Maize is one of the most important food and feed crops in China due to the high demand for its use by both humans and animals. The Huang-Huai-Hai region is a major maize cultivation area in China, and the special cropping rotation system of wheat and maize requires a suitable reproductive period for maize. The AUX/IAA and ARF transcription factors are two key genes that regulate auxin signals in plants, which play an important role during the process of auxin regulation in plant growth and development. In this study, we obtained two overexpressed lines of ZmIAA29 belonging to the AUX/IAA transcription factor family. Compared with the Wide type, the overexpressed strains of ZmIAA29 were significantly regulated in maize during the flowering time and had increased ear weight. Moreover, ZmIAA29 was assayed via the yeast two-hybrid and BiLUC systems for interaction, and the results showed that ZmIAA29 interacted with several ZmARF transcription factors. Furthermore, RNA-seq and DAP-seq analysis revealed that ZmIAA29 regulates maize growth and development by influencing pathways such as those for plant signal transduction and the key genes related to maize flowering. Taken together, our results suggest that ZmIAA29 plays a key role in the development of maize flowering. This study provides new insight for better understanding the combined regulation of the AUX/IAA and ARF transcription factors during flowering time in maize.

Phosphorus (P) is an essential macroelement supporting maize productivity and low-P stress is a limiting factor of maize growth and yield. Improving maize plant tolerance to low P through molecular breeding is an effective alternative to increase crop productivity. In this study, a total of 111 diverse maize inbred lines were used to identify the favorable alleles and nucleotide diversity of candidate ZmNAC9, which plays an important role in response to low P and regulation in root architecture. A significant difference was found under low- and sufficient-P conditions for each of the 22 seedling traits, and a total of 41 polymorphic sites including 32 single nucleotide polymorphisms (SNPs) and 9 insertion and deletions (InDels) were detected in ZmNAC9 among 111 inbred lines. Among the 41 polymorphic studied sites, a total of 39 polymorphic sites were associated with 20 traits except for the dry weight of shoots and forks, of which six sites were highly significantly associated with a diverse number of low-P tolerant root trait index values by using a mixed linear model (MLM) at −log10 P = 3.61. In addition, 29 polymorphic sites under P-sufficient and 32 polymorphic sites under P-deficient conditions were significantly associated with a diverse number of seedling traits, of which five polymorphic sites (position S327, S513, S514, S520, and S827) were strongly significantly associated with multiple seedling traits under low-P and normal-P conditions. Among highly significant sites, most of the sites were associated with root traits under low-P, normal-P, and low-P trait index values. Linkage disequilibrium (LD) was strong at (r2 > 1.0) in 111 inbred lines. Furthermore, the effect of five significant sites was verified for haplotypes in 111 lines and the favorable allele S520 showed a positive effect on the dry weight of roots under the low-P condition. Furthermore, the expression pattern confirmed that ZmNAC9 was highly induced by low P in the roots of the P-tolerant 178 inbred line. Moreover, the subcellular localization of ZmNAC9 encoded by protein was located in the cytoplasm and nucleus. Haplotypes carrying more favorable alleles exhibited superior effects on phenotypic variation and could be helpful in developing molecular markers in maize molecular breeding programs. Taken together, the finding of this study might lead to further functions of ZmNAC9 and genes that might be involved in responses to low-P stress in maize.