieties with contrasting drought tolerance. Comparative transcriptome analysis revealed widespread differences in the response of the two varieties at early and late time points of exposure to drought stress and in the recovery after rewatering. Major differences in the response of the two varieties occurred at the early time point, suggesting the speed of response is crucial. In the leaves and roots of the tolerant variety, we observed rapid upregulation of ABA-related genes, which did not occur until later in the susceptible variety and indicated not only more effective ABA synthesis and mobilization, but more effective feedback regulation to limit detrimental effects of too much ABA. Roots of both varieties showed differential expression of genes involved in cell wall reinforcement and remodeling to maintain cell wall strength, hydration and growth under drought stress, including genes involved in lignification and wall expansion, though the response was stronger in the tolerant variety. Such changes in leaf and root may help to limit water losses in the tolerant variety, while limiting the reduction in photosynthetic rate. These findings provide insights into molecular bases of drought tolerance mechanisms and pave the way for their reintroduction into modern cultivars with improved resistance to drought stress and yield stability under drought conditions.

Keywords: abiotic stress; drought; potato; rehydration; transcriptome.

Figure 1

Transcriptomic overview of progressive drought response in two potato varieties. Principal component analysis (PCA) of leaf (A) and root (B) in tolerant (Tol) and susceptible (Sus) varieties in the non-stressed control and across three drought-stressed time points (early T1, late T2 and recovery after rewatering T3). The number of DEGs in each time point compared with the non-stressed control that are up-regulated in leaf (C) or root (E) or downregulated in leaf (D) or root (F). Volcano plot showing differential expression of genes in T1 in leaf (G) or root (H) compared with the control. Vertical dashed lines indicate absolute log2FC ≥2. Horizontal dashed lines indicate padj. equal to 5%. Genes passing neither threshold are shown in grey, while non-significant genes passing the FC threshold are shown in green. In blue are genes with a small but significant fold change and in red are genes passing both thresholds.

Figure 2

Commonalities and differences in DEGs across drought treatment time points in two potato varieties. Up and down-regulated DEGs in leaf (A, B) and root (C, D) in tolerant (Tol) and susceptible (Sus) varieties in three drought-stressed time points (early T1, late T2 and recovery after rewatering T3) compared with the non-stressed control condition.

Figure 3

Commonalities and differences in drought-responsive DEGs between tolerant and susceptible varieties. Overlap between up- and down- regulated DEGs in leaf and root in tolerant (Tol) and susceptible (Sus) varieties in at least one drought-stressed time point (T1-T3) (A), or in each of the early T1 (B), late T2 (C) or recovery after rewatering T3 (D) time points compared with the non-stressed control condition.

Figure 4

Heatmap of the log2 fold change for DEGs related to the ABA response. Shown is the log2FC compared to the non-stressed control for all DEGs annotated with GO:0009737 and all NCED genes. In grey are genes with no significant change in the respective time point (early T1, late T2, and recovery T3), tissue, or variety.

Figure 5

Heatmap of the log2 fold change of DEGs related to lignin biosynthesis in roots. Shown is the log2FC compared to the non-stressed control for all DEGs annotated with lignin biosynthetic process (GO:0009809), lignin catabolic process (GO:0046274) or as laccase genes in the potato genome v6.1. In grey are genes with no significant change in the respective time point (early T1, late T2, and recovery T3), tissue, or variety.

Figure 6

Heatmap of the log2 fold change of WRKY genes. Shown is the log2FC expression of WRKY genes differentially expressed in either tissue in two potato varieties at any time point compared to the non-stressed control.