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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (7): 1658-1668.doi: 10.3724/SP.J.1006.2022.14115

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

Screening candidate genes involved in potato tuber development using WGCNA

JIAN Hong-Ju1,2,3(), ZHANG Mei-Hua1(), SHANG Li-Na1, WANG Ji-Chun1,2,3, HU Bai-Geng4, Vadim Khassanov5, LYU Dian-Qiu1,2,3,*()   

  1. 1College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
    2State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
    3Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
    4National Engineering Research Center for Potato, Dezhou 253600, Shandong, China
    5S. Seifullin Kazakh Agrotechnical University, Zhenis Avenue 010011, Astana, Republic of Kazakhstan
  • Received:2021-07-02 Accepted:2021-10-19 Online:2022-07-12 Published:2021-11-15
  • Contact: LYU Dian-Qiu E-mail:hjjian518@swu.edu.cn;mhzhang77@163.com;smallpotatoes@126.com
  • About author:First author contact:

    ** Contributed equally to this work

  • Supported by:
    Science and Technology Partnership Program, Minis-try of Science and Technology of China(KY201904016);National Key Research and Development Program of China(2018YFE0127900);National Natural Science Foundation of China(32101659);Talent Introduction Program of Southwest University Project(SWU019008);Special research project on Germplasm Innovation of Southwest University

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Abstract:

Tuber is the main economic organ of potato. It is of great significance to illustrate its formation and development mechanism for high yield breeding of potato. Although some related genes have been reported, there are still a large number of genes involved in tuber production which need to be further excavated and identified. With the continuous innovation and development of sequencing technology, transcriptome data has become more abundant and complicated. The method of screening genes related to specific traits, tissues or developmental stages using Weighted Gene Co-expression Network Analysis (WGCNA) has been widely used. In this study, to construct co-expression networks and screen co-expression modules related to tuber development, WGCNA was used to analyze transcriptome data of potato DM 1-3516 R44 (DM) material and RH89-039-16 (RH) material from 15 tissues and organs, respectively. GO and KEGG pathway enrichment were performed on the genes in the screening expression module. The top 10 genes in the module were taken as the hub genes, annotated by PGSC database and NCBI, and verified by qRT-PCR. 13 co-expression modules were obtained in both DM and RH materials, among which the Cray module in DM material analysis and the Black module in RH material analysis were significantly correlated with tubers by WGCNA. The analysis showed that the genes of the two modules were significantly enriched in related processes such as hormone metabolism, starch and sucrose metabolism, and cell formation. In addition, gene StGA2ox1, which had been proved to be related to tuber development, was noted in Cyan, and StGA2ox1 was correlated with 10 hub genes in the module in the co-expression analysis. The qRT-PCR results of the hub genes were basically consistent with the results of RNA-seq. In this study, two co-expression modules related to tuber development were identified by WGCNA, and several candidate genes related to tuber development were screened out, which laid a foundation for high yield potato breeding.

Key words: potato, WGCNA, tuber development, regulatory network, hub genes

Table 1

Primers of hub genes"

模块
Module		 基因编号
Gene ID		 正向引物
Forward primer (5°-3°)		 反向引物
Reverse primer (5°-3°)
Cyan PGSC0003DMG400021191 GTGCTGCTTAGGAATATGGTTG GAATGAAGATCCGAACAGCTTC
Cyan PGSC0003DMG400005704 CGACAACGATGAAGAAGATGAC ATGACGATGGTACTCTCTTCAC
Cyan PGSC0003DMG400005659 CAACGATTGGAGGCATTTCTAG GAGCTCATATGCAGTAGTTTGC
Cyan PGSC0003DMG400017696 AGTCGCAGTGATCGTGAATA CCACCACCATACCTATCATCTC
Cyan PGSC0003DMG401009395 GATGGCCGTATTCTTGTATCAT AGACCTGTTATGGTTCCAAATG
Cyan PGSC0003DMG400021095 CTTTTGGGGACTTGTGAAAGAG CTGGACATGGTGGATAGTGATT
Black PGSC0003DMG400030431 CTAAGGGTCATTACACTGAGGG CTTGTAGGCAGTCACAGTTTTC
Black PGSC0003DMG400010293 ATTTAGGCTTCTTTGTCTTGCG CGCCATCAAGTCAAATAAACCA
Black PGSC0003DMG400009401 ACAAGTGCTTACTATCGAGGAG GTCAGTATGATCTCTGAGCTCC
Black PGSC0003DMG400007997 TCCCTTCATTCCCTGTCTTA AATGTAGGCTCCACTTCCAC
Black PGSC0003DMG400008491 CTCTCCAACTGTGAAGTCTAGG AAGGAGAACATGATTTCCGTCT
Black PGSC0003DMG400012238 CAATGTCAAGGCCAAGATTCAA AAGTCGACTCTTTCTGGATGTT

