Transcriptomic Analysis of Maize Inbred Lines with Different Leaf Shapes Reveals Candidate Genes and Pathways Involved in Density Tolerance

Abstract

Maize is an important food and feed crop. Under limited arable land area, the cultivation of high-density-tolerance crops is a key factor in promoting yield improvement. Leaf width and stalk strength are important influences on density tolerance in maize. However, no comprehensive transcriptomic analysis has focused on maize’s leaf width and stalk strength formation mechanisms. In this study, comparative transcriptomic analyses demonstrated that significant transcriptome changes occurred regarding leaf width and stalk strength of narrow-leaved and wide-leaved maize inbred lines, with a total of 5001 differentially expressed genes (DEGs) identified. Enrichment analysis showed that phenylpropanoid biosynthesis, starch and sucrose metabolism, phytohormone signaling, amino acid metabolism, and brassinosteroid biosynthesis were significantly correlated with the formation of maize leaf shape and stalk strength and that the genes in these pathways were primarily involved in cell wall formation. Weighted gene co-expression network analysis identified 2 modules significantly correlated with leaf width and stalk strength, from which 11 hub genes were further identified. The 11 leaf and stem development genes in different pathways were validated using qRT-PCR. These findings can provide a theoretical basis for the mechanism of narrow-leaf and high-strength stalk formation in high-density-tolerance maize and contribute to the proposal of a breeding strategy for yield improvement.