Transcriptomic analysis reveals the regulation of early ear-length development in maize

Ear length is an important component of maize grain yield. However, the ear length is a complex quantitative trait, and the underlying molecular mechanisms remain poorly understood. Here, the chromosome segment substitution line (CSSL) 1283 displayed a longer ear length compared with the recipient parent Xu178. An RNA sequencing analysis of Xu178 and CSSL1283 ears during three undifferentiated ear developmental stages identified 1,991 differentially expressed genes (DEGs). A gene ontology analysis of the DEGs showed that genes related to transcription factors and response to abiotic stimulus were significantly enriched. Furthermore, the expression of DEGs associated with AP2/EREBP and WRKY transcription factors and heat shock proteins was upregulated in CSSL1283. In addition, several genes encoding protein kinase were differentially expressed between Xu178 and CSSL1283. Our study provided a genetic resource for the dissection of the molecular mechanisms of ear-length development and for uncovering candidate genes to increase maize ear length.