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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (7): 1033-1051.doi: 10.3724/SP.J.1006.2020.94130


Identification of drought-related co-expression modules and hub genes in potato roots based on WGCNA

Tian-Yuan QIN1,2,**,Chao SUN1,2,**,Zhen-Zhen BI1,2,Wen-Jun LIANG1,2,Peng-Cheng LI1,2,Jun-Lian ZHANG1,Jiang-Ping BAI1,2,*()   

  1. 1 Gansu Provincial Key Laboratory of Aridland Crop Science / Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou 730070, Gansu, China;
    2 College of Agronomy, Gansu Agricultural University, Lanzhou 730070, Gansu, China
  • Received:2019-08-27 Accepted:2019-12-26 Online:2020-07-12 Published:2020-01-14
  • Contact: Jiang-Ping BAI E-mail:baijp@gsau.edu.cn
  • About author:** Contributed equally to this work
  • Supported by:
    National Natural Science Foundation of China(31660432);National Natural Science Foundation of China(31460369);China Agricultural Research System (Potato)(CARS-09-P14);Gansu Agricultural Research System (Potato)(GARS-03-P1);“Light of the West” Talent Training Program of the Chinese Academy of Sciences(2014-01);Lanzhou Science and Technology Development Plan(2015-3-62);Gansu Provincial Department of Education(2019B-073);Gansu Science and Technology Fund(18JR3RA174);Gansu Provincial Key Laboratory of Aridland Crop Science, GAU(GSCS-2017-9);GAU Fund(GAU-XKJS-2018-085)


Weighted gene co-expression network analysis (WGCNA) is a research method in systematic biology. It is widely used to identify gene modules related to target traits in multi-sample transcriptome data. In order to further explore the molecular mechanism of potato response to drought stress, two cultivars (C16: CIP 397077.16 and C119: CIP 398098.119) introduced from the International Potato Center were used as experimental materials, and five drought stress gradients were treated for 0 h, 2 h, 6 h, 12 h, and 24 h, with the untreated material as a control. A total of 30 samples of root system were used for transcriptome sequencing, with three biological replicates. Based on the above transcriptome data, we constructed a co-expression network of weighted genes associated with stress-resistant physiological traits by WGCNA, and obtained 15 gene co-expression modules closely related to root drought resistance. In addition, a number of hub genes involved in drought stress regulation pathways were discovered from the four modules with the highest correlation with target traits. These results provide clues for further study on the molecular genetic mechanisms of potato root drought resistance.

Key words: potato, drought stress, weighted gene co-expression network, transcriptome

Table 1

Experimental materials"

CIP number
Maternal parent
Paternal parent
C16 CIP397077.16 392025.7=(LR93.221) 392820.1=(C93.154)
C119 CIP398098.119 393371.58 392639.31

Fig. 1

Upregulated and down-regulated genes in roots of C16 and C119 under different treatments A, B: the number of differentially expressed genes up-regulated in C16 and C 119 roots; C, D: the down-regulated genes. The yellow column represents the total number of genes in the sample, the black column represents the number of differentially expressed genes in the sample corresponding to the black dots, and the black line between the black dots represents the same differentially expressed genes between the samples."

Supplementary table 1

Biochemical indicator data for C16 and C119 at different treatment times"

处理时间Treatment time 超氧化物歧化酶
Superoxide dismutase (U g-1)
Peroxidase (U g-1 min-1)
Catalase (U g-1 min-1)
Root vitality (mg g-1 h-1)
Average value
Average value
Average value
Average value
C16-0 h 9.57 2.00 2637.50 135.95 116.75 6.72 457.74 35.21
C16-2 h 14.13 1.55 3375.00 187.90 129.93 7.68 457.75 30.18
C16-6 h 15.63 1.81 3862.50 162.71 144.84 13.26 496.57 33.10
C16-12 h 16.42 1.75 4262.50 149.01 155.83 15.39 627.09 30.73
C16-24 h 22.22 1.35 8575.00 142.27 209.34 20.20 815.49 62.11
C119-0 h 46.02 5.15 1312.50 190.92 244.25 15.10 712.44 36.99
C119-2 h 48.92 6.91 3200.00 262.15 274.48 22.32 811.53 64.44
C119-6 h 49.16 6.29 3500.00 218.72 276.74 14.75 826.29 81.45
C119-12 h 56.62 7.72 3687.50 206.59 341.57 16.84 901.41 23.47
C119-24 h 75.53 8.95 6112.50 210.12 370.75 19.51 924.88 70.89

Fig. 2

Dendrogram of samples A: dendrogram of all 30 samples; B: dendrogram of samples after removing outlier."

