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.

Maize tassel spindle length is closely related to the number of pollen grains and the duration of the flowering stage, ultimately affecting maize yield and adaptations to stress conditions. In this study, 182 maize inbred lines were included in an association population. A genome-wide association study was conducted on maize tassel spindle length using the Q + K model. With p ≤ 1.0 × 10⁻⁴ applied as the significance threshold, 240 SNPs significantly associated with tassel spindle length were detected, which were associated with 99 quantitative trait loci (QTLs), with 21 QTLs detected in two or more environments. Moreover, 51 candidate genes were detected in 21 co-localized QTLs. A KEGG enrichment analysis and candidate gene expression analysis indicated that Zm00001d042312 affects plant hormone signal transduction and is highly expressed in maize tassels. A haplotype analysis of Zm00001d042312 revealed three main haplotypes, with significant differences between Hap1 and Hap2. In conclusion, we propose that Zm00001d042312 is a gene that regulates maize tassel spindle length. This study has further elucidated the genetic basis of maize tassel spindle length, while also providing excellent genetic targets and germplasm resources for the genetic improvement of maize tassel spindle length and yield.