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. 2017 Jun 22:8:914.
doi: 10.3389/fpls.2017.00914. eCollection 2017.

Comparative Transcriptome Analysis Reveals Critical Function of Sucrose Metabolism Related-Enzymes in Starch Accumulation in the Storage Root of Sweet Potato

Kai Zhang  1   2   3 , Zhengdan Wu  1   3 , Daobin Tang  1   2   3 , Kai Luo  1   3 , Huixiang Lu  1   3 , Yingying Liu  1   3 , Jie Dong  1   3 , Xin Wang  1   3 , Changwen Lv  1   2   3 , Jichun Wang  1   2   3 , Kun Lu  1   2
Affiliations

Comparative Transcriptome Analysis Reveals Critical Function of Sucrose Metabolism Related-Enzymes in Starch Accumulation in the Storage Root of Sweet Potato

Kai Zhang et al. Front Plant Sci. .

Abstract

The starch properties of the storage root (SR) affect the quality of sweet potato (Ipomoea batatas (L.) Lam.). Although numerous studies have analyzed the accumulation and properties of starch in sweet potato SRs, the transcriptomic variation associated with starch properties in SR has not been quantified. In this study, we measured the starch and sugar contents and analyzed the transcriptome profiles of SRs harvested from sweet potatoes with high, medium, and extremely low starch contents, at five developmental stages [65, 80, 95, 110, and 125 days after transplanting (DAP)]. We found that differences in both water content and starch accumulation in the dry matter affect the starch content of SRs in different sweet potato genotypes. Based on transcriptome sequencing data, we assembled 112336 unigenes, and identified several differentially expressed genes (DEGs) involved in starch and sucrose metabolism, and revealed the transcriptional regulatory network controlling starch and sucrose metabolism in sweet potato SRs. Correlation analysis between expression patterns and starch and sugar contents suggested that the sugar-starch conversion steps catalyzed by sucrose synthase (SuSy) and UDP-glucose pyrophosphorylase (UGPase) may be essential for starch accumulation in the dry matter of SRs, and IbβFRUCT2, a vacuolar acid invertase, might also be a key regulator of starch content in the SRs. Our results provide valuable resources for future investigations aimed at deciphering the molecular mechanisms determining the starch properties of sweet potato SRs.

Keywords: RNA-seq; expression profile; starch; storage root; sucrose; sweet potato.

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Figures

Figure 1
Figure 1
Dynamic changes of dry matter, starch properties, and SR weight during SR development. Dynamic changes of (A) dry matter content per SR fresh weight, (B) starch content per SR fresh weight, (C) SR fresh weight, (D) starch content of SR dry matter, (E) amylose content, and (F) amylose to amylopectin ratio in the SR starch during SR development in the SQ52-7, XS22, and YS33 genotypes. Error bars indicate the standard deviation from three independent replicates.
Figure 2
Figure 2
Dynamic changes of sugar content during SR development.
Figure 3
Figure 3
Gene ontology classification of assembled unigenes.
Figure 4
Figure 4
Comparison of the transcriptomes among the tested SR samples. (A) Heatmap plotting and cluster analysis of 15 SR databases based on the expression pattern and abundance of unigenes; (B) Box plot showing the RPKM distribution of unigenes in the 15 samples; (C) Correlation analysis among samples. The correlation matrix was performed by comparing the values of the whole transcriptome in 15 samples, and Pearson's correlation coefficient among samples was analyzed using R scripts.
Figure 5
Figure 5
Expressed unigenes identified in the 15 sweet potato SRs. Venn diagrams were generated to identify sweet potato (A) genotype- and (B) developmental stage-specific expressed unigenes and common expressed unigenes.
Figure 6
Figure 6
Expression patterns of unigenes encoding enzymes involved in starch and sucrose metabolism during SR development in three sweet potato genotypes. Cluster analysis was performed to group DEGs with similar expression levels and patterns based on the normalized log2-transformed RPKM values of DEGs. The abbreviations of enzymes and transporters encoded by DEGs are shown in Figure S2. GS, glycogen (starch) synthase (EC 2.4.1.11); IbAGPa1, IbAGPa2, IbAGPb1A, IbAGPb1B, IbAGPb2, ADP-glucose pyrophosphorylase (AGPase, EC 2.7.7.27) small subunit 1, 2, and large subunit 1, 2, and 3, respectively; IbβFRUCT2, β-fructofuranosidase (EC 3.2.1.26); INVInh, invertase inhibitor; SBEI and SBEII, class I and II starch branching enzyme (EC 2.4.1.18), respectively. Red, dark red, green, and pale green rectangles on the right side indicate DEGs involved in starch granule formation and degradation, sucrose metabolism, sucrose synthesis and conversion, and DEGs encoding transporters, respectively.
Figure 7
Figure 7
Dynamic changes in the starch content and the expression pattern of Ibβfruct2 during SR development in the three sweet potato varieties. SC, starch content per SR fresh weight; RE, relative expression (ΔCt) of Ibβfruct2.
Figure 8
Figure 8
Heatmap showing expression patterns of pyrophosphate-energized vacuolar membrane proton pump encoding unigenes. Normalized log2-transformed RPKM gene expression values were used to plot the heatmap.
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