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作物学报 ›› 2020, Vol. 46 ›› Issue (7): 1033-1051.doi: 10.3724/SP.J.1006.2020.94130

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

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

秦天元1,2,**,孙超1,2,**,毕真真1,2,梁文君1,2,李鹏程1,2,张俊莲1,白江平1,2,*()   

  1. 1 甘肃省干旱生境作物学重点实验室 / 甘肃省作物遗传改良与栽培种创新重点实验室, 甘肃兰州 730070
    2 甘肃农业大学农学院, 甘肃兰州 730070
  • 收稿日期:2019-08-27 接受日期:2019-12-26 出版日期:2020-07-12 发布日期:2020-01-14
  • 通讯作者: 白江平 E-mail:baijp@gsau.edu.cn
  • 作者简介:秦天元, E-mail: 1637835362@qq.com|孙超, E-mail: sunc@gsau.edu.cn
    ** 同等贡献
  • 基金资助:
    国家自然科学基金项目(31660432);国家自然科学基金项目(31460369);国家现代农业产业技术体系(马铃薯)建设专项(CARS-09-P14);甘肃省马铃薯产业体系(GARS-03-P1);中国科学院“西部之光”人才培养计划(2014-01);兰州市科技发展计划(2015-3-62);甘肃省教育厅项目(2019B-073);甘肃省自然科学基金(18JR3RA174);甘肃农业大学国重实验室开放基金(GSCS-2017-9);甘肃农业大学创新基金(GAU-XKJS-2018-085)

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)

摘要:

权重基因共表达网络分析(Weighted Gene Co-expression Network Analysis, WGCNA)是系统生物学的一种研究方法, 在多样本转录组数据中挖掘与目标性状相关的基因模块有较广泛的应用。为了深入探究马铃薯应对干旱胁迫的分子机制, 本研究以国际马铃薯中心引进栽培种C16 (CIP 397077.16)和C119 (CIP 398098.119)为试验材料, 将其无菌组培苗利用甘露醇模拟干旱胁迫, 处理0 h、2 h、6 h、12 h和24 h, 取其根系进行转录组测序, 每样设3个生物学重复, 共30个样本。基于以上转录组数据, 利用WGCNA构建与抗逆生理性状相关联的权重基因共表达网络, 得到15个与根系抗旱密切相关的基因共表达模块, 并从4个与目标性状关联度最高的模块中发掘到数个核心基因, 功能注释表明其中大部分参与干旱胁迫调控通路。这些结果为进一步研究马铃薯根系抗旱的分子遗传机制提供了线索。

关键词: 马铃薯, 干旱胁迫, 权重基因共表达网络, 转录组学

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

表1

试验材料"

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

图1

不同处理时间下C16与C119根系中上调和下调的差异表达基因数 A, B: C16和C119根中上调表达的差异基因数目; C, D: C16和C119根中下调表达的差异基因数目。黄色柱代表该样本的总基因数目, 黑色柱代表黑色圆点所对应的样本中的差异基因数目, 黑色圆点间的连线代表样本之间拥有的相同差异表达基因。"

附表 1

C16和C119在不同处理时间下的生化指标数据"

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)
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

图2

样本的聚类树 A: 所有的样本的聚类树; B: 去除离群样本后的聚类树。"

图3

基因共表达网络软阈值的确定 图A和图B的横坐标均代表软阈值(β), 图A的纵坐标代表无尺度网络模型指数, 图B的纵坐标代表每一个软阈值对应的网络平均连接程度。"

图4

基因共表达网络基因聚类数和模块切割 基因聚类树的每一个分支对应一个模块。"

图5

基因共表达网络模块与生理生化性状的关联热图 横轴表示不同处理时间下的生理生化性状, 纵轴表示每一个模块的特征向量。红色的格子代表性状与模块具有正相关性, 绿色的格子代表性状与模块具有负相关性。0 h表示未进行干旱处理。"

图6

ME聚类树"

图7

不同模块两两之间ME的相关性"

图8

各样本中不同模块的所有基因与相应ME的表达水平 上图(热图)为各个样本在模块中所有基因的表达水平。A: Red模块; B: Yellow模块; C: Turquoise模块; D: Blue模块。行代表该模块内的所有基因, 列代表不同的样本。下图(柱状图)为对应的样本中该模块ME的表达水平。"

图9

目标模块内基因GO注释"

表2

目标模块的部分GO富集分析结果"

模块
Module
GO条目
GO term
基因本体
Ontology
描述
Description
P
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
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

图10

Red和Yellow模块内的基因共表达网络及其核心基因"

图11

Turquoise和Blue模块内的基因共表达网络及其核心基因"

表3

不同模块中核心基因的功能注释"

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

表4

字母与基因的对应表"

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

图12

核心基因的RT-qPCR验证"

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