The drought tolerance and capacity to recover after drought are important for plant growth and yield. In this study, two maize lines with different drought resistance were used to investigate the effects of different drought durations and subsequent re-watering on photosynthetic capacity, electron transfer and energy distribution, and antioxidative defense mechanisms of maize. Under short drought, maize plants decreased stomatal conductance and photosynthetic electron transport rate, and increased NPQ (Non-photochemical quenching) to dissipate excess excitation energy in time and protect the photosynthetic apparatus. With the increased drought duration, NPQ, antioxidase activity, PI_total (total performance index), ∆I/Io, ψ_Eo (quantum yield for electron transport)_, φ_Eo (efficiency/probability that an electron moves further than Q_A⁻), δ_Ro (efficiency/probability with which an electron from the intersystem electron carriers is transferred to reduce end electron acceptors at the PSI acceptor side) and φ_Ro (the quantum yield for the reduction of the end electron acceptors at the PSI acceptor side) were significantly reduced, while Y(NO) (quantum yield of nonregulated energy dissipation) and MDA (malondialdehyde) began to quickly increase. The photosynthetic rate and capacity of photosynthetic electron transport could not recover to the level of the plants subjected to normal water status after re-watering. These findings indicated that long drought damaged the PSI (photosystem I) and PSII (photosystem II) reaction center and decreased the electron transfer efficiency, and this damage could not be recovered by re-watering. Different drought resistance and recovery levels of photosynthetic performance were achieved by different maize lines. Compared with D340, D1798Z had higher NPQ and antioxidase activity, which was able to maintain functionality for longer in response to progressive drought, and it could also recover at more severe drought after re-watering, which indicated its higher tolerance to drought. It was concluded that the capacity of the energy dissipation and antioxidant enzyme system is crucial to mitigate the effects caused by drought, and the capacity to recover after re-watering was dependent on the severity and persistence of drought, adaptability, and recovery differences of the maize lines. The results provide a profound insight to understand the maize functional traits’ responses to drought stresses and re-watering.

DNA methylation affects agronomic traits and the environmental adaptability of crops, but the natural polymorphisms in DNA methylation–related genes and their contributions to phenotypic variation in maize (Zea mays) remain elusive. Here, we show that a polymorphic 10-bp insertion/deletion variant in the 3′UTR of Zea methyltransferase2 (ZMET2) alters its transcript level and accounts for variation in the number of maize husk layers. ZMET2 encodes a chromomethylase and is required for maintaining genome-wide DNA methylation in the CHG sequence context. Disruption of ZMET2 increased the number of husk layers and resulted in thousands of differentially methylated regions, a proportion of which were also distinguishable in natural ZMET2 alleles. Population genetic analyses indicated that ZMET2 was a target of selection and might play a role in the spread of maize from tropical to temperate regions. Our results provide important insights into the natural variation of ZMET2 that confers both global and locus-specific effects on DNA methylation, which contribute to phenotypic diversity in maize.

Ear architecture is determined by two stable heritable traits, kernel row number (KRN) and kernel number per row (KNPR), but its relationship with drought resistance is still vague. To this end, we obtained 16 and 11 hybrids with slender (less KRN but more KNPR) and stubby (more KRN but less KNPR) ears by intentionally crossbreeding, respectively. These hybrids were exposed to a seven-day water deficit (WD) since silk emergence coupled with synchronous (SP) and continuous pollination (CP) to alter the pollination time gaps on ears. The results showed that the emerged silks in CP were 9.1 and 9.0% less than in the SP treatment in the stubby and slender ears, respectively, suggesting the suppression of asynchronous pollination on silk emergence. The stubby ears performed higher silking rate and yield compared with the slender ears with or without drought stress. To eliminate the inherent difference in sink capacities, we selected four hybrids for each ear type with similar silk and kernel numbers for further analyses. Interestingly, the stubby ears were less affected in silking rate and thus performed higher yield under drought compared with the slender ears. The finding suggests that ear architecture matters in the determination of drought resistance that deserves more attention in breeding.

