Maize (Zea mays): a model organism for basic and applied research in plant biology

The Zea mays PeptideAtlas: A New Maize Community Resource

This study presents the Maize PeptideAtlas resource (www.peptideatlas.org/builds/maize) to help solve questions about the maize proteome. Publicly available raw tandem mass spectrometry (MS/MS) data for maize collected from ProteomeXchange were reanalyzed through a uniform processing and metadata annotation pipeline. These data are from a wide range of genetic backgrounds and many sample types and experimental conditions. The protein search space included different maize genome annotations for the B73 inbred line from MaizeGDB, UniProtKB, NCBI RefSeq, and for the W22 inbred line. 445 million MS/MS spectra were searched, of which 120 million were matched to 0.37 million distinct peptides. Peptides were matched to 66.2% of proteins in the most recent B73 nuclear genome annotation. Furthermore, most conserved plastid- and mitochondrial-encoded proteins (NCBI RefSeq annotations) were identified. Peptides and proteins identified in the other B73 genome annotations will improve maize genome annotation. We also illustrate the high-confidence detection of unique W22 proteins. N-terminal acetylation, phosphorylation, ubiquitination, and three lysine acylations (K-acetyl, K-malonyl, and K-hydroxyisobutyryl) were identified and can be inspected through a PTM viewer in PeptideAtlas. All matched MS/MS-derived peptide data are linked to spectral, technical, and biological metadata. This new PeptideAtlas is integrated in MaizeGDB with a peptide track in JBrowse.

Consistent prokaryotic community patterns along the radial root axis of two Zea mays L. landraces across two distinct field locations

The close interconnection of plants with rhizosphere- and root-associated microorganisms is well recognized, and high expectations are raised for considering their symbioses in the breeding of future crop varieties. However, it is unclear how consistently plant-mediated selection, a potential target in crop breeding, influences microbiome members compared to selection imposed by the agricultural environment. Landraces may have traits shaping their microbiome, which were lost during the breeding of modern varieties, but knowledge about this is scarce. We investigated prokaryotic community composition along the radial root axis of two European maize (Zea mays L.) landraces. A sampling gradient included bulk soil, a distal and proximal rhizosphere fraction, and the root compartment. Our study was replicated at two field locations with differing edaphic and climatic conditions. Further, we tested for differences between two plant developmental stages and two precipitation treatments. Community data were generated by metabarcoding of the V4 SSU rRNA region. While communities were generally distinct between field sites, the effects of landrace variety, developmental stage, and precipitation treatment were comparatively weak and not statistically significant. Under all conditions, patterns in community composition corresponded strongly to the distance to the root. Changes in α- and β-diversity, as well as abundance shifts of many taxa along this gradient, were similar for both landraces and field locations. Most affected taxa belonged to a core microbiome present in all investigated samples. Remarkably, we observed consistent enrichment of Actinobacteriota (particularly Streptomyces, Lechevalieria) and Pseudomonadota (particularly Sphingobium) toward the root. Further, we report a depletion of ammonia-oxidizers along this axis at both field sites. We identified clear enrichment and depletion patterns in microbiome composition along the radial root axis of Z. mays. Many of these were consistent across two distinct field locations, plant developmental stages, precipitation treatments, and for both landraces. This suggests a considerable influence of plant-mediated effects on the microbiome. We propose that the affected taxa have key roles in the rhizosphere and root microbiome of Z. mays. Understanding the functions of these taxa appears highly relevant for the development of methods aiming to promote microbiome services for crops.

SPX family response to low phosphorus stress and the involvement of ZmSPX1 in phosphorus homeostasis in maize

Phosphorus (P) is a crucial macronutrient for plant growth and development, and low-Pi stress poses a significant limitation to maize production. While the role of the SPX domain in encoding proteins involved in phosphate (Pi) homeostasis and signaling transduction has been extensively studied in other model plants, the molecular and functional characteristics of the SPX gene family members in maize remain largely unexplored. In this study, we identified six SPX members, and the phylogenetic analysis of ZmSPXs revealed a close relationship with SPX genes in rice. The promoter regions of ZmSPXs were abundant in biotic and abiotic stress-related elements, particularly associated with various hormone signaling pathways, indicating potential intersections between Pi signaling and hormone signaling pathways. Additionally, ZmSPXs displayed tissue-specific expression patterns, with significant and differential induction in anthers and roots, and were localized to the nucleus and cytoplasm. The interaction between ZmSPXs and ZmPHRs was established via yeast two-hybrid assays. Furthermore, overexpression of ZmSPX1 enhanced root sensitivity to Pi deficiency and high-Pi conditions in Arabidopsis thaliana. Phenotypic identification of the maize transgenic lines demonstrated the negative regulatory effect on the P concentration of stems and leaves as well as yield. Notably, polymorphic sites including 34 single-nucleotide polymorphisms (SNPs) and seven insertions/deletions (InDels) in ZmSPX1 were significantly associated with 16 traits of low-Pi tolerance index. Furthermore, significant sites were classified into five haplotypes, and haplotype5 can enhance biomass production by promoting root development. Taken together, our results suggested that ZmSPX family members possibly play a pivotal role in Pi stress signaling in plants by interacting with ZmPHRs. Significantly, ZmSPX1 was involved in the Pi-deficiency response verified in transgenic Arabidopsis and can affect the Pi concentration of maize tissues and yield. This work lays the groundwork for deeper exploration of the maize SPX family and could inform the development of maize varieties with improved Pi efficiency.

