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

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–2 and 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.