? Discovery of leaf region and time point related modules and genes in maize (<em>Zea mays</em> L.) leaves by Weighted Gene Co-expression Network analysis (WGCNA) of gene expression profiles of carbon metabolism
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    2019, Vol. 18 Issue (02): 350-360     DOI: 10.1016/S2095-3119(18)62029-5
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Discovery of leaf region and time point related modules and genes in maize (Zea mays L.) leaves by Weighted Gene Co-expression Network analysis (WGCNA) of gene expression profiles of carbon metabolism
WANG Jing-lu*, ZHANG Ying*, PAN Xiao-di, DU Jian-jun, MA Li-ming, GUO Xin-yu
Beijing Key Lab of Digital Plant/Beijing Research Center for Information Technology in Agriculture/National Engineering Research Center for Information Technology in Agriculture/Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R.China
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Abstract 
Maize (Zea mays L.) yield depends not only on the conversion and accumulation of carbohydrates in kernels, but also on the supply of carbohydrates by leaves.  However, the carbon metabolism process in leaves can vary across different leaf regions and during the day and night.  Hence, we used Weighted Gene Co-expression Network analysis (WGCNA) with the gene expression profiles of carbon metabolism to identify the modules and genes that may associate with particular regions in a leaf and time of day.  There were a total of 45 samples of maize leaves that were taken from three different regions of a growing maize leaf at five time points.  Robust Multi-array Average analysis was used to pre-process the raw data of GSE85963 (accession number), and quality control of data was based on Pearson correlation coefficients.  We obtained eight co-expression network modules.  The modules with the highest significance of association with LeafRegion and TimePoint were selected.  Functional enrichment and gene-gene interaction analyses were conducted to acquire the hub genes and pathways in these significant modules.  These results can support the findings of similar studies by providing evidence of potential module genes and enriched pathways associated with leaf development in maize.
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WANG Jing-lu
ZHANG Ying
PAN Xiao-di
DU Jian-jun
MA Li-ming
GUO Xin-yu
Key wordsWGCNA     maize leaf     gene expression     gene modules     pathways     
Received: 2017-12-08; Accepted: 2018-06-04
Fund: This study was funded by the National Nature Science Foundation of China (31671577), the Natural Science Foundation of Beijing, China (5174033), the Scientific and Technological Innovation Capacity Construction Project of Beijing Academy of Agricultural and Forestry Sciences, China (KJCX20170404), the Scientific and Technological Innovation Team of Beijing Academy of Agricultural and Forestry Sciences, China (JNKYT201604), and the Beijing Postdoctoral Research Foundation, China (2016 ZZ-66).
Corresponding Authors: Correspondence GUO Xin-yu, Tel/Fax: +86-10-51503422, E-mail: guoxy@nercita.org.cn   
About author: WANG Jing-lu, Tel: +86-10-51503618, E-mail: wangjl@nercita.org.cn; ZHANG Ying, Tel: +86-10-51503618, E-mail: zhangying@nercita.org.cn;* These authors contributed equally to this study.
Cite this article:   
WANG Jing-lu, ZHANG Ying, PAN Xiao-di, DU Jian-jun, MA Li-ming, GUO Xin-yu. 2019. Discovery of leaf region and time point related modules and genes in maize (Zea mays L.) leaves by Weighted Gene Co-expression Network analysis (WGCNA) of gene expression profiles of carbon metabolism. Journal of Integrative Agriculture, 18(02): 350-360.
URL:  
http://www.chinaagrisci.com/Jwk_zgnykxen/EN/ 10.1016/S2095-3119(18)62029-5      or     http://www.chinaagrisci.com/Jwk_zgnykxen/EN/Y2019/V18/I02/350
 
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