Callus-specific CRISPR/Cas9 system to increase heritable gene mutations in maize

MAIN CONCLUSION

A callus-specific CRISPR/Cas9 (CSC) system with Cas9 gene driven by the promoters of ZmCTA1 and ZmPLTP reduces somatic mutations and improves the production of heritable mutations in maize. The CRISPR/Cas9 system, due to its editing accuracy, provides an excellent tool for crop genetic breeding. Nevertheless, the traditional design utilizing CRISPR/Cas9 with ubiquitous expression leads to an abundance of somatic mutations, thereby complicating the detection of heritable mutations. We constructed a callus-specific CRISPR/Cas9 (CSC) system using callus-specific promoters of maize Chitinase A1 and Phospholipid transferase protein (pZmCTA1 and pZmPLTP) to drive Cas9 expression, and the target gene chosen for this study was the bZIP transcription factor Opaque2 (O2). The CRISPR/Cas9 system driven by the maize Ubiquitin promoter (pZmUbi) was employed as a comparative control. Editing efficiency analysis based on high-throughput tracking of mutations (Hi-TOM) showed that the CSC systems generated more target gene mutations than the ubiquitously expressed CRISPR/Cas9 (UC) system in calli. Transgenic plants were generated for the CSC and UC systems. We found that the CSC systems generated fewer target gene mutations than the UC system in the T0 seedlings but reduced the influence of somatic mutations. Nearly 100% of mutations in the T1 generation generated by the CSC systems were derived from the T0 plants. Only 6.3-16.7% of T1 mutations generated by the UC system were from the T0 generation. Our results demonstrated that the CSC system consistently produced more stable, heritable mutants in the subsequent generation, suggesting its potential application across various crops to facilitate the genetic breeding of desired mutations.

Enhanced pan-genomic resources at the maize genetics and genomics database

Pan-genomes, encompassing the entirety of genetic sequences found in a collection of genomes within a clade, are more useful than single reference genomes for studying species diversity. This is especially true for a species like Zea mays, which has a particularly diverse and complex genome. Presenting pan-genome data, analyses, and visualization is challenging, especially for a diverse species, but more so when pan-genomic data is linked to extensive gene model and gene data, including classical gene information, markers, insertions, expression and proteomic data, and protein structures as is the case at MaizeGDB. Here, we describe MaizeGDB's expansion to include the genic subset of the Zea pan-genome in a pan-gene data center featuring the maize genomes hosted at MaizeGDB, and the outgroup teosinte Zea genomes from the Pan-Andropoganeae project. The new data center offers a variety of browsing and visualization tools, including sequence alignment visualization, gene trees and other tools, to explore pan-genes in Zea that were calculated by the pipeline Pandagma. Combined, these data will help maize researchers study the complexity and diversity of Zea, and to use the comparative functions to validate pan-gene relationships for a selected gene model.

Zea mays genotype influences microbial and viral rhizobiome community structure

Plant genotype is recognized to contribute to variations in microbial community structure in the rhizosphere, soil adherent to roots. However, the extent to which the viral community varies has remained poorly understood and has the potential to contribute to variation in soil microbial communities. Here we cultivated replicates of two Zea mays genotypes, parviglumis and B73, in a greenhouse and harvested the rhizobiome (rhizoplane and rhizosphere) to identify the abundance of cells and viruses as well as rhizobiome microbial and viral community using 16S rRNA gene amplicon sequencing and genome resolved metagenomics. Our results demonstrated that viruses exceeded microbial abundance in the rhizobiome of parviglumis and B73 with a significant variation in both the microbial and viral community between the two genotypes. Of the viral contigs identified only 4.5% (n = 7) of total viral contigs were shared between the two genotypes, demonstrating that plants even at the level of genotype can significantly alter the surrounding soil viral community. An auxiliary metabolic gene associated with glycoside hydrolase (GH5) degradation was identified in one viral metagenome-assembled genome (vOTU) identified in the B73 rhizobiome infecting Propionibacteriaceae (Actinobacteriota) further demonstrating the viral contribution in metabolic potential for carbohydrate degradation and carbon cycling in the rhizosphere. This variation demonstrates the potential of plant genotype to contribute to microbial and viral heterogeneity in soil systems and harbors genes capable of contributing to carbon cycling in the rhizosphere.