Biochar amendment is considered a sustainable agricultural strategy to improve crop yields. However, information on grain yield, fine roots and in relation to rhizosphere microbial communities in maize under plastic film mulching is very limited. Herein, biochar applied every 2 years (8.4 t ha⁻¹, B1) and biochar applied every 5 years (21 t ha⁻¹, B2) combined with nitrogen (225 kg ha⁻¹), or nitrogen alone, were tested in a field experiment. The results showed that a biochar–fertilizer application significantly decreased the root length at the V9 stage, but biochar applied every 5 years significantly maintained the root length at the R6 stage. Biochar–fertilizer application increased grain yield under the B1 treatment while slightly decreasing under the B2 treatment. The rhizosphere of maize was preferentially colonized by Proteobacteria, Firmicutes, Sphingomonas, and Bradyrhizobium. Dominant phyla including Proteobacteria were enriched in bulk soils, while Bacteroidetes and Firmicutes were depleted in rhizosphere and bulk soils under the biochar–fertilizer application. Changes in root morphology and soil properties were responsible for bacterial community structure in response to different biochar applications. Thus, we concluded that the differential responses of maize yield and root attributes might be related to the specific biochar dose-specific effects on soil microbiome diversity.

Northern corn leaf blight (NCLB), caused by the fungal pathogen Exserohilum turcicum, poses a grave threat to maize production worldwide. The resistance gene in A619Ht3, discovered decades ago, is an important genetic resource for NCLB control. By using a pair of near-isogenic lines (NILs) A619Ht3 and A619, together with the resistant and susceptible bulks derived from the cross of A619Ht3 and L3162 lines, we initially detected a Ht3-like (Ht3L) locus in bin 8.06 that was closely associated with NCLB resistance. We then performed five rounds of fine-mapping, which ultimately delimited the Ht3L locus to a 577-kb interval flanked by SNP markers KA002081 and KA002084. Plants homozygous for the Ht3L/Ht3L genotype exhibited an average reduction in diseased leaf area (DLA) by 16.5% compared to plants lacking Ht3L locus. The Ht3L locus showed extensive variation in genomic architecture among different maize lines and did not appear to contain any genes encoding canonical cell wall-associated kinases against NCLB. Moreover, the Ht3L locus was located ∼2.7 Mb away from the known Htn1 locus. We speculate that the Ht3L locus may contain a bona fide Ht3 gene or a novel NCLB resistance gene closely linked to Ht3. In practice, the Ht3L locus is a valuable resource for improving maize resistance to NCLB.

Fusarium ear rot (FER), caused by F. verticillioides, is a devastating disease in maize, leading to substantial yield losses and mycotoxin contamination. Therefore, revealing the molecular mechanisms underlying FER resistance is essential for crop breeding. Here, we performed integrated transcriptomic and metabolomic analyses on two maize inbred lines with contrasting FER resistance: the resistant line ZL30-12 (ZL30) and the susceptible line 92C0468U (92C). Following F. verticillioides inoculation, ZL30 exhibited sustained inhibition of fungal colonization and fumonisin accumulation, whereas 92C showed progressive disease development and elevated fumonisin levels. Both transcriptomic and metabolomic analyses converged on the phenylpropanoid pathway, with DEGs enriched in phenylpropanoid metabolism and DAMs enriched in phenylpropanoid biosynthesis, highlighting its central role in resistance. Further integrative analysis revealed that the lignin biosynthetic process, a key branch of phenylpropanoid metabolism, plays an important role in resistance. Several key DEGs (ZmPAL, ZmHCT, peroxidases, and ZmCOMT) and DAMs (sinapic acid, sinapaldehyde, coniferin, cinnamic acid, and caffeic acid) were differentially regulated between the two lines. Correlation analysis revealed a significant correlation between ZmCOMT expression and sinapic acid accumulation. RT-qPCR validation confirmed the expression patterns of key lignin-associated genes. The elevated activation of lignin biosynthesis in ZL30, via time-dependent induction of key genes (ZmPAL, ZmHCT, and peroxidases), suggests an increase in lignin accumulation, which likely reinforces cell wall integrity and restricts fungal invasion, thereby contributing to FER resistance. Collectively, these findings provide insights into the molecular mechanisms of FER resistance and identify key lignin-associated genes as promising targets for maize breeding.