Genome-Wide Identification of Height-Related Genes Using Three Maize Dwarfs and RNA-Seq

Plant height is an important grain yield-associated trait in maize. To date, few genes related to plant height have been characterized in maize. To better understand the genetic mechanisms of plant height in maize, we revealed the transcriptional changes of three dwarf mutants compared to the wild type. By ethyl methane sulfonate treatment of the wild-type maize cultivar PH6WC, we obtained three dwarfs—PH6WCdwarf1 (pd1), PH6WCdwarf2 (pd2), and PH6WCdwarf3 (pd3)—and their plant heights were reduced by 42%, 38%, and 24%, respectively. RNA-Seq data suggested that 1641 differentially expressed genes (DEGs) overlapped with each other among the three dwarfs at the seedling stage. Further analysis showed that the DEGs were divided into four groups with different expression patterns. Functional analysis revealed that these DEGs were commonly enriched in 47 GO terms mainly involved in cytokinesis, hormone, and energy metabolism pathways. Among them, An1, involved in the GA biosynthesis pathway, and mutations in An1 result in reduced plant height. EREB182 encodes ethylene-responsive element binding protein 2, which is critical for internode elongation. Microtubule-related genes Zmtub2, Zmtub3, Zmtub5, Zmtub6, and TUBG2 were commonly enriched among the three comparisons. Previous studies have shown that mutations in microtubule-associated genes cause the dwarf phenotype. However, nearly half of the common DEGs had no functional information, such as Zm00001d000107, Zm00001d000279, etc., implying their novel and specific functions in maize. Overall, this study identifies several potential plant height-related genes and contributes to linking genetic resources with maize breeding.