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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (3): 385-394.doi: 10.3724/SP.J.1006.2020.93021


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 Online:2020-03-12 Published:2020-03-01
  • Contact: Hui-Yong LI E-mail:lihuiyong1977@126.com
  • 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)


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

Fig. 1

Determination of soft threshold β at 45,000 plants hm-2 (A) and 67,500 plants hm-2 (B) A and B: The ordinate represents the index of scale free network model in left figure. The ordinate represents the average link degree of each soft threshold in right figure. The abscissa represents the soft threshold β."

Fig. 2

Plant height and ear height of eight materials at 45,000 plants hm-2 and 67,500 plants hm-2 Number represents mean±SE. Bars with different letters are significantly different at P < 0.05 as determined by Duncan’s multiple comparison. * denotes significant at the 0.05 probability level."

Fig. 3

Gene cluster dendrograms and modules construction at 45,000 plants hm-2(A) and 67,500 plants hm-2 (B)"

Fig. 4

Co-expression modules, gene number, and correlation coefficient for plant height (PH) and ear height (EH) at 45,000 plants hm-2"

Fig. 5

Co-expression modules, gene number, and correlation coefficient for plant height (EH) and ear height (EH) at 67,500 plants hm-2"

Fig. 6

Gene networks of hub genes for significant co-expression modules Colors in figure represent Turquoise, Lightgreen, and Pink modules."

Fig. 7

Gene networks of known plant height genes D8, DWF1, ZmGRF10, An1, and GA20ox3 Colors in figure represent Turquoise, Brown, and Pink modules."

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