Comparative transcriptome analysis reveals potential regulatory genes involved in the development and strength formation of maize stalks.

Abstract

Background: Stalk strength is a critical trait in maize that influences plant architecture, lodging resistance and grain yield. The developmental stage of maize, spanning from the vegetative stage to the reproductive stage, is critical for determining stalk strength. However, the dynamics of the genetic control of this trait remains unclear.

Results: Here, we report a temporal resolution study of the maize stalk transcriptome in one tropical line and one non-stiff-stalk line using 53 transcriptomes collected covering V7 (seventh leaf stage) through silking stage. The time-course transcriptomes were categorized into four phases corresponding to stalk early development, stalk early elongation, stalk late elongation, and stalk maturation. Fuzzy c-means clustering and Gene Ontology (GO) analyses elucidated the chronological sequence of events that occur at four phases of stalk development. Gene Ontology analysis suggests that active cell division occurs in the stalk during Phase I. During Phase II, processes such as cell wall extension, lignin deposition, and vascular cell development are active. In Phase III, lignin metabolic process, secondary cell wall biogenesis, xylan biosynthesis process, cell wall biogenesis, and polysaccharide biosynthetic process contribute to cell wall strengthening. Defense responses, abiotic stresses, and transport of necessary nutrients or substances are active engaged during Phase IV. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the two maize lines presented significant gene expression differences in the phenylpropanoid biosynthesis pathway and the flavonoid biosynthesis pathway. Certain differentially expressed genes (DEGs) encoding transcription factors, especially those in the NAC and MYB families, may be involved in stalk development. In addition, six potential regulatory genes associated with stalk strength were identified through weighted gene co-expression network analysis (WGCNA).

Conclusion: The data set provides a high temporal-resolution atlas of gene expression during maize stalk development. These phase-specific genes, differentially expressed genes, and potential regulatory genes reported in this study provide important resources for further studies to elucidate the genetic control of stalk development and stalk strength formation in maize.