Fig. 1

Gene cluster tree and module construction"

Fig. 2

Number of genes contained in different modules"

Fig. 3

Association analysis of gene co-expression network modules with traits A: DM material; B: RH material. The horizontal axis represents different tissues, and the vertical axis represents the eigenvectors of each module. The red lattice represents a positive correlation between the physiological traits with the module, while the blue lattice represents a negative correlation."

Fig. 4

GO enrichment analysis of genes in target module A: Cyan module of DM material; B: Black module of RH material."

Fig. 5

KEGG enrichment analysis of genes in target module A: Cyan module of DM material; B: Black module of RH material."

Fig. 6

Gene co-expression network and hub genes in Cyan and Black module"

Table 2

Functional annotations of hub genes in different modules"

模块
Module		 核心基因
Hub gene		 拟南芥同源基因
Homologous gene in Arabidopsis thaliana		 基因注释
Gene annotation
Cyan PGSC0003DMG400021191 AT1G30480 DNA损伤修复/耐受蛋白DRT111, 叶绿体 DNA-damage-repair/toleration protein DRT111, chloroplastic
Cyan PGSC0003DMG400004278 AT3G63390 功能未知的保守基因
Conserved gene of unknown function
Cyan PGSC0003DMG400005704 AT1G03280 转录起始因子IIE亚基α样亚型X2
Transcription initiation factor IIE subunit alpha-like isoform X2
Cyan PGSC0003DMG400005659 AT3G18165 Pre-mRNA剪接因子SPF27同源物
Pre-mRNA-splicing factor SPF27 homolog
Cyan PGSC0003DMG400031139 AT1G71780 功能未知的保守基因
Conserved gene of unknown function
Cyan PGSC0003DMG400011912 — 功能未知的基因
Gene of unknown function
Cyan PGSC0003DMG400017696 AT3G26420 RNA结合蛋白RZ-1
RNA binding protein RZ-1
Cyan PGSC0003DMG400006479 — Myb-like蛋白A同工型X2
Myb-like protein A isoform X2
Cyan PGSC0003DMG400000409 AT4G01560 RNA加工因子1
RNA processing factor 1
Cyan PGSC0003DMG401009395 AT4G28450 DDB1和CUL4相关因子13
DDB1- and CUL4-associated factor 13
Cyan PGSC0003DMG400021095 AT1G30040 赤霉素2-氧化酶1
Gibberellin 2-oxidase 1 (GA2OX1)
Black PGSC0003DMG400030431 AT2G29550 β微管蛋白2
Beta-tubulin 2
模块
Module		 核心基因
Hub gene		 拟南芥同源基因
Homologous gene in Arabidopsis thaliana		 基因注释
Gene annotation
Black PGSC0003DMG401002397 AT5G56670 核糖体蛋白S30
Ribosomal protein S30
Black PGSC0003DMG400017722 AT1G35780 功能未知的保守基因
Conserved gene of unknown function
Black PGSC0003DMG400010293 AT2G20490 H/ACA核糖核蛋白复合物亚基3-like蛋白同工型X2
H/ACA ribonucleoprotein complex subunit 3-like protein isoform X2
Black PGSC0003DMG400009401 AT5G60860 Ras相关蛋白RABA1f
Ras-related protein RABA1f
Black PGSC0003DMG400003723 AT5G39600 功能未知的保守基因
Conserved gene of unknown function
Black PGSC0003DMG400007997 AT2G34520 核糖体蛋白S14, 线粒体
Rbosomal protein S14, mitochondrial
Black PGSC0003DMG400007257 AT1G67785 功能未知的保守基因
Conserved gene of unknown function
Black PGSC0003DMG400008491 AT2G38160 内切几丁质酶A
Endochitinase A
Black PGSC0003DMG400012238 AT3G52590 泛素超群, 核糖体蛋白L40e
Ubiquitin supergroup, ribosomal protein L40e

Fig. 7

qRT-PCR validation of Hub genes The relative expression of RNA-Seq=log10 (FPKM+1)."

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