Identification of QTLs and new candidate genes affecting ear shank length via BSA-seq and transcriptomic analysis in maize

A total of 14 QTLs for ear shank length were detected, which included 334 non-synonymous mutants, synonymous mutants and frameshift mutant genes. Among these loci, five were known to be associated with ear shank length, while nine were newly identified. 3,460 differentially expressed genes (DEGs) were screened through RNA-seq analysis of the ear shank at the silking stage in both parents. Thirteen new candidate genes were identified through the combined analysis of BSA-seq and RNA-seq, as well as gene function annotation and gene expression analysis. Based on functional predictions, the candidate genes <i>Zm00001eb023400</i>, <i>Zm00001eb023420</i> and <i>Zm00001eb050490</i>, which encoded lytic transglycosylases, significantly associated with cell wall remodeling and degradation. The candidate genes <i>Zm00001eb282410</i> and <i>Zm00001eb282430</i> enriched the phenylpropanoid biosynthesis pathway and played important roles in the formation of the maize ear shank. These findings provided a foundation for understanding the molecular mechanisms regulating ear shank length in maize.