Bioinformatics Analysis of Microarray Data to Reveal Novel Genes Related to Cold-Resistance of Maize

Abstract

Low temperature has become a major abiotic stress factor that can reduce maize yield and cause a number of economic loss. This study was designed to identify key genes and pathways associated with coldresistance of maize. The gene expression profile GSE46704, including 4 control temperature treated plants and 4 low temperature treated plants, was downloaded from the Gene Expression Omnibus database. Differentially-expressed genes (DEGs) were identified by limma package. Then, protein-protein interaction (PPI) network and module selection were constructed using Cytoscape. Moreover, the DEGs were re-matched based on the Zea mays L. gene ID and symbol data from PlantRegMap. Finally, the re-matched DEGs were performed functional and pathway enrichment analyses by the DAVID online tool. A total of 750 DEGs were screened (including 387 up-regulated and 363 down-regulated genes) In the PPI network, GRMZM2G070837_P01 and GRMZM2G114578_P01 had higher degrees. Besides, carbohydrate metabolic process, starch and sucrose metabolism and biosynthesis of secondary metabolites were significantly enriched in functional and pathway enrichment analysis. GRMZM2G070837_P01 and GRMZM2G114578_P01 might play a critical role in cold-resistance of maize. Meanwhile, carbohydrate metabolic process, starch and sucrose metabolism and biosynthesis of secondary metabolites might function in cold-resistance of maize.