基于WGCNA的马铃薯根系抗旱相关共表达模块鉴定和核心基因发掘

doi:10.3724/SP.J.1006.2020.94130

Abstract

Abstract:

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

QIN Tian-Yuan, SUN Chao, BI Zhen-Zhen, LIANG Wen-Jun, LI Peng-Cheng, ZHANG Jun-Lian, BAI Jiang-Ping. Identification of drought-related co-expression modules and hub genes in potato roots based on WGCNA[J].Acta Agronomica Sinica, 2020, 46(7): 1033-1051.

Figures/Tables 17

Table 1

Fig. 1

Supplementary table 1

Fig. 2

Fig. 3

Fig. 4

Fig. 5

Fig. 6

Fig. 7

Fig. 8

Fig. 9

Table 2

Partial GO enrichment analysis of target modules"

模块 Module	GO条目 GO term	基因本体 Ontology	描述 Description	P值 P-value
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.	2.90E-09
Red	GO:0004866	F	内肽酶抑制剂活性。 Endopeptidase inhibitor activity.	0.00062
Red	GO:0030414	F	肽酶抑制剂活性。 Peptidase inhibitor activity.	0.00062
Red	GO:0005515	F	蛋白质结合。 Protein binding.	0.0012
Yellow	GO:0005515	F	蛋白质结合。 Protein binding.	2.20E-13
Turquoise	GO:0015979	P	光合作用。 Photosynthesis.	7.10E-07
模块 Module	GO条目 GO term	基因本体 Ontology	描述 Description	P值 P-value
Turquoise	GO:0019684	P	光合作用, 光反应。 Photosynthesis, light reaction.	5.90E-06
Turquoise	GO:0006694	P	类固醇生物合成过程。 Steroid biosynthetic process.	5.60E-05
Turquoise	GO:0010033	P	对有机物质的反应。 Response to organic substance.	0.00023
Turquoise	GO:0005515	F	蛋白结合。 Protein binding.	4.00E-27
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.	3.00E-07
Turquoise	GO:0003854	F	3-β-羟基-Δ5-类固醇脱氢酶活性。 3-beta-hydroxy-delta5-steroid dehydrogenase activity.	3.30E-05
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.	3.30E-05
Turquoise	GO:0016229	F	类固醇脱氢酶活性。 Steroid dehydrogenase activity.	3.30E-05
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.	7.10E-05
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.	0.00026
Turquoise	GO:0051287	F	NAD或NADH结合。 NAD or NADH binding.	0.00039
Turquoise	GO:0008092	F	细胞骨架蛋白结合。 Cytoskeletal protein binding.	0.00062
Blue	GO:0007010	P	细胞骨架组织。 Cytoskeleton organization.	1.20E-05
Blue	GO:0005515	F	蛋白结合。 Protein binding.	2.70E-29
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.	2.50E-10
Blue	GO:0016021	C	膜结合。 Integral to membrane.	7.30E-05
Blue	GO:0015629	C	肌动蛋白细胞骨架。 Actin cytoskeleton.	0.00021
Blue	GO:0031224	C	膜固有的。 Intrinsic to membrane.	0.00036

Table 2

Fig. 10

Fig. 11

Table 3

Functional annotations of hub genes in different modules"

模块 Module	核心基因 Hub gene	核心基因在拟南芥同源基因 Hub gene in A. thaliana	基因功能 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).
模块 Module	核心基因 Hub gene	核心基因在拟南芥同源基因 Hub gene in A. thaliana	基因功能 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 3

Table 4

Fig. 12

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

处理时间Treatment time	超氧化物歧化酶 Superoxide dismutase (U g^-1)		过氧化物酶 Peroxidase (U g^-1 min^-1)		过氧化氢酶 Catalase (U g^-1 min^-1)		根活力 Root vitality (mg g^-1 h^-1)
处理时间Treatment time	平均值 Average value	标准差 Standard deviation	平均值 Average value	标准差 Standard deviation	平均值 Average value	标准差 Standard deviation	平均值 Average value	标准差 Standard deviation
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

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

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