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Background Leaf angle is a key trait for maize plant architecture that plays a significant role in its morphological development, and ultimately impacting maize grain yield. Although many studies have been conducted on the association and localization of genes regulating leaf angle in maize, most of the candidate genes identified are associated with the regulation of ligule-ear development and phytohormone pathways, and only a few candidate genes have been reported to enhance the mechanical strength of leaf midrib and vascular tissues. Results To address this gap, we conducted a genome-wide association study (GWAS) using the leaf angle phenotype and genotyping-by-sequencing data generated from three recombinant inbred line (RIL) populations of maize. Through GWAS analysis, we identified 156 SNPs significantly associated with the leaf angle trait and detected a total of 68 candidate genes located within 10 kb upstream and downstream of these individual SNPs. Among these candidate genes, Zm00001d045408 , located on chromosome 9 emerged as a key gene controlling the angles of both the ear leaf and the second leaf above the ear leaf. Notably, this new gene’s homolog in Arabidopsis promotes cell division and vascular tissue development. Further analysis revealed that a SNP transversion (G/T) at 7.536 kb downstream of the candidate gene Zm00001d045408 may have caused a reduction in leaf angles of the ear and the second leaf above the ear leaf. Our analysis of the 10 kb region downstream of this candidate gene revealed a 4.337 kb solo long-terminal reverse transcription transposon (solo LTR), located 3.112 kb downstream of Zm00001d045408 , with the SNP located 87 bp upstream of the solo LTR. Conclusions In summary, we have identified a novel candidate gene, Zm00001d045408 and a solo LTR that are associated with the angles of both the ear leaf and the second leaf above the ear leaf. The future research holds great potential in exploring the precise role of newly identified candidate gene in leaf angle regulation. Functional characterization of this gene can help in gaining deeper insights into the complex genetic pathways underlying maize plant architecture.

Background Drought is a serious causal factor of reduced crop yields than any other abiotic stresses. As one of the most widely distributed crops, maize plants frequently suffer from drought stress, which causes great losses in the final kernel yield. Drought stress response in plants showed tissue- and developmental stage-specific characteristics. Results In this study, the ears at the V9 stage, kernels and ear leaf at the 5DAP (days after pollination) stage of maize were used for morphological, physiological and comparative transcriptomics analysis to understand the different features of “sink” or “source” organs and the effects on kernel yield under drought stress conditions. The ABA-, NAC-mediate signaling pathway, osmotic protective substance synthesis and protein folding response were identified as common drought stress response in the three organs. Tissue-specific drought stress responses and the regulators were identified, they were highly correlated with growth, physiological adaptation and yield loss under drought stress. For ears, drought stress inhibited ear elongation, led to the abnormal differentiation of the paired spikelet, and auxin signaling involved in the regulation of cell division and growth and primordium development changes. In the kernels, reduced kernel size caused by drought stress was observed, and the obvious differences of auxin, BR and cytokine signaling transduction appeared, which indicated the modification in carbohydrate metabolism, cell differentiation and growth retardation. For the ear leaf, dramatically and synergistically reduced the expression of photosynthesis genes were observed when suffered from drought stress, the ABA- and NAC- mediate signaling pathway played important roles in the regulation of photosynthesis. Conclusions Transcriptomic changes caused by drought were highly correlated with developmental and physiological adaptation, which was closely related to the final yield of maize, and a sketch of tissue- and developmental stage-specific responses to drought stress in maize was drafted.

The spatial morphological structure of plant leaves is an important index to evaluate crop ideotype. In this study, we characterized the three-dimensional (3D) data of the ear leaf midrib of maize at the grain-filling stage using the 3D digitization technology and obtained the phenotypic values of 15 traits covering four different dimensions of the ear leaf midrib, of which 13 phenotypic traits were firstly proposed for featuring plant leaf spatial structure. Cluster analysis results showed that the 13 traits could be divided into four groups, Group I, -II, -III and -IV. Group I contains HorizontalLength, OutwardGrowthMeasure, LeafAngle and DeviationTip; Group II contains DeviationAngle, MaxCurvature and CurvaturePos; Group III contains LeafLength and ProjectionArea; Group IV contains TipTop, VerticalHeight, UpwardGrowthMeasure, and CurvatureRatio. To investigate the genetic basis of the ear leaf midrib curve, 13 traits with high repeatability were subjected to genome-wide association study (GWAS) analysis. A total of 828 significantly related SNPs were identified and 1365 candidate genes were annotated. Among these, 29 candidate genes with the highest significant and multi-method validation were regarded as the key findings. In addition, pathway enrichment analysis was performed on the candidate genes of traits to explore the potential genetic mechanism of leaf midrib curve phenotype formation. These results not only contribute to further understanding of maize leaf spatial structure traits but also provide new genetic loci for maize leaf spatial structure to improve the plant type of maize varieties.