Uncovering microsatellite markers associated with agronomic traits of South Sudan landrace maize

BACKGROUND

Maize has great importance in South Sudan as the most cultivated cereal after sorghum; however, numerous challenges are encountered in its production. To raise maize production, it is critical to exploit the wealth of its genetic variation for grain yield enhancement.

OBJECTIVE

This study aimed to conduct association analysis to identify specific simple sequence repeat (SSR) markers associated with quantitative agronomic traits.

METHODS

Genetic variation and population structure were investigated among 31 maize accessions by association analysis using 50 SSR markers and seven quantitative agronomic traits.

RESULTS

The genotypes exhibited abundant genetic variation, and 418 alleles were detected with an average of 8.4 alleles per locus. The average genetic diversity, major allele frequency, and polymorphic information content were 0.754, 0.373, and 0.725, respectively. The population structure based on 50 SSR markers divided the maize accessions into two main groups and an admixed group without considering their descent. Association analysis was performed using a general linear model (Q GLM) and a mixed linear model (Q + K MLM). Q GLM detected 44 trait-marker associations involving 23 SSR markers. Q + K MLM detected four marker-trait associations involving three SSR markers (umc2286, umc1303, umc1429) associated with days to tasseling, days to silking, leaf length, and leaf width.

CONCLUSIONS

The detected significant SSR markers related to agronomic traits could be useful for future genetic studies. Additionally, markers affecting several agronomic traits and overlapped SSR markers require further testing on a wide range of genotypes prior to their consideration as candidate markers for marker assisted selection for South Sudan maize improvement.

Systematic analysis of the Rboh gene family in seven gramineous plants and its roles in response to arbuscular mycorrhizal fungi in maize

BACKGROUND

Plant respiratory burst oxidase homolog (Rboh) gene family produces reactive oxygen species (ROS), and it plays key roles in plant-microbe interaction. Most Rboh gene family-related studies mainly focused on dicotyledonous plants; however, little is known about the roles of Rboh genes in gramineae.

RESULTS

A total of 106 Rboh genes were identified in seven gramineae species, including Zea mays, Sorghum bicolor, Brachypodium distachyon, Oryza sativa, Setaria italica, Hordeum vulgare, and Triticum aestivum. The Rboh protein sequences showed high similarities, suggesting that they may have conserved functions across different species. Duplication mode analysis detected whole-genome/segmental duplication (WGD)/(SD) and dispersed in the seven species. Interestingly, two local duplication (LD, including tandem and proximal duplication) modes were found in Z. mays, S. italica and H. vulgare, while four LD were detected in T. aestivum, indicating that these genes may have similar functions. Collinearity analysis indicated that Rboh genes are at a stable evolution state in all the seven species. Besides, Rboh genes from Z. mays were closely related to those from S. bicolor, consistent with the current understanding of plant evolutionary history. Phylogenetic analysis showed that the genes in the subgroups I and II may participate in plant-AM fungus symbiosis. Cis-element analysis showed that different numbers of elements are related to fungal induction in the promoter region. Expression profiles of Rboh genes in Z. mays suggested that Rboh genes had distinct spatial expression patterns. By inoculation with AM fungi, our transcriptome analysis showed that the expression of Rboh genes varies upon AM fungal inoculation. In particularly, ZmRbohF was significantly upregulated after inoculation with AM fungi. pZmRbohF::GUS expression analyses indicated that ZmRbohF was induced by arbuscular mycorrhizal fungi in maize. By comparing WT and ZmRbohF mutant, we found ZmRbohF had limited impact on the establishment of maize-AM fungi symbiosis, but play critical roles in regulating the proper development of arbuscules.

CONCLUSIONS

This study provides a comprehensive analysis of the evolution relationship of Rboh genes in seven gramineae species. Results showed that several Rboh genes regulate maize-AM fungal symbiosis process. This study provides valuable information for further studies of Rboh genes in gramineae.