Fig. 3

Soft threshold determination of gene co-expression network The abscissae in both Figures A and B represent the soft threshold, the ordinate of Figure A represents the scale-free network model index, the ordinate of Figure B represents the average degree of network connectivity for each soft threshold."

Fig. 4

Gene co-expression network gene clustering number and modular cutting Each branch of the gene clustering tree corresponds to one module."

Fig. 5

Association analysis of gene co-expression network modules with physiological and biochemical traits The horizontal axis represents different characteristics, 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 green lattice represents a negative correlation. 0 h means no drought treatment, as the control."

Fig. 6

ME cluster tree"

Fig. 7

ME correlation between different modules"

Fig. 8

Expression levels of all genes and corresponding ME in different modules of each sample The above figure (heat map) shows the expression level of all genes in modules. A: Red module; B: Yellow module; C: Turquoise module; D: Blue module. The row represents all genes in the module, and the column represents each sample. The below figure shows the ME expression level of the module in the sample."

Fig. 9

Gene GO annotation in target module"

Table 2

Partial GO enrichment analysis of target modules"

GO term
Red GO:0016705 F 氧化还原酶活性, 作用于成对供体, 与分子氧结合或还原。
Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen.
Red GO:0004866 F 内肽酶抑制剂活性。
Endopeptidase inhibitor activity.
Red GO:0030414 F 肽酶抑制剂活性。
Peptidase inhibitor activity.
Red GO:0005515 F 蛋白质结合。
Protein binding.
Yellow GO:0005515 F 蛋白质结合。
Protein binding.
Turquoise GO:0015979 P 光合作用。
GO term
Turquoise GO:0019684 P 光合作用, 光反应。
Photosynthesis, light reaction.
Turquoise GO:0006694 P 类固醇生物合成过程。
Steroid biosynthetic process.
Turquoise GO:0010033 P 对有机物质的反应。
Response to organic substance.
Turquoise GO:0005515 F 蛋白结合。
Protein binding.
Turquoise GO:0016705 F 氧化还原酶活性, 作用于成对供体, 与分子氧结合或还原。
Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen.
Turquoise GO:0003854 F 3-β-羟基-Δ5-类固醇脱氢酶活性。
3-beta-hydroxy-delta5-steroid dehydrogenase activity.
Turquoise GO:0033764 F 类固醇脱氢酶活性, 作用于供体的羟基, NAD或NADP作为受体。
Steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor.
Turquoise GO:0016229 F 类固醇脱氢酶活性。
Steroid dehydrogenase activity.
Turquoise GO:0016614 F 氧化还原酶活性, 作用于供体的羟基。
Ooxidoreductase activity, acting on CH-OH group of donors.
Turquoise GO:0016616 F 氧化还原酶活性, 作用于供体的羟基, NAD或NADP作为受体。
Oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor.
Turquoise GO:0051287 F NAD或NADH结合。
NAD or NADH binding.
Turquoise GO:0008092 F 细胞骨架蛋白结合。
Cytoskeletal protein binding.
Blue GO:0007010 P 细胞骨架组织。
Cytoskeleton organization.
Blue GO:0005515 F 蛋白结合。
Protein binding.
Blue GO:0016705 F 氧化还原酶活性, 作用于成对供体, 与分子氧结合或还原。
Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen.
Blue GO:0016021 C 膜结合。
Integral to membrane.
Blue GO:0015629 C 肌动蛋白细胞骨架。
Actin cytoskeleton.
Blue GO:0031224 C 膜固有的。
Intrinsic to membrane.

Fig. 10

Gene co-expression network and hub genes in Red and Yellow modules"

Fig. 11

Gene co-expression network and hub genes in Turquoise and Blue modules"

Table 3

Functional annotations of hub genes in different modules"

