Transcriptome response of cassava leaves under natural shade

Abstract

Cassava is an important staple crop in tropical and sub-tropical areas. As a common farming practice, cassava is usually cultivated intercropping with other crops and subjected to various degrees of shading, which causes reduced productivity. Herein, a comparative transcriptomic analysis was performed on a series of developmental cassava leaves under both full sunlight and natural shade conditions. Gene expression profiles of these two conditions exhibited similar developmental transitions, e.g. genes related to cell wall and basic cellular metabolism were highly expressed in immature leaves, genes involved in lipid metabolism and tetrapyrrole synthesis were highly expressed during the transition stages, and genes related to photosynthesis and carbohydrates metabolism were highly expressed in mature leaves. Compared with the control, shade significantly induced the expression of genes involved in light reaction of photosynthesis, light signaling and DNA synthesis/chromatin structure; however, the genes related to anthocyanins biosynthesis, heat shock, calvin cycle, glycolysis, TCA cycle, mitochondrial electron transport, and starch and sucrose metabolisms were dramatically depressed. Moreover, the shade also influenced the expression of hormone-related genes and transcriptional factors. The findings would improve our understanding of molecular mechanisms of shade response, and shed light on pathways associated with shade-avoidance syndrome for cassava improvement.

Figure 1. Light spectrum of cassava expanded leaves.

The curves represent transmission (A,B), reflection (C,D) and absorption (E,F) percentage of expanded leaves in both natural (control) and shade conditions, respectively. Leaves from young to old: CL3-CL9 for control and SL3-SL9 for shade.

Figure 2. Samples of cassava leaves used in this study.

In each graph, sample in the top was derived from control, while sample in the bottom was derived from shade. A-I represent eighteen RNA-seq leaf samples (CL1-CL9 vs. SL1-SL9) used in this study respectively. Bars represent 0.5 cm (A,B) and 5 cm (C–I), respectively.

Figure 3. Dynamic transcriptome of cassava leaves.

(A) Expression patterns of 12 clusters along different developmental leaves. The samples are (from left to right): CL1-CL9 in black for control, and SL1-SL9 in red for shade conditions, respectively. Error bars represent standard deviation. The number of genes included in each cluster is shown at the upper-right corner. (B) Functional category enrichment of each cluster in (A).

Figure 4. Percentage of up- and down- regulated genes in shade compared with control.

The categories were derived from MapMan annotation. Star (*) indicates p < 0.05 based on binomial test.

Figure 5. Heatmap of the genes related to light reaction, light signaling and DNA synthesis/chromatin structure.

Figure 6

Anthocyanin biosynthesis pathway (A) and heatmap of its related genes (B). Anthocyanin biosynthesis pathway was modified from Gou et al. (2011) and Petroni and Tonelli (2011).

Figure 7. Heatmap of the genes associated with heat shock protein, calvin cycle, starch and sucrose synthesis, glycolysis, TCA and mitochondrial electron transport.

Figure 8

Heatmap of hormone genes (A) and transcription factors (B) related to leaf development and shade response.

Figure 9. Putative gene interaction model of shade response in cassava.