Construction of Gene Co-expression Network and Identification of Hub Genes Related to Anthocyanin Biosynthesis Based on RNA-seq and WGCNA in Sweetpotato

doi:10.13523/j.cb.2106048

China Biotechnology

2021, Vol. 41

Issue (9): 27-36 DOI: 10.13523/j.cb.2106048

Construction of Gene Co-expression Network and Identification of Hub Genes Related to Anthocyanin Biosynthesis Based on RNA-seq and WGCNA in Sweetpotato

HE Li-heng¹,ZHANG Yi²,ZHANG Jie¹,REN Yu-chao¹,XIE Hong-e³,TANG Rui-min¹,JIA Xiao-yun^2,^**(

),WU Zong-xin^3,^**(

)

1 College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
2 College of Life Science, Shanxi Agricultural University, Taigu 030801, China
3 Institute of Cotton Research, Shanxi Agricultural University, Yuncheng 044000, China

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Abstract

Weighted gene co-expression network analysis (WGCNA) is a systematic biological method. It can be used to explore the relationship between genes and related traits by the identification of co-expressed modules and hub genes in the network. Sweetpotato [Ipomoea batatas (L.)Lam.] is one of the nutritious tuberous crops in the world. Purple-fleshed sweetpotato (PFSP) is a special variety of sweetpotato. In addition to the nutritional components of common sweetpotato, PFSP is also enriched in anthocyanin with antioxidant function that is beneficial to health. Therefore, the cultivation of PFSP with high anthocyanin content has always been the goal of scientists. Although some PFSP varieties have been bred by traditional hybridization breeding techniques, which has some disadvantages, such as long breeding cycle, labor consuming and low efficiency. Therefore, it is urgent to develop PFSP with high yield and quality by molecular design breeding. Studying on key genes related to anthocyanin biosynthesis of sweetpotato can shed light on molecular breeding of PFSP. In order to explore genes related to anthocyanin biosynthesis in sweetpotato, white-fleshed sweetpotato‘Xushu-18'and PFSP‘Xuzishu-3' were used for transcriptome sequencing in this study. By integrated analysis of the published genomic information of sweetpotato and the transcriptome sequencing data of 43 purple-fleshed and 45 non purple-fleshed tuberous roots in public database, the top 50% differentially expressed genes (26 760) with large variation in different samples were identified and selected for WGCNA. A total of 28 gene co-expression modules were identified, in which four modules were specific in purple-fleshed sweetpotato (Grey60 module and Black module are significantly positively correlated to PFSP, while Brown modules and Blue modules are significantly negatively correlated to PFSP). GO analysis showed that the Grey60 module was significantly enriched in the metabolic process of flavonoids and anthocyanin. A total of 47 core hub genes related to anthocyanin biosynthesis were screened in Grey60 module by calculating gene connectivity in the corresponding networks. Of them, MYB113, CHS, three CHI and F3H, GST and LDOX have been previously reported to be related to anthocyanins biosynthesis. The expression patterns of seven of the 47 hub genes were verified by qRT-PCR, which were consistent with the results by transcriptome sequencing. Analysis of the interaction network of hub genes indicated that MYB interacts not only with the known genes related to anthocyanin biosynthesis, such as bHLH, CHI, GST, F3'H and CHS, but also with the transporter genes DUF914 and ABCC4, etc. WRKY3 interacts with many core genes, such as LODX, GST, and CHS. In summary, this study will provide new ideas for the cultivation of high anthocyanin content purple-fleshed sweetpotato varieties and theoretical foundation for dissection of anthocyanin biosynthesis mechanism.

Key words： Purple-fleshed sweetpotato Anthocyanin WGCNA Transcriptome sequencing Hub genes

Received: 27 June 2021 Published: 30 September 2021

ZTFLH:

Q812

Corresponding Authors: Xiao-yun JIA,Zong-xin WU E-mail: jiaxiaoyun@sxau.edu.cn;mhswzx@126.com

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	Li-heng HE
	Yi ZHANG
	Jie ZHANG
	Yu-chao REN
	Hong-e XIE
	Rui-min TANG
	Xiao-yun JIA
	Zong-xin WU

Cite this article:

HE Li-heng,ZHANG Yi,ZHANG Jie,REN Yu-chao,XIE Hong-e,TANG Rui-min,JIA Xiao-yun,WU Zong-xin. Construction of Gene Co-expression Network and Identification of Hub Genes Related to Anthocyanin Biosynthesis Based on RNA-seq and WGCNA in Sweetpotato. China Biotechnology, 2021, 41(9): 27-36.

URL:

https://manu60.magtech.com.cn/biotech/10.13523/j.cb.2106048 OR https://manu60.magtech.com.cn/biotech/Y2021/V41/I9/27

Fig.1 The choice of the soft thresholding power (a) Soft thresholding (power) and corresponding R² The red line represents R² = 0.80 (b) Soft thresholding (power) and corresponding mean connectivity

Fig.2 The gene cluster dendrogram and corresponding modules (a) Gene clustering (b) Gene modules (c) The resulting merged modules

Fig.3 The gene number in each module

Fig.4 Distribution of the number of transcription factors in modules

Fig.5 The correlation heat map for modules and purple trait The columns displayed different modules. The row was purple trait. The numbers were correlation coefficients and P values

Fig. 6 Bubble diagram of GO enrichment of genes specificity related with purple-flesded sweetpotato in the Grey60 module The vertical axis displayed the enriched GO categorys, and the horizontal axis displayed the enrichment score. The gene number and statistical significance -lgP were showed with point size and color, respectively

Table 1 Hub genes and functional annotations related with anthocyanin biosynthesis in Grey60 module

Fig.7 Gene interaction network of hub genes associated with anthocyanin biosynthesis in the Grey60 module The red triangles represented core genes, and the yellow triangle represented the core gene was also transcription factor. The green circles represented other non core interaction genes, and the yellow circles represented non core transcription factors

Fig.8 Expression analysis of seven randomly selected hub genes The upper and lower vertical axises represented the relative expression level and TPM value by qRT-PCR and RNA-seq, respectively. * Represented significantly difference at P<0.05


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