Multi-trait and multi-environment genomic prediction for flowering traits in maize: a deep learning approach

Maize (Zea mays L.), the third most widely cultivated cereal crop in the world, plays a critical role in global food security. To improve the efficiency of selecting superior genotypes in breeding programs, researchers have aimed to identify key genomic regions that impact agronomic traits. In this study, the performance of multi-trait, multi-environment deep learning models was compared to that of Bayesian models (Markov Chain Monte Carlo generalized linear mixed models (MCMCglmm), Bayesian Genomic Genotype-Environment Interaction (BGGE), and Bayesian Multi-Trait and Multi-Environment (BMTME)) in terms of the prediction accuracy of flowering-related traits (Anthesis-Silking Interval: ASI, Female Flowering: FF, and Male Flowering: MF). A tropical maize panel of 258 inbred lines from Brazil was evaluated in three sites (Cambira-2018, Sabaudia-2018, and Iguatemi-2020 and 2021) using approximately 290,000 single nucleotide polymorphisms (SNPs). The results demonstrated a 14.4% increase in prediction accuracy when employing multi-trait models compared to the use of a single trait in a single environment approach. The accuracy of predictions also improved by 6.4% when using a single trait in a multi-environment scheme compared to using multi-trait analysis. Additionally, deep learning models consistently outperformed Bayesian models in both single and multiple trait and environment approaches. A complementary genome-wide association study identified associations with 26 candidate genes related to flowering time traits, and 31 marker-trait associations were identified, accounting for 37%, 37%, and 22% of the phenotypic variation of ASI, FF and MF, respectively. In conclusion, our findings suggest that deep learning models have the potential to significantly improve the accuracy of predictions, regardless of the approach used and provide support for the efficacy of this method in genomic selection for flowering-related traits in tropical maize.

Revisiting maize Brittle endosperm-2 reveals new insights in BETL development and starchy endosperm filling

Rerouting the starch biosynthesis pathway in maize can generate specialty types, like sweet corn and waxy corn, with a drastically increasing global demand. Hence, a fine-tuning of starch metabolism is relevant to create diverse maize cultivars for end-use applications. Here, we characterized a new maize brittle endosperm mutant, referred to as bt1774, which exhibited decreased starch content but a dramatic increase of soluble sugars at maturity. Both endosperm and embryo development was impaired in bt1774 relative to the wild-type (WT), with a prominently arrested basal endosperm transfer layer (BETL). Map-based cloning revealed that BRITTLE ENDOSPERM2 (Bt2), which encodes a small subunit of ADP-glucose pyrophosphorylase (AGPase), is the causal gene for bt1774. A MuA2 element was found to be inserted into intron 2 of Bt2, leading to a severe decrease of its expression, in bt1774. This is in line with the irregular and loosely packed starch granules in the mutant. Transcriptome of endosperm at grain filling stage identified 1, 013 differentially expressed genes in bt1774, which were notably enriched in the BETL compartment, including ZmMRP1, Miniature1, MEG1, and BETLs. Gene expression of the canonical starch biosynthesis pathway was marginally disturbed in Bt1774. Combined with the residual 60% of starch in this nearly null mutant of Bt2, this data strongly suggests that an AGPase-independent pathway compensates for starch synthesis in the endosperm. Consistent with the BETL defects, zein accumulation was impaired in bt1774. Co-expression network analysis revealed that Bt2 probably has a role in intracellular signal transduction, besides starch synthesis. Altogether, we propose that Bt2 is likely involved in carbohydrate flux and balance, thus regulating both the BETL development and the starchy endosperm filling.

Identification of ultrastructural and biochemical cuticular markers influencing temperature of ice nucleation in selected genotypes of corn

Corn is an economically important yet frost-sensitive crop, injured at the moment of ice nucleation. However, the influence of autumn temperatures on subsequent ice nucleation temperature is unknown. A 10-day chilling treatment under phytotron conditions ("mild", 18/6°C) or ("extreme", 10/5°C) generated no-visible damage but induced changes in the cuticle of the four genotypes in this study. The putatively more cold hardy Genotypes 884 and 959 leaves nucleated at colder temperatures compared to the more sensitive Genotypes 675 and 275. After chilling treatment, all four genotypes displayed warmer ice nucleation temperatures, with Genotype 884 expressing the largest shift to warmer nucleation temperatures. Cuticular hydrophobicity reduced while cuticular thickness remained unchanged under the chilling treatment. By contrast, under five-week field conditions, cuticle thickness increased in all genotypes, with Genotype 256 expressing a significantly thinner cuticle. FTIR spectroscopy revealed increases in the spectral regions of cuticular lipids in all genotypes after phytotron chilling treatment, while those spectral regions decreased under field conditions. A total of 142 molecular compounds were detected, with 28 compounds significantly induced under either phytotron or field conditions. Of these, seven compounds were induced under both conditions (Alkanes C31-C33, Ester C44, C46, β-amyrin, and triterpene). While clear differential responses were observed, chilling conditions preceding a frost modified physical and biochemical properties of the leaf cuticle under both phytotron and field conditions indicating this response is dynamic and could be a factor in selecting corn genotypes better adapted to avoiding frost with lower ice nucleation temperature.