Poultry litter (PL) is known to have residual effects on crop productivity long after applications cease. Whether this advantage is greater if applied by subsurface vs. surface broadcast is unknown. The objective of this study was to determine whether the residual benefit of PL to corn and cotton production is greater if applied in subsurface bands vs. surface broadcast and identify PL components contributing to this effect. The residual effect of PL applied by the two methods or synthetic nitrogen (sN) at seven plant available N rates (0–292 kg ha−1 yr−1) in 2014–2015 was tested on corn and cotton in 2016–2019. Corn was grown without applying PL or sN in 2016, and cotton was grown in 2017–2019 after applying 90 kg ha−1 yr−1 sN to all plots. Corn produced 40% greater grain and cotton produced 29% more lint yield due to residuals from PL than sN. Residuals from PL distinctly increased cotton leaf K over sN regardless of the method of application. Corn and cotton yield benefits from PL residual were greater if applied by subsurface banding vs. surface broadcast. This difference diminished with time. The overall results show PL components persist in the soil for up to 4 years and affect corn and cotton production, but this persistence is greater if the PL is applied by subsurface banding. This study identified K as the key PL nutrient that persisted in the soil and benefited cotton yield 4 years after the last application.

Chlorophyll is an essential component that captures light energy to drive photosynthesis. Chlorophyll content can affect photosynthetic activity and thus yield. Therefore, mining candidate genes of chlorophyll content will help increase maize production. Here, we performed a genome-wide association study (GWAS) on chlorophyll content and its dynamic changes in 378 maize inbred lines with extensive natural variation. Our phenotypic assessment showed that chlorophyll content and its dynamic changes were natural variations with a moderate genetic level of 0.66/0.67. A total of 19 single-nucleotide polymorphisms (SNPs) were found associated with 76 candidate genes, of which one SNP, 2376873-7-G, co-localized in chlorophyll content and area under the chlorophyll content curve (AUCCC). Zm00001d026568 and Zm00001d026569 were highly associated with SNP 2376873-7-G and encoded pentatricopeptide repeat-containing protein and chloroplastic palmitoyl-acyl carrier protein thioesterase, respectively. As expected, higher expression levels of these two genes are associated with higher chlorophyll contents. These results provide a certain experimental basis for discovering the candidate genes of chlorophyll content and finally provide new insights for cultivating high-yield and excellent maize suitable for planting environment.

The ear leaf veins are an important transport structure in the maize \"source\" organ; therefore, the microscopic phenotypic characteristics and genetic analysis of the leaf veins are particularly essential for promoting the breeding of ideal maize varieties with high yield and quality. In this study, the microscopic image of the complete blade cross section was realized using X-ray micro-computed tomography (micro-CT) technology with a resolution of 13.5 µm. Moreover, the veins’ phenotypic traits in the cross section of the complete maize leaf, including the number of leaf veins, midvein area, leaf width, and density of leaf veins, were automatically and accurately detected by a deep-learning-integrated phenotyping pipeline. Then, we systematically collected vein phenotypes of 300 inbred lines at the silking stage of the ear leaves. It was found that the leaf veins’ microscopic characteristics varied among the different subgroups. The number of leaf veins, the density of leaf veins, and the midvein area in the stiff-stalk (SS) subgroup were significantly higher than those of the other three subgroups, but the leaf width was the smallest. The leaf width in the tropical/subtropical (TST) subgroup was the largest, but there was no significant difference in the number of leaf veins between the TST subgroup and other subgroups. Combined with a genome-wide association study (GWAS), 61 significant single-nucleotide polymorphism markers (SNPs) and 29 candidate genes were identified. Among them, the candidate gene Zm00001d018081 regulating the number of leaf veins and Zm00001d027998 regulating the midvein area will provide new theoretical support for in-depth analysis of the genetic mechanism of maize leaf veins.

Improper nutrient management reduces the yield and affects the nutrient status of crops. This study aimed to diagnose the nutrients limitation in maize. A three-year multi-location (348 sites) nutrient experiments were conducted in randomized block design to analyse nutrients limitation for maize production under conventional fertilizer recommendation system in Nigeria using DRIS, and to identify soil factors that influence DRIS indices using random forest model. DRIS indices for nutrients were calculated from the results of ear leaf samples collected from the experimental plots. The DRIS indices were summed, and used to cluster plots using k-means cluster algorithm. The results show large differences in average yield between the clusters. The clusters also differed based on frequency with which nutrients are most limiting. B was the most limiting in cluster one and three, Mn in cluster two and K in cluster four. Random forest results show that soil pH, B and Mg had the largest influence on DRIS indices in cluster one. DRIS indices were most influenced by soil N and B in cluster two. To a lesser extent, the soil Fe, K, Mg and S contents also influenced DRIS indices in cluster two. Soil K, B and Zn were the most significant factors influencing the DRIS indices in cluster four. Bulk Density, Fe, Na, ECEC, and organic carbon had a moderate influence on the indices in this cluster. Nutrient limitation in plants can be diagnose using the DRIS. Soil properties have a definite influence on maize nutrient status.

