The regulation of adaptive responses to phosphorus (P) deficiency by the microRNA399 (miR399)/PHOSPHATE2 (PHO2) pathway has been well studied in Arabidopsis thaliana but not in maize (Zea mays). Here, we show that miR399 transcripts are strongly induced in maize by phosphate (Pi) deficiency. Transgenic maize plants that over-expressed MIR399b accumulated excessive amounts of P in their shoots and displayed typical Pi-toxicity phenotypes. We re-annotated ZmPHO2 with an additional 1165 bp of the 59-untranslated region. miR399-guided post-transcriptional repression of ZmPHO2 was mainly observed in the P-efficient lines. We identified Pi-deficiency-induced long non-coding RNA 1 (PILNCR1) from our strand-specific RNA libraries. Transient expression assays in Nicotiana benthamiana and maize leaf protoplasts demonstrated that PILNCR1 inhibits ZmmiR399-guided cleavage of ZmPHO2. The abundance of PILNCR1 was significantly higher in P-inefficient lines than in P-efficient lines, which is consistent with the abundance of ZmmiR399 transcripts. These results indicate that the interaction between PILNCR1 and miR399 is important for tolerance to low Pi in maize.

Iron (Fe) deficiency remains widespread among people in developing countries. To help solve this problem, breeders have been attempting to develop maize cultivars with high yields and high Fe concentrations in the kernels. We conducted a genome-wide association study and identified a gene, ZmNAC78 ( NAM/ATAF/CUC DOMAIN TRANSCRIPTION FACTOR 78 ), that regulates Fe concentrations in maize kernels. We cultivated maize varieties with both high yield and high Fe concentrations in their kernels by using a molecular marker developed from a 42–base pair insertion or deletion (indel) in the promoter of ZmNAC78 . ZmNAC78 expression is enriched in the basal endosperm transfer layer of kernels, and the ZmNAC78 protein directly regulates messenger RNA abundance of Fe transporters. Our results thus provide an approach to develop maize varieties with Fe-enriched kernels.

Although microRNA408 (miR408) is a highly conserved miRNA, the miR408 response to salt stress differs among plant species. Here, we show that miR408 transcripts are strongly repressed by salt stress and methyl viologen treatment in maize (Zea mays). Application of N, N¹-dimethylthiourea partly relieved the NaCl-induced down-regulation of miR408. Transgenic maize overexpressing MIR408b is hypersensitive to salt stress. Overexpression of MIR408b enhanced the rate of net Na⁺ efflux, caused Na⁺ to locate in the inter-cellular space, reduced lignin accumulation, and reduced the number of cells in vascular bundles under salt stress. We further demonstrated that miR408 targets ZmLACCASE9 (ZmLAC9). Knockout of MIR408a or MIR408b or overexpression of ZmLAC9 increased the accumulation of lignin, thickened the walls of pavement cells, and improved salt tolerance of maize. Transcriptome profiles of the wild-type and MIR408b-overexpressing transgenic maize with or without salt stress indicated that miR408 negatively regulates the expression of cell wall biogenesis genes under salt conditions. These results indicate that miR408 negatively regulates salt tolerance by regulating secondary cell wall development in maize.

Phosphorus (P) stress is a global problem in maize production. Although macro/microarray technologies have greatly increased our general knowledge of maize responses to P stress, a greater understanding of the diversity of responses in maize genotypes is still needed. In this study, we first evaluated the tolerance to low P of 560 accessions under field conditions, and selected the low P-tolerant line CCM454 and the low P-sensitive line 31778 for further research. We then generated 24 strand-specific RNA libraries from shoots and roots of CCM454 and 31778 that had been subjected to P stress for 2 and 8 days. The P deficiency-responsive genes common to CCM454 and 31778 were involved in various metabolic processes, including acid phosphatase (APase) activity. Determination of root-secretory APase activities showed that the induction of APase by P stress occurred much earlier in CCM454 than that in 31778. Gene Ontology analysis of differentially expressed genes (DEGs) and CAT/POD activities between CCM454 and 31778 under P-sufficient and -deficient conditions demonstrated that CCM454 has a greater ability to eliminate reactive oxygen species (ROS) than 31778. In addition, 16 miRNAs in roots and 12 miRNAs in shoots, including miRNA399s, were identified as DEGs between CCM454 and 31778. The results indicate that the tolerance to low P of CCM454 is mainly due to the rapid responsiveness to P stress and efficient elimination of ROS. Our findings increase the understanding of the molecular events involved in the diversity of responses to P stress among maize accessions.

ZmEHD1 regulates auxin homeostasis by mediating clathrin-mediated endocytosis and is crucial for maize normal development.

Photoperiod sensitivity poses a major obstacle to the expansion, breeding, and production of maize (Zea mays) in temperate regions. While the photoperiod-dependent FLOWERING LOCUS T (FT)/ZCNs pathway modulates floral development, the mechanism by which crops perceive specific light wavelengths and regulate flowering remains largely unknown. In this study, we demonstrate that the rhythmic expression of the blue light receptor FLAVIN-BINDING KELCH REPEAT F-BOX 1a (ZmFKF1a) is finely controlled by the Evening Complex (EC) components of LUX ARRHYTHMO 2 (ZmLUX2). ZmFKF1a interacts with GIGANTEA 1 (ZmGI1), stabilizing it and promoting its nuclear localization via a blue light-dependent mechanism. In the nucleus, ZmGI1 directly binds and activates Zea mays MADS-box 4 (ZMM4), a MADS-box gene specifically expressed in the shoot apical meristem, which drives floral transition. Genetic analyses revealed that ZmGI1 is epistatic to ZmFKF1a in promoting shoot apex development and accelerating flowering in maize. Our findings elucidate a ZmLUX2-ZmFKF1a–ZmGI1-ZMM4 regulatory module that fine-tunes photoperiodic flowering of day-neutral temperate maize lines, functioning independently of ZEA CENTRORADIALISs (ZCNs). Furthermore, transgenic maize overexpressing ZmFKF1a exhibited accelerated flowering and enhanced yield specifically in photoperiod-sensitive tropical maize lines under extreme natural long-day conditions, underscoring its potential application in improving maize production through precise manipulation of flowering traits. These insights advance our understanding of how blue light signaling orchestrates flowering time in maize and offer a promising strategy for optimizing crop performance in diverse environments.