Mitigating the repercussions of climate change on diseases affecting important crop commodities in Southeast Asia, for food security and environmental sustainability—A review

Southeast Asia is a fertile land with a warm and humid climate which tends to accommodate various food crops. The development and advancement of the agricultural sector not only allows the countries in the region to feed the increasing population, but are also able to boost the nation's economy through exportation of the crops. Some of the well-known and economically-significant plant commodities found in the region include rice, oil palm, rubber, coconut, banana, sugarcane, pineapple, black pepper, maize, cocoa, durian, and jackfruit. Due to the high production of crops, Southeast Asia is able to stand among the top world producers of these commodities. Nevertheless, the widespread of pathogenic microorganisms has posed a serious threat to the industry over the years; with hundreds of millions of money wasted and total yield being lost due to the devastating diseases associated with each type of the plants. A lot of attention and effort have been continuously devoted to find effective plant management strategies to combat plant diseases, starting from traditional physical and chemical methods to the increasing discoveries on biological approaches made in recent decades. Due to the challenges and limitations faced by conventional approaches and the rising awareness toward the environment, more work has been focused on establishing the application of beneficial microorganisms to tackle plant diseases through direct mechanisms. Thus, by bringing the common plant commodities in Southeast Asia, their associated diseases and various physical, chemical and biological control measures together, this review aims to provide clearer insights and practical information to those who seek to limit the damages caused by plant diseases.

Key role of reactive oxygen species-scavenging system in nitric oxide and hydrogen sulfide crosstalk-evoked thermotolerance in maize seedlings

Nitric oxide (NO) and hydrogen sulfide (H₂S) are novel signaling molecules, which participate in plant growth, development, and response to stress. In this study root-irrigation with 0.15 mM sodium nitroprusside (SNP, NO donor) up-regulated gene expression of L-CYSTEINE DESULFHYDRASE1 (LCD1), activities of L-cysteine desulfhydrase (LCD) and D-cysteine desulfhydrase (DCD), as well as an endogenous H₂S level, compared to control seedlings. The SNP-up-regulated effects were enhanced by 0.5 mM sodium hydrosulfide (NaHS, H₂S donor), but weakened by NO scavenger 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO) and H₂S scavenger hypotaurine (HT) alone. NaHS had no significant effect on gene expression and activity of nitrate reductase (NR, a NO candidate producing enzyme). These data indicate that NO could trigger the LCD/H₂S signaling pathway in maize seedlings. To further investigate the effect of NO and H₂S crosstalk on thermotolerance in maize seedlings, thermotolerance parameters and reactive oxygen species (ROS)-scavenging system were estimated. The results show that SNP increased survival rate and tissue viability, decreased malondialdehyde (MDA) accumulation, and electrolyte leakage in maize seedlings under heat stress (HS), implying NO could improve thermotolerance in maize seedlings. The NO-improved thermotolerance was impaired by H₂S inhibitor DL-propargylglycine (PAG) and scavenger HT alone. Similarly, SNP up-regulated the gene expression of DEHYDROASCORBATE REDUCTASE (DHAR) and GLUTATHIONE REDUCTASE1 (GR1); activities of ascorbate peroxidase, glutathione reductase, and catalase; as well as levels of ascorbic acid, glutathione, flavonoids, carotenoids, and total phenols. SNP also reduced hydrogen peroxide and superoxide radical accumulation in maize seedlings under HS compared to the control. The effects of SNP on ROS and their scavenger system were weakened by PAG and HT alone. These data hint that NO could evoke thermotolerance in maize seedlings by triggering the LCD/H₂S signaling pathway, and the ROS-scavenging system played a key role in the NO and H₂S crosstalk-evoked thermotolerance.

Involvement of osmoregulation, glyoxalase, and non-glyoxalase systems in signaling molecule glutamic acid-boosted thermotolerance in maize seedlings

Glutamic acid (Glu) is not only an important protein building block, but also a signaling molecule in plants. However, the Glu-boosted thermotolerance and its underlying mechanisms in plants still remain unclear. In this study, the maize seedlings were irrigated with Glu solution prior to exposure to heat stress (HS), the seedlings' thermotolerance as well as osmoregulation, glyoxalase, and non-glyoxalase systems were evaluated. The results manifested that the seedling survival and tissue vitality after HS were boosted by Glu, while membrane damage was reduced in comparison with the control seedlings without Glu treatment, indicating Glu boosted the thermotolerance of maize seedlings. Additionally, root-irrigation with Glu increased its endogenous level, reinforced osmoregulation system (i.e., an increase in the levels of proline, glycine betaine, trehalose, and total soluble sugar, as well as the activities of pyrroline-5-carboxylate synthase, betaine dehydrogenase, and trehalose-5-phosphate phosphatase) in maize seedlings under non-HS and HS conditions compared with the control. Also, Glu treatment heightened endogenous methylglyoxal level and the activities of glyoxalase system (glyoxalase I, glyoxalase II, and glyoxalase III) and non-glyoxalase system (methylglyoxal reductase, lactate dehydrogenase, aldo-ketoreductase, and alkenal/alkenone reductase) in maize seedlings under non-HS and HS conditions as compared to the control. These data hint that osmoregulation, glyoxalase, and non-glyoxalase systems are involved in signaling molecule Glu-boosted thermotolerance of maize seedlings.

