Drought stress presents a significant threat to the growth and development of maize. It is important to study the genes and mechanisms that contribute to drought tolerance. In this study, we identified ZmHDT103 (that encodes a histone deacetylase) by conducting a homologous sequence comparison and found that the expression of ZmHDT103 in maize seedlings is responsive to treatment with polyethylene glycol (PEG). We utilized CRISPR/Cas9 gene editing technology to generate three distinct knockout lines and obtained the ChinaMU mutant of the ZmHDT103 gene. Under drought conditions, the seedlings of ZmHDT103 mutants exhibited significantly lower water loss rate (WLR), relative electrolytic leakage (REL), hydrogen peroxide (H₂O₂) level, and malonaldehyde (MDA) level than those of their wild-type (WT) counterparts. Additionally, the seedlings of ZmHDT103 mutants exhibited significantly higher levels of abscisic acid (ABA), relative water content (RWC), peroxidase (POD), and proline (Pro) than those of the WT control. These findings indicate that ZmHDT103 acts as a negative regulator of drought tolerance in maize.

Drought is one of the major abiotic stresses with a severe negative impact on maize production globally. Understanding the genetic architecture of drought tolerance in maize is a crucial step towards the breeding of drought-tolerant varieties and a targeted exploitation of genetic resources. In this study, 511 quantitative trait loci (QTL) related to grain yield components, flowering time, and plant morphology under drought conditions, as well as drought tolerance index were collected from 27 published studies and then projected on the IBM2 2008 Neighbors reference map for meta-analysis. In total, 83 meta-QTL (MQTL) associated with drought tolerance in maize were identified, of which 20 were determined as core MQTL. The average confidence interval of MQTL was strongly reduced compared to that of the previously published QTL. Nearly half of the MQTL were confirmed by co-localized marker-trait associations from genome-wide association studies. Based on the alignment of rice proteins related to drought tolerance, 63 orthologous genes were identified near the maize MQTL. Furthermore, 583 candidate genes were identified within the 20 core MQTL regions and maize–rice homologous genes. Based on KEGG analysis of candidate genes, plant hormone signaling pathways were found to be significantly enriched. The signaling pathways can have direct or indirect effects on drought tolerance and also interact with other pathways. In conclusion, this study provides novel insights into the genetic and molecular mechanisms of drought tolerance in maize towards a more targeted improvement of this important trait in breeding.

Genotype-by-environment interaction (G-by-E) is a common but potentially problematic phenomenon in plant breeding. In this study, we investigated the genotypic performance and two measures of plasticity on a phenotypic and genetic level by assessing 234 maize doubled haploid lines from six populations for 15 traits in seven macro-environments with a focus on varying soil phosphorus levels. It was found intergenic regions contributed the most to the variation of phenotypic linear plasticity. For 15 traits, 124 and 31 quantitative trait loci (QTL) were identified for genotypic performance and phenotypic plasticity, respectively. Further, some genes associated with phosphorus use efficiency, such as Zm00001eb117170, Zm00001eb258520, and Zm00001eb265410, encode small ubiquitin-like modifier E3 ligase were identified. By significantly testing the main effect and G-by-E effect, 38 main QTL and 17 interaction QTL were identified, respectively, in which MQTL38 contained the gene Zm00001eb374120, and its effect was related to phosphorus concentration in the soil, the lower the concentration, the greater the effect. Differences in the size and sign of the QTL effect in multiple environments could account for G-by-E. At last, the superiority of G-by-E in genomic selection was observed. In summary, our findings will provide theoretical guidance for breeding P-efficient and broadly adaptable varieties.