Hub gene
Hub gene in A. thaliana
Gene function
Red PGSC0003DMG400030368 AT1G07140 编码假定的RAN结合蛋白。
Encodes a putative RAN-binding protein (siRANBP).
Red PGSC0003DMG400003662 AT1G20270; AT5G66060 2-氧戊二酸和铁依赖性加氧酶超家族蛋白; 铁离子结合/氧化还原酶/氧化还原酶蛋白。
2-oxoglutarate and Fe-dependent oxygenase superfamily protein; Ironion binding/oxidoreductase/oxidoreductase protein.
Red PGSC0003DMG402020462 AT5G25360 假设性蛋白质。
Hypothetical protein (source: Araport 11).
Red PGSC0003DMG400005154 X 未知功能。Unknown.
Red PGSC0003DMG400020562 AT2G40470 含LOB结构域的蛋白质。参与木质部分化的调节——作为VND7的调节器, VND7是木质部细胞分化的主要调节器。
LOB-domain containing protein. Involved in regulation of xylem differentiation—acts as a regulator of VND7 which is a master regulator of xylem cell differentiation.
Yellow PGSC0003DMG400029350 AT1G05680[15] 编码一个UDP-葡萄糖基转移酶, ugt74e2, 作用于IBA (吲哚-3-丁酸)并影响生长素的稳态。这种酶的转录和蛋白质水平被H2O2强烈诱导, 可能允许ROS (活性氧物种)和生长素信号的整合。
Encodes a UDP-glucosyltransferase, ugt74e2, that acts on IBA (indole-3-butyric acid) and affects auxin homeostasis. The transcript and protein levels of this enzyme are strongly induced by H2O2 and mayallow integration of ROS (reactive oxygen species) and auxin signaling.
Yellow PGSC0003DMG400024717 AT3G05545 超家族蛋白。
RING/U-box superfamily protein (source: Araport 11).
Yellow PGSC0003DMG400026572 AT3G51730[16] 含皂苷B结构域的蛋白质。
Saposin B domain-containing protein (source: Araport 11).
Yellow PGSC0003DMG400006704 AT5G35200[17] 超家族蛋白。
ENTH/ANTH/VHS superfamily protein (source: Araport 11).
Yellow PGSC0003DMG400015386 AT2G42610 光依赖性短下胚轴样蛋白。
LIGHT-DEPENDENT SHORT HYPOCOTYLS-like protein (DUF640) (source: Araport 11).
Yellow PGSC0003DMG400026238 AT3G60410 假设性蛋白质。
Hypothetical protein (DUF1639) (source: Araport 11).
Hub gene
Hub gene in A. thaliana
Gene function
Yellow PGSC0003DMG400020683 AT3G25910 MAP激酶
Mitogen-activated protein kinases (DUF1644)(source: Araport 11).
Yellow PGSC0003DMG400024687 AT1G55000[18] 含蛋白的肽聚糖结合赖氨酸域。
Peptidoglycan-binding LysM domain-containing protein (source: Araport 11).
Yellow PGSC0003DMG400006516 AT1G55570 SKU5 similar 12 (source: Araport 11).
Turquoise PGSC0003DMG400013391 AT3G22990 含有蛋白质的犰狳重复序列, 位于核内, 广泛表达于植物。
Armadillo-repeat containing protein, located in nucleus, broadly expressed throughout vegetative.
Turquoise PGSC0003DMG400003792 AT3G14110[19] 编码一种新的盘绕线圈, 含有TPR结构域的蛋白质, 定位于叶绿体膜并参与叶绿素的生物合成。
Encodes a novel coiled-coil, TPR domain containing protein that is localized to the chloroplast membrane and is involved in chlorophyll biosynthesis.
Turquoise PGSC0003DMG400024698 AT5G27620 核心细胞周期基因的mRNA是细胞间流动的。
Core cell cycle genes the mRNA is cell-to-cell mobile.
Turquoise PGSC0003DMG402011550 AT5G23200 C5orf35 (source: Araport 11).
Blue PGSC0003DMG400018372 X 未知功能。Unknown.
Blue PGSC0003DMG400026187 AT3G50950 编码一种典型的CC型NLR蛋白, 该蛋白是识别病原菌丁香中T3SE-Hopz1a所必需的。
Encodes a canonical CC-type NLR protein that is required for the recognition of the T3SE HopZ1a from the pathogenic bacteria P. syringae

Table 4

Correspondence between letters and genes"

A PGSC0003DMG400026572 E PGSC0003DMG400030368 I PGSC0003DMG400006704
B PGSC0003DMG400005154 F PGSC0003DMG400003792 J PGSC0003DMG400020683
C PGSC0003DMG400029350 G PGSC0003DMG402011550 K PGSC0003DMG400024687
D PGSC0003DMG400020462 H PGSC0003DMG400013391 L PGSC0003DMG400026238

Fig. 12

RT-qPCR validation of Hub genes"

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doi: 10.1105/tpc.109.071316 pmid: 20798329
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