Genome-Wide Identification and Characterization of Heat Shock Protein 20 Genes in Maize

Maize is an important cereal crop worldwide and is sensitive to abiotic stresses in fluctuant environments that seriously affect its growth, yield, and quality. The small heat shock protein (HSP20) plays a crucial role in protecting plants from abiotic stress. However, little is known about HSP20 in maize (ZmHSP20). In this study, 44 ZmHSP20s were identified, which were unequally distributed over 10 chromosomes, and 6 pairs of ZmHSP20s were tandemly presented. The gene structure of ZmHSP20s was highly conserved, with 95% (42) of the genes having no more than one intron. The analysis of the cis-element in ZmHSP20s promoter demonstrated large amounts of elements related to hormonal and abiotic stress responses, including abscisic acid (ABA), high temperature, and hypoxia. The ZmHSP20s protein had more than two conserved motifs that were predictably localized in the cytoplasm, nucleus, endoplasmic reticulum, peroxisome, mitochondria, and plasma. Phylogenetic analysis using HSP20s in Arabidopsis, rice, maize, and Solanum tuberosum indicated that ZmHSP20s were classified into 11 categories, of which each category had unique subcellular localization. Approximately 80% (35) of ZmHSP20 were upregulated under heat stress at the maize seedling stage, whereas the opposite expression profiling of 10 genes under 37 and 48 °C was detected. A total of 20 genes were randomly selected to investigate their expression under treatments of ABA, gibberellin (GA), ethylene, low temperature, drought, and waterlogging, and the results displayed that more than half of these genes were downregulated while ZmHSP20-3, ZmHSP20-7, ZmHSP20-24, and ZmHSP20-44 were upregulated under 1 h treatment of ethylene. A yeast-one-hybrid experiment was conducted to analyze the binding of four heat stress transcription factors (ZmHSFs) with eight of the ZmHSP20s promoter sequences, in which ZmHSF3, ZmHSF13, and ZmHSF17 can bind to most of these selected ZmHSP20s promoters. Our results provided a valuable resource for studying HSP20s function and offering candidates for genetic improvement under abiotic stress.

Biopriming of Maize Seeds with a Novel Bacterial Strain SH-6 to Enhance Drought Tolerance in South Korea

Maize is the third most common cereal crop worldwide, after rice and wheat, and plays a vital role in preventing global hunger crises. Approximately 50% of global crop yields are reduced by drought stress. Bacteria as biostimulants for biopriming can improve yield and enhance sustainable food production. Further, seed biopriming stimulates plant defense mechanisms. In this study, we isolated bacteria from the rhizosphere of Artemisia plants from Pohang beach, Daegu, South Korea. Twenty-three isolates were isolated and screened for growth promoting potential. Among them, bacterial isolate SH-6 was selected based on maximum induced tolerance to polyethylene glycol-simulated drought. SH-6 showed ABA concentration = 1.06 ± 0.04 ng/mL, phosphate solubilizing index = 3.7, and sucrose concentration = 0.51 ± 0.13 mg/mL. The novel isolate SH-6 markedly enhanced maize seedling tolerance to oxidative stress owing to the presence of superoxide dismutase, catalase, and ascorbate peroxidase activities in the culture media. Additionally, we quantified and standardized the biopriming effect of SH-6 on maize seeds. SH-6 significantly increased maize seedling drought tolerance by up to 20%, resulting in 80% germination potential. We concluded that the novel bacterium isolate SH-6 (gene accession number (OM757882) is a biostimulant that can improve germination performance under drought stress.

