Mesocotyl plays a key role in the seedling emergence of maize; however, the mechanism of mesocotyl elongation is still unclear. Moreover, different maize inbred lines and cultivars have varied mesocotyl lengths positively correlated with deep sowing tolerance. In this study, we selected one inbred line with long mesocotyl (LM) and two maize inbred lines with short mesocotyl (SM1 and SM2) from more than 400 maize inbred lines. The mesocotyl length of the LM line was about three-fold longer than those of the SM1 and SM2 lines. Microstructure observation showed that the reason for short mesocotyl in the SM1 and SM2 lines was few cell numbers and short cell length, respectively. Subsequently, we used RNA-seq to investigate the mechanism of mesocotyl elongation by regulating cell number and cell length at the transcriptome level. Compared with the LM line, the SM1 line displayed stronger downregulation of Cytochrome P450 and peroxidase genes than the SM2 line. Moreover, plant hormone signal transduction plays a vital role in mesocotyl elongation. Taken together, we propose a model for mesocotyl elongation of maize inbred lines with different cell lengths and cell numbers, which provide new insights into mesocotyl elongation in maize.
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