Drought severely limits crop yield every year, making it critical to clarify the genetic basis of drought tolerance for breeding of improved varieties. As drought tolerance is a complex quantitative trait, we analyzed three phenotypic groups: (1) agronomic traits under well-watered (WW) and water-deficit (WD) conditions, (2) stress tolerance indices of these traits, and (3) phenotypic plasticity, using a multi-parent doubled haploid (DH) population assessed in multi-environment trials. Genome-wide association studies (GWAS) identified 130, 171, and 71 quantitative trait loci (QTL) for the three groups of phenotypes, respectively. Only one QTL was shared among all trait groups, 25 between stress indices and agronomic traits, while the majority of QTL were specific to their group. Functional annotation of candidate genes revealed distinct pathways of the three phenotypic groups. Candidate genes under WD conditions were enriched for stress response and epigenetic regulation, while under WW conditions for protein synthesis and transport, RNA metabolism, and developmental regulation. Stress tolerance indices were enriched for transport of amino/organic acids, epigenetic regulation, and stress response, whereas plasticity showed enrichment for environmental adaptability. Transcriptome analysis of 26 potential candidate genes showed tissue-specific drought responses in leaves, ears, and tassels. Collectively, these results indicated both shared and independent genetic mechanisms underlying drought tolerance, providing novel insights into the complex phenotypes related to drought tolerance and guiding further strategies for molecular breeding in maize.

Phosphorus is one of the key limiting factors for maize growth and productivity, and low-phosphorus stress severely restricts crop yield and stability. Enhancing the ability of maize to grow under low-phosphorus stress and improving phosphorus use efficiency (PUE) are crucial for achieving high and stable yields. Phosphate transporter (PHT) family proteins play a crucial role in the absorption, transport, and utilization of phosphorus in plants. In this study, we systematically identified the PHT gene family in maize, followed by the phylogenetic, gene structure, and expression profiles. The results show that these genes are widely distributed across the 10 chromosomes of maize, forming multiple subfamilies, with the PHT1 subfamily having the largest number. Cis-regulatory element analysis revealed that these genes might play key roles in plant stress responses and hormone regulation. Transcriptome analysis under phosphorus-deficient and normal conditions demonstrated developmental stage- and tissue-specific expression patterns, identifying candidate genes, such as ZmPHT1-3, ZmPHT1-4, ZmPHT1-10, and ZmPHO1-H3, involved in phosphorus stress response. This study presents a comprehensive and systematic analysis of the PHT gene family in maize, providing key molecular resources for improving phosphorus use efficiency and breeding phosphorus-efficient maize varieties.

Maize is one of the first crops to benefit from heterosis, significantly enhancing commercial breeding. Despite extensive research, the molecular mechanisms of heterosis remain elusive. This study integrates a novel genetic framework with transcriptomic and phenotypic analyses to identify heterosis-related genes and uncover their regulatory mechanisms. Single-segment substitution lines (SSSLs) were combined with a novel double single-factor differential subtraction (DSDS) strategy to identify heterosis-related differentially expressed genes (DEGs). Unlike traditional parent-hybrid comparisons, DSDS subtracts background expression noise and identifies heterosis-related genes within a controlled genomic context. Five hybrid groups, including mini-F₁ and sub-F₁ hybrids, were generated and analyzed. RNA sequencing was conducted at 15 days after pollination (DAP) to profile gene expression. Motif enrichment and dual-luciferase assays were used for functional validation. Heterosis exhibited a nonlinear trajectory with parental genetic distance, displaying a rapid increase at low genomic heterogeneity levels before reaching a saturation point at moderate divergence. DSDS identified 359 and 80 heterosis-related DEGs in two mini-F₁ hybrids, with most DEGs located outside the substitution regions, supporting a trans-regulatory mechanism. GO (gene ontology) analysis revealed enrichment in transport and cell expansion pathways, aligning with key processes in early kernel development. Notably, ZmWRKY67 was the only DEG in the substitution segment of mini-F₁ CL137 × Ye478. Initial functional assays confirmed its regulation of Incw1, a key sucrose metabolism gene. The findings suggest a transcriptional "butterfly effect", where minor genomic variations in heterozygous regions trigger genome-wide expression changes to drive heterosis. This study demonstrates the effectiveness of SSSL-based DSDS in identifying heterosis-related genes and provides a framework for dissecting transcriptional regulation in heterosis. The observed transcriptional "butterfly effect" offers a novel perspective on how small genomic variations contribute to heterosis. Future research should explore additional substitution-region DEGs to further unravel the molecular basis of heterosis in maize.