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作物学报 ›› 2020, Vol. 46 ›› Issue (3): 385-394.doi: 10.3724/SP.J.1006.2020.93021

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

利用WGCNA鉴定玉米株高和穗位高基因共表达模块

马娟,曹言勇,王利锋,李晶晶,王浩,范艳萍,李会勇()   

  1. 河南省农业科学院粮食作物研究所, 河南郑州 450002
  • 收稿日期:2019-04-02 接受日期:2019-09-26 出版日期:2020-03-12 网络出版日期:2020-03-01
  • 通讯作者: 李会勇
  • 作者简介:

    E-mail:majuanjuan85@126.com

  • 基金资助:
    本研究由国家重点研发计划项目(2016YFD100103);河南省科技攻关项目资助(192102110008)

Identification of gene co-expression modules of maize plant height and ear height by WGCNA

Juan MA,Yan-Yong CAO,Li-Feng WANG,Jing-Jing LI,Hao WANG,Yan-Ping FAN,Hui-Yong LI()   

  1. Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China
  • Received:2019-04-02 Accepted:2019-09-26 Published:2020-03-12 Published online:2020-03-01
  • Contact: Hui-Yong LI
  • Supported by:
    This study was supported by the National Key Research and Development Program of China(2016YFD100103);the Science and Technology Project of Henan province(192102110008)

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摘要：

株高和穗位高是玉米株型的重要影响因子, 与产量性状紧密相关。加权基因共表达网络分析(weighted gene co-expression network analysis, WGCNA)是探索基因网络与特定性状间关联关系的重要方法, 为株高和穗位高相关基因的挖掘提供新途径。本研究利用郑58、掖478、昌7-2和黄早四及其组配的杂交种郑单958、安玉5号、郑58/黄早四和掖478/黄早四, 结合其在45,000株 hm -2和67,500株 hm -2条件下的转录组数据, 采用WGCNA构建了2种密度条件下的共表达网络, 分别得到24个和21个共表达模块, 并鉴定到与株高和穗位高显著且高度相关(相关系数的绝对值>0.50)的共表达模块15个, 其中两性状相同的模块共6个。基因功能富集分析结果表明, 株高和穗位高共表达模块主要参与生长发育、光合作用、响应光刺激、植物激素、碳水化合物合成/代谢等重要活动。根据模块内基因的连接度, 发现乙烯响应因子EREB14、硫胺素酶TENA2、磷酸甘油酸激酶PGK、谷胱甘肽转移酶GST2和琥珀酸脱氢酶SUDH7等是模块内的核心基因。通过构建其局部网络, 发现EREB14与已报道株高基因D8、DWF1和ZmGRF10以及C3H转录因子C3H35、C2C2-GATA转录因子GATA4和乙烯受体同源子ETR40等存在关联关系。此外, 已报道株高基因An1和GA20ox3也存在于共表达模块中。以这5个已报道株高基因为核心, 构建其基因网路, 发现生长素转录因子ARFTF7、ARFTF26、GST39、光合系统II氧进化多肽PspB2和光合系统I N亚基PasN1等与其存在关联。15个共表达模块和核心基因的挖掘以及基因生物学功能和互作网络的解析有助于揭示玉米株高和穗位高的遗传基础。

关键词: 玉米, 加权基因共表达网络, 转录组, 株高, 穗位高

Abstract:

Plant height (PH) and ear height (EH) are important factors for maize plant type and grain yield. Weighted gene co-expression network analysis (WGCNA) is an important method to explain the relationships between gene network and complicated traits and identify the PH and EH associated genes. In this study, we used Zheng 58, Ye 478, Chang 7-2, Huangzaosi and its combinations Zhengdan 958, Anyu 5, Zheng 58/Huangzaosi, and Ye 478/Huangzaosi as materials and utilized transcriptome data under the planting densities of 45,000 plants hm -2and 67,500 plants hm -2 to construct a co-expression network by WGCNA, getting 24 and 21 co-expression modules, respectively. Among them, a total of 15 co-expression modules were significantly correlated with PH and EH, with the absolute correlation coefficients higher than 0.50. Six modules were overlapped between PH and EH. By gene function analysis, these overlapped modules were significantly enriched in development, photosynthesis, response to light stimulus, plant hormone, and carbohydrate biosynthesis/metabolism related activities. According to connectivity of genes in modules, AP2-EREBP transcription factor EREB14, thiaminase TENA2, phosphoglyceric kinase PGK, glutathione transferase GST2, and succinate dehydrogenase SUDH7 were considered as hub genes. From gene networks, EREB14 was connected with three known PH genes D8, DWF1, ZmGRF10, and C3H35 (C3H transcription factor), GATA4 (C2C2-GATA transcription factor), and ethylene homology ETR40. Reported PH genes An1 and GA20ox3 were also found in our co-expression modules. From the networks of the five known PH genes, ARF-transcription factor 7 (ARFTF7), ARFTF26, GST39, photosystem II oxygen evolving polypeptide PspB2, and photosystem I N subunit PasN1 had connections with these known PH genes. The identification of 15 co-expression modules and their hub genes, and analysis of their gene function and gene networks of key genes will be helpful for revealing the genetic basis of PH and EH.

Key words: maize, weighted gene co-expression network, transcriptome, plant height, ear height

图1

45,000株 hm-2(A) 和67,500株 hm-2(B)条件下软阈值β的确定 A和B: 左图纵坐标是无尺度网络模型指数; 右图纵坐标每一个软阈值对应的平均连接度; 横坐标均代表软阈值β。"

图2

45,000株 hm-2和67,500株 hm-2条件下8个材料株高和穗位高 图中数字表示均值±标准误。柱中字母为Duncan’s多重比较结果, 不同字母表示材料间在P < 0.05水平差异显著。*表示0.05显著水平。"

图3

45,000株 hm-2(A)和67,500株 hm-2(B)条件下基因聚类树和模块构建"

图4

45,000株hm-2条件下株高(PH)和穗位高(EH)共表达模块及其基因个数和相关系数"

图5

67,500株hm-2条件下株高(PH)和穗位高(EH)共表达模块及其基因个数和相关系数"

图6

显著共表达模块内核心基因的基因网络 图中青绿色、浅绿色和粉红色分别表示Turquoise、Lightgreen和Pink模块。"

图7

已报道株高基因D8、DWF1、ZmGRF10、An1和GA20ox3的基因网络 图中青绿色、棕色和粉红色分别表示Turquoise、Brown和Pink模块。"

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