Soil waterlogging resulting from extreme precipitation events creates anaerobic conditions that may inhibit plant growth and increase N losses. A three-year (2013–2015) field experiment was conducted in poorly-drained claypan soils to assess the effects of waterlogging [0 or 7-days waterlogging at V3 growth stage of corn (Zea mays L.)] and pre-plant application of different N fertilizer sources and post-waterlogging rescue N application (0 or 84 kg N ha−1 of urea plus urease inhibitor (NCU + UI) at V7) on chlorophyll SPAD meter (CM) readings, stomatal conductance, ear leaf and silage N concentrations, N uptake and apparent N recovery efficiency (ARE) of two corn hybrids with varying amounts of flood tolerance. Pre-plant N fertilizer sources included a non-treated control (CO), urea (NCU), urea plus nitrification inhibitor (NCU + NI) and polymer coated urea (PCU) applied at 168 kg N ha−1. In 7-days waterlogged plots, rescue N applications increased N uptake in PCU treatments 33% and 40% in 2013 and 2014, respectively, as well as in NCU by 48% in 2013. In 7-days waterlogged plots which received rescue N applications, NCU and PCU in 2013 resulted in higher N uptake than CO and NCU + NI by 47 to 77 kg ha−1. PCU had higher N uptake than NCU and NCU + NI by 78 and 72 kg ha−1 in 7-days waterlogged plots that received rescue N applications in 2014. Corn hybrid showed no differences in N uptake and ARE in our study. Our results indicate combining pre-plant N fertilizer source selection and rescue N applications may be a strategy to reduce possible decreases in corn N uptake caused by early season soil waterlogging in average rainfall years.

Background The plant architecture traits of maize determine the yield. Plant height, ear position, leaf angle above the primary ear and internode length above the primary ear together determine the canopy structure and photosynthetic efficiency of maize and at the same time affect lodging and disease resistance. A flat and tall plant architecture confers an obvious advantage in the yield of a single plant but is not conducive to dense planting and results in high rates of lodging; thus, it has been gradually eliminated in production. Although using plants that are too compact, short and density tolerant can increase the yield per unit area to a certain extent, the photosynthetic efficiency of such plants is low, ultimately limiting yield increases. Genetic mapping is an effective method for the improvement of plant architecture to identify candidate genes for regulating plant architecture traits. Results To find the best balance between the yield per plant and the yield per unit area of maize, in this study, the F2:3 pedigree population and a RIL population with the same male parent were used to identify QTL for plant height (PH), ear height (EH), leaf angle and internode length above the primary ear (LAE and ILE) in Changchun and Gongzhuling for 5 consecutive years (2016–2020). A total of 11, 13, 23 and 13 QTL were identified for PH, EH, LAE, and ILE, respectively. A pleiotropic consistent QTL for PH overlapped with that for EH on chromosome 3, with a phenotypic variation explanation rate from 6.809% to 21.96%. In addition, there were major consistent QTL for LAE and ILE, and the maximum phenotypic contribution rates were 24.226% and 30.748%, respectively. Three candidate genes were mined from the three consistent QTL regions and were involved in the gibberellin-activated signal pathway, brassinolide signal transduction pathway and auxin-activated signal pathway, respectively. Analysis of the expression levels of the three genes showed that they were actively expressed during the jointing stage of vigorous maize growth. Conclusions In this study, three consistent major QTL related to plant type traits were identified and three candidate genes were screened. These results lay a foundation for the cloning of related functional genes and marker-assisted breeding of related functional genes.

Leaf morphological characteristics are critical factors affecting plant architecture and canopy photosynthesis, all of which ultimately affect grain yield. Elucidation of the genetic basis of maize leaf-related traits could assist breeders in designing effective breeding strategies. Genomic selection (GS) is an effective method to accelerate the breeding process. We performed a genome-wide association study (GWAS) and GS for leaf-related traits in a natural maize population consisting of 291 inbred lines. The GWAS panel was phenotyped at four environments for the leaf length of the first leaf above the upmost ear (L1), the upmost ear leaf (L2), the first leaf below the upmost ear (L3), leaf width of L1, L2, and L3, leaf area of L2 (LAr2), and leaf number above the upmost ear (LNAE), and genotyped by sequencing. The heritability of leaf-related traits was ranged from 77.93% to 87.54%. A total of 24 unique significant SNPs were identified for leaf length at the -value threshold of 2.968 × 10 by FarmCPU and BLINK models. The phenotypic variation explained (PVE) by each SNP ranged from 4.82% to 20.7%. A total of 34 unique significant SNPs were identified for leaf width, each with a PVE ranging from 0.01% to 17.2%. A total of 14 unique significant SNPs were identified for LAr2, each with a PVE ranging from 0.7% to 21.8%. A total of 19 unique significant SNPs were identified for LNAE, each with a PVE ranging from 1.21% to 25.01%. Eleven pleiotropic SNPs controlling leaf-related traits were identified, indicating that the leaf length and width at different leaf positions may be influenced by one or more common loci. A total of 122 candidate genes were retrieved, among which , , , , and are key candidate genes for leaf-related traits. The results of GS indicated that a training population size of 70% and a set of 3000 SNPs were adequate for the application of GS in maize leaf-related traits. This study provides important reference information for further elucidating the genetic basis of leaf-related traits and applying GS in maize breeding programs.