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. 2022 Dec 12;23(24):15774.
doi: 10.3390/ijms232415774.

Understanding the Potential Gene Regulatory Network of Starch Biosynthesis in Tartary Buckwheat by RNA-Seq

Juan Huang  1 , Bin Tang  1 , Rongrong Ren  1 , Min Wu  1 , Fei Liu  1 , Yong Lv  1 , Taoxiong Shi  1 , Jiao Deng  1 , Qingfu Chen  1
Affiliations

Understanding the Potential Gene Regulatory Network of Starch Biosynthesis in Tartary Buckwheat by RNA-Seq

Juan Huang et al. Int J Mol Sci. .

Abstract

Starch is a major component of crop grains, and its content affects food quality and taste. Tartary buckwheat is a traditional pseudo-cereal used in food as well as medicine. Starch content, granule morphology, and physicochemical properties have been extensively studied in Tartary buckwheat. However, the complex regulatory network related to its starch biosynthesis needs to be elucidated. Here, we performed RNA-seq analyses using seven Tartary buckwheat varieties differing in starch content and combined the RNA-seq data with starch content by weighted correlation network analysis (WGCNA). As a result, 10,873 differentially expressed genes (DEGs) were identified and were functionally clustered to six hierarchical clusters. Fifteen starch biosynthesis genes had higher expression level in seeds. Four trait-specific modules and 3131 hub genes were identified by WGCNA, with the lightcyan and brown modules positively correlated with starch-related traits. Furthermore, two potential gene regulatory networks were proposed, including the co-expression of FtNAC70, FtPUL, and FtGBSS1-3 in the lightcyan module and FtbHLH5, C3H, FtBE2, FtISA3, FtSS3-5, and FtSS1 in the brown. All the above genes were preferentially expressed in seeds, further suggesting their role in seed starch biosynthesis. These results provide crucial guidance for further research on starch biosynthesis and its regulatory network in Tartary buckwheat.

Keywords: DEGs; RNA-seq; Tartary buckwheat; amylopectin; amylose; gene regulatory network; starch biosynthesis; transcription factor.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Starch content in late-filling-stage seeds of seven Tartary buckwheat varieties. (a) Amylose content; (b) amylopectin content; (c) amylopectin/amylose. The data represent the mean ± SD that came from three biological replicates and at least two technical replicates for each biological replicate.
Figure 2
Figure 2
Analyses of differentially expressed genes (DEGs) in seven Tartary buckwheat varieties. (a) Upset plot of the DEGs in six comparisons. Black bars on the lower left represent the number of DEGs in comparisons of seven selected varieties. The black dots on the lower right represent the common DEGs existing in six comparisons. Black bars above represent the number of common DEGs in six comparisons; (b) Functional category of DEGs by hierarchical cluster; (c) Gene expression patterns of the six clusters that correspond to the hierarchical cluster result. Six main clusters were presented as C1–C6. Gene expression values are normalized to log10 (FPKM).
Figure 3
Figure 3
Expression patterns of genes related to the starch biosynthesis pathway. The light-brown rectangles and dark-brown ovals represent the substrates and the enzymes in the starch biosynthesis pathway, respectively. The heatmap shows the expression patterns of genes in the starch biosynthesis pathway. Genes marked with “*” were identified as DEGs. AGPase, ADP-glucose pyrophosphorylase; AGPL, large subunit of AGPase; AGPS, small subunit of AGPase; GBSS, granule-bound starch synthase; SS, soluble starch synthase; BE, starch branching enzyme; DBE, starch debranching enzyme; ISA, isoamylase; PUL, pullulanase.
Figure 4
Figure 4
Weighted gene correlation network analysis (WGCNA) for DEGs and the enriched pathways of trait-specific modules in Tartary buckwheat seeds. (a) Module–trait relationships by WGCNA analysis. The correlations and the corresponding p-values (in parentheses) are indicated in the heatmap. The panel on the left side shows nine identified modules. amylose/amylopectin is shorten for the ratio of amylose to amylopectin; amylopectin/amylose is short for the ratio of amylopectin to amylose; (b) Expression patterns of the trait-specific modules (p-value < 0.05) in correspondence to the module–trait relationship heatmap; (c) KEGG enrichment analysis of the lightcyan and brown modules. Rich factor is the ratio of the number of DEGs to that of all genes annotated to a pathway term. A higher rich factor indicates greater intensity.
Figure 5
Figure 5
TFs identified in four trait-specific modules and their co-expression networks related to the starch biosynthesis pathway. (a) Distribution of transcription factor families in four trait-specific modules. C3H, CCCH-type Zn-finger protein; (b,c) Co-expression networks of TFs in the hub genes in the top 50 in intramodule connectivity (represented by dark-red ovals) and starch biosynthesis genes in the hub genes of the top 30% in intramodule connectivity (represented by clay-brown ovals) in the lightcyan (b) and brown (c) modules. Edge width indicates the weight of the relationship between two genes. (d,e) Pearson correlation between the genes in correspondence to (b,e). ** indicates that the correlation reached a significant level of 0.01. FtPUL, FtPinG0000055300.01; FtNAC70, FtPinG0002339300.01; FtGBSS1-3, FtPinG0000359400.01; FtBE2, FtPinG0000080700.01; FtISA3, FtPinG0009517500.01; C3H, FtPinG0003310400.01; FtbHLH5, FtPinG0000281400.01; FtSS3-5, FtPinG0003226800.01; FtSS1, FtPinG0005939600.01.
Figure 6
Figure 6
Tissue-specific expression patterns of nine candidate genes in the regulatory network of the starch biosynthesis pathway.
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References

    1. Luthar Z., Zhou M., Golob A., Germ M. Breeding buckwheat for increased levels and improved quality of protein. Plants. 2021;10:14. doi: 10.3390/plants10010014. - DOI - PMC - PubMed
    1. Zhu F. Chemical composition and health effects of Tartary buckwheat. Food Chem. 2016;203:231–245. doi: 10.1016/j.foodchem.2016.02.050. - DOI - PubMed
    1. Luthar Z., Golob A., Germ M., Vombergar B., Kreft I. Tartary buckwheat in human nutrition. Plants. 2021;10:700. doi: 10.3390/plants10040700. - DOI - PMC - PubMed
    1. Lu C.L., Zheng Q., Shen Q., Song C., Zhang Z.M. Uncovering the relationship and mechanisms of Tartary buckwheat (Fagopyrum tataricum) and Type II diabetes, hypertension, and hyperlipidemia using a network pharmacology approach. PeerJ. 2017;5:e4042. doi: 10.7717/peerj.4042. - DOI - PMC - PubMed
    1. Zhu F. Buckwheat starch: Structures, properties, and applications. Trends Food Sci. Technol. 2016;49:121–135. doi: 10.1016/j.tifs.2015.12.002. - DOI