Translocation, bioaccumulation, and distribution of perfluoroalkyl and polyfluoroalkyl substances (PFASs) in plants

Perfluoroalkyl and polyfluoroalkyl substances (PFASs) are persistent in the environment and have been detected in a variety of plants such as vegetables, cereals, and fruits. Increasing evidence shows that plants are at a risk of being adversely affected by PFASs. This review concludes that PFASs are predominantly absorbed by roots from sources in the soil; besides, the review also discusses several factors such as soil properties and the species of PFASs and plants. In addition, following uptake by root, long-chain PFASs (C ≥ 7 for PFCA and C ≥ 6 for PFSA) were preferentially retained within the root, whereas the short-chain PFASs were distributed across tissues above the ground — according to the studies. The bioaccumulation potential of PFASs within various plant structures are further expressed by calculating bioaccumulation factor (BAF) across various plant species. The results show that PFASs have a wide range of BAF values within root tissue, followed by straw, and then grain. Furthermore, owing to its high water solubility than other PFASs, PFOA is the predominant compound accumulated in both the soil itself and within the plant tissues. Among different plant groups, the potential BAF values rank from highest to lowest as follows: leaf vegetables > root vegetables > flower vegetables > shoot vegetables. Several PFAS groups such as PFOA, PFBA, and PFOS, may have an increased public health risk based on the daily intake rate (ID). Finally, future research is suggested on the possible PFASs degradation occurring in plant tissues and the explanations at genetic-level for the metabolite changes that occur under PFASs stress.

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Long-chain PFASs are preferentially retained in the roots

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BAF values were ranked as root > straw > grain in one plant

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PFOA is the main compound in soil and within plant tissues

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PFOA, PFBA, and PFOS have a potential risk to humans through dietary exposure

Transcriptome response of maize (Zea mays L.) seedlings to heat stress

Among stresses, heat stress (HS) is a prime factor restricting plant growth and productivity. However, the molecular mechanisms of plants' response to HS need to be further uncovered. Here, the transcriptome response of maize seedlings to HS was dissected using transcriptome data analysis. The data exhibited that a total of 43,221 genes in maize seedlings had been found, 37,534 of which were referred, while 5686 were not. Under HS, comparison with the control without HS, there were 13,607 genes that were differentially expressed (DEGs, 6195 upregulated and 7412 downregulated). In addition, Gene Ontology (GO) enrichment analysis indicated that there were 220, 478, and 1300 terms that were enriched in cellular component, molecular function, and biological process, respectively. Significantly enriched GO terms were involved in 23 cellular components, 27 molecular functions, and 124 biological processes. Also, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis suggested that there were 2613 DEGs that were assigned to 131 pathways, 14 of which (enriched 1068 DEGs in total) were significantly upregulated. These pathways were mainly related to protein renaturation, biomembrane repair, osmotic adjustment, and redox balance. Among them, protein processing in endoplasmic reticulum was the most significantly upregulated. The transcriptome data decoded that protein renaturation, biomembrane repair, osmotic adjustment, and redox balance played a key role in the response of maize seedlings to HS.

Nitric oxide donor, sodium nitroprusside modulates hydrogen sulfide metabolism and cysteine homeostasis to aid the alleviation of chromium toxicity in maize seedlings (Zea mays L.)

The current research aimed to assess the protective role of nitric oxide (NO) against chromium (Cr) toxicity in maize seedlings. Chromium (200 µM) lowered osmotic potential in epicotyls and mostly in radicles (by 38% and 63%, respectively) as compared to the control. Sodium nitroprusside (SNP, NO donor) restored seedling biomass (+90% for both organs) and water potential, whereas application of Nω-nitro-L-arginine methylester (_L-NAME, a NOS inhibitor) increased sensitivity to Cr. SNP suppressed Cr-triggered proline accumulation by inhibiting Δ¹-pyrroline-5-carboxylate synthetase activity and stimulating proline dehydrogenase activity, leading to glutamate over-accumulation (~30% for both organs). Cr stimulated cysteine metabolism and this was further enhanced by SNP which stimulated serine acetyl-transferase and O-acetylserine (thiol) lyase activities. This was followed by an increase in endogenous hydrogen sulfide (H₂S) generation by up-regulating L-cysteine desulfhydrase (+205%), D-cysteine desulfhydrase (+150%) and cyanoalanine synthase (+65%) activities in radicles compared to Cr-treatments plants. These positive effects were reduced in _L-NAME compared to control. Combined Cr+SNP affected the levels of compounds involved in glutathione metabolism (γ-glutamyl-cysteinyl, γ-glutamyl-cysteinyl-clycine, γ-cysteinyl-glycine, and glycine.). All together, our findings indicate that NO and elicited cellular H₂S act synergistically to alleviate Cr stress in maize seedlings by influencing a metabolic interplay between cysteine, proline, and glutathione.

