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Figure 1. 

Representative symptoms of different daylily cultivars at different days after waterlogging treatment. The symptoms were recorded every two d post treatment. After waterlogging for 10 d, each daylily cultivar was subjected to recovery (Rec.) for 40 d of normal maintenance.

Figure 2. 

Transcriptome analysis of daylily roots under waterlogging treatment. (a) Principal component analysis (PCA) of daylily root transcriptome data for each sample. B1 and B5, 'Here Lies Butch' root samples at 0 and 24 h after waterlogging; S1 and S5, 'Bonibrae Sharky' root samples at 0 and 24 h after waterlogging. (b) The correlation test among samples in daylily root transcriptome data. (c) Cluster analysis of all samples based on sample-to-sample distances. (d) Number of differentially expressed genes (DEGs) for different pairwise comparisons. (e), (f) Venn diagrams of DEGs for different pairwise comparisons.

Figure 3. 

GO and KEGG analysis of daylily root transcriptome data in response to waterlogging stress. (a) The GO functional classification of differentially expressed genes (DEGs) in all pairwise comparisons. (b) KEGG pathway enrichment of DEGs between different groups.

Figure 4. 

Expression profiles of differentially expressed genes in various pathways associated with waterlogging stress responses through transcriptome analysis. These differentially expressed genes (DEGs) are indicated by italics. Different colors in the heatmap represent variable transcription ranged from low to high levels for each transcript. Transcript levels of DEGs were Log₂-transformed. Solid lines ending with arrows indicate positive regulation, whereas the ones ending with short perpendicular lines represent negative regulation.

Figure 5. 

Analysis of differentially expressed transcription factors in waterlogging-treated daylily roots through transcriptome analysis. (a) Number of differentially expressed transcription factors in response to waterlogging stress. (b) Transcript levels of a number of transcription factors from ERF, ARF, bHLH, MADS, MYB, NAC, WRKY, and ZFP families, in various samples under waterlogging treatment. Error bars indicate standard deviation (SD) of the means from three biological replicates. Different letters above the bars suggest statistical significance, which is determined by Duncan's multiple range test at p < 0.05.

Figure 6. 

Principle component analysis of the selected differentially expressed transcription factors with the genes in various pathways associated with waterlogging tolerance. The functional genes in various pathways of (a) ethylene biosynthesis, (b) reactive oxygen species (ROS) production and scavenging, (c) alcoholic fermentation, (d) abscisic acid (ABA) biosynthesis, (e) gibberellin (GA) biosynthesis, and (f) programmed cell death, are denoted by red solid circles, while the selected transcription factors from various families are marked by green solid circles. The genes with relatively close correlation distance are indicated by dashed circles.

Figure 7. 

An interaction network between the selected differentially expressed transcription factors with the genes in various pathways associated with waterlogging tolerance. Grey solid or dashed lines indicate positive or negative regulation, respectively. Larger circles or triangles with more nodes indicate more significant correlations, whereas smaller ones with less nodes represent the opposite correlations. The genes with relatively close correlation distance are indicated by dashed circles.