Transcriptome and co-expression network analysis reveal the genetic basis of cell wall components in maize stalks

Abstract

Cellulose (CEL), hemicellulose (HCE), and lignin (LIG) are crucial constituents of the cell wall in maize stalks, significantly influencing stalk resistance to lodging and external stresses. The proportion of these contents also determines the application of maize stalks in animal feed, energy production, and other fields. Herein, two maize inbred lines with contrasting cell wall component contents in the stalk, MO190 (high CEL, HCE, and LIG contents) and MO194 (low CEL, HCE, and LIG contents), were subjected to analysis of transcriptomes at the seedling, jointing, silking, and grain stages. By comparing the differentially expressed genes (DEGs) during stalk development between the two lines, 11,546 genes were identified as the specific DEGs in each line. Using traits-associated WGCNA (weight gene co-expression network analysis), we identified a hub co-expression module and 26 key genes regulating the CEL, HCE, and LIG contents in the stalk. Based on the eigengene-based connectivity value in the module, the four genes Zm00001d019317, Zm00001d027313, Zm00001d043965, and Zm00001d019149 were confirmed as the hub genes affecting these contents. Among these, Zm00001d019317 that encodes CEL synthase-8 was significantly associated with CEL content in the stalk via gene-based association studies. Maize lines carrying the “deletion” allele in the promoter region of Zm00001d019317 exhibited significantly higher CEL content compared to those with the “C” allele. Our study helps to understand the variation mechanism of cell wall component contents in maize stalks and contributes to genetic modification of maize resistance to stalk lodging.

Supplementary Information: The online version contains supplementary material available at 10.1186/s12864-025-11816-2.

Keywords: Cellulose (CEL); Hemicellulose (HCE); Lignin (LIG); Maize; RNA-Seq; Stalk; WGCNA.

Fig. 1

Comparison of cellulose, hemicellulose, and lignin contents between the lines MO190 and MO194 at four stages. Seedling, seedling stage; Jointing, jointing stage; Silking, silking stage; Filling, grain filling stage. CEL, cellulose. HCE, hemicellulose. LIG, lignin

Fig. 2

Statistics of differentially expressed genes in maize stalk. A Pearson correlations between biological replicates from RNA sequencing. The depth of color corresponds to the level of correlation. B Up- and down-regulated genes at each treatment stage. C Venn diagram of DEGs between MO190 and MO194 at each stage. D KEGG pathways enriched with the 11,546 specific DEGs in each line. DEGs, differentially expressed genes. Seedling, seedling stage; Jointing, jointing stage; Silking, silking stage; Filling, grain filling stage. Rep, replicates. Up, upregulated genes; down, downregulated genes

Fig. 3

The results of weighted gene co expression network analysis (WGCNA) using the transcriptome data and phenotypes of two lines. A The gene co-expression modules in maize stalk using WGCNA. B Correlations between modules and phenotypes. Numbers without parentheses are the correlation coefficients between the module and phenotype; numbers inside the parentheses represent the P-values of the correlation. The red boxes show the selected modules most significantly correlated with the traits. CEL, cellulose. HCE, hemicellulose. LIG, lignin. C GO terms enriched in the salmon module

Fig. 4

Co-expression network of the 26 specific DEGs in the salmon module. A Co-expression network of the 26 specific genes in the salmon module. The size of the node represents the weight of the gene, node color represents the value of KME. value. B Gene expression patterns of the 26 genes in maize stalk

Fig. 5

Variant in Zm00001d019317 promoter was significantly correlated with cellulose. A Frequency distribution diagram of 100 lines in three areas. Xinxiang, XX; Chengdu, CD; Xishuangbanna, XSBN. B Significant variant associated with cellulose and the pairwise LDs between the markers. The horizontal dashed black line depicts the significance threshold at log₁₀(P) = 3.05 for Zm00001d019317-based association analysis; red dashed lines denote significant variants. C Comparison of cellulose between the groups with allele “deletion” and allele “C”, respectively, in 2023 XSBN. The pairwise LDs between the markers. D qRT-PCR of Zm00001d019317, 5/15/25 DAP refers to the maize grains on 5/15/25 days after pollination