Determination of morpho-physiological and yield traits of maize inbred lines (Zea mays L.) under optimal and drought stress conditions

Globally, climate change could hinder future food security that concurrently implies the importance of investigating drought stress and genotype screening under stressed environments. Hence, the current study was performed to screen 45 diverse maize inbred lines for 18 studied traits comprising phenological, physiological, morphological, and yield characters under optimum and water stress conditions for two successive growing seasons (2018 and 2019). The results showed that growing seasons and water regimes significantly influenced (p < 0.01) most of the studied traits, while inbred lines had a significant effect (p < 0.01) on all of the studied traits. The findings also showed a significant increase in all studied characters under normal conditions compared to drought conditions, except chlorophyll content, transpiration rate, and proline content which exhibited higher levels under water stress conditions. Furthermore, the results of the principal component analysis indicated a notable distinction between the performance of the 45 maize inbred lines under normal and drought conditions. In terms of grain yield, the drought tolerance index (DTI) showed that Nub60 (1.56), followed by Nub32 (1.46), Nub66 (1.45), and GZ603 (1.44) were the highest drought-tolerant inbred lines, whereas Nub46 (0.38) was the lowest drought-tolerant inbred line. These drought-tolerant inbred lines were able to maintain a relatively high grain yield under normal and stress conditions, whereas those drought-sensitive inbred lines showed a decline in grain yield when exposed to drought conditions. The hierarchical clustering analysis based on DTI classified the forty-five maize inbred lines and eighteen measured traits into three column- and row-clusters, as inbred lines in cluster-3 followed by those in cluster-2 exhibited greater drought tolerance in most of the studied traits. Utilizing the multi-trait stability index (MTSI) criterion in this study identified nine inbred lines, including GZ603, as stable genotypes in terms of the eighteen studied traits across four environments. The findings of the current investigation motivate plant breeders to explore the genetic potential of the current maize germplasm, especially in water-stressed environments.

Analytical Characterization and Inhibitor Detection in Liquid Phases Obtained After Steam Refining of Corn Stover and Maize Silage

The utilization of agricultural products and residues for the production of value-added and biobased products is a highly relevant topic in present research. Due to the natural recalcitrance of lignocellulosic biomass against enzymatic degradation, pretreatments are important requirement for further processes. For the raw material in this study, corn stover (CS) as highly available agricultural residue and maize silage (MS) as model substrate for an ensiled agricultural product were pretreated by steam refining. However, after processing a liquid fraction and fibers are present. Subsequent to steaming the fiber fraction is well characterized. Nonetheless, in depth characterizations of the filtrates are also important for their subsequent utilization. Decreasing molar masses from 7,900 g/mol to 1,100 g/mol for CS filtrates and 100.000–12.900 g/mol for MS filtrates were determined with increasing severity. Due to their proven inhibitory effect on microorganisms weak acids, furans and phenolic compounds within the liquid phased were analyzed. Especially formic acid increases with increasing severity from 0.27 to 1.20% based on raw material for CS and from 0.07 to 0.23% based on raw material for MS. Further GC/MS measurements indicate, that up to 8.25% (CS filtrate) and 5.23% (MS filtrates) of the total peak area is related to inhibitory phenols. Considering the data, detoxification strategies are of non-negligible importance for filtrates after steam refining and should be considered for further research and process or parameter optimizations. An alternative may be the application of milder process conditions in order to prevent the formation of inhibitory degradation products or the dilution of the gained filtrates.

Maize Transformation: From Plant Material to the Release of Genetically Modified and Edited Varieties

Over the past decades, advances in plant biotechnology have allowed the development of genetically modified maize varieties that have significantly impacted agricultural management and improved the grain yield worldwide. To date, genetically modified varieties represent 30% of the world's maize cultivated area and incorporate traits such as herbicide, insect and disease resistance, abiotic stress tolerance, high yield, and improved nutritional quality. Maize transformation, which is a prerequisite for genetically modified maize development, is no longer a major bottleneck. Protocols using morphogenic regulators have evolved significantly towards increasing transformation frequency and genotype independence. Emerging technologies using either stable or transient expression and tissue culture-independent methods, such as direct genome editing using RNA-guided endonuclease system as an in vivo desired-target mutator, simultaneous double haploid production and editing/haploid-inducer-mediated genome editing, and pollen transformation, are expected to lead significant progress in maize biotechnology. This review summarises the significant advances in maize transformation protocols, technologies, and applications and discusses the current status, including a pipeline for trait development and regulatory issues related to current and future genetically modified and genetically edited maize varieties.

A pan-genomic approach to genome databases using maize as a model system

Research in the past decade has demonstrated that a single reference genome is not representative of a species' diversity. MaizeGDB introduces a pan-genomic approach to hosting genomic data, leveraging the large number of diverse maize genomes and their associated datasets to quickly and efficiently connect genomes, gene models, expression, epigenome, sequence variation, structural variation, transposable elements, and diversity data across genomes so that researchers can easily track the structural and functional differences of a locus and its orthologs across maize. We believe our framework is unique and provides a template for any genomic database poised to host large-scale pan-genomic data.

Developing Portulaca oleracea as a model system for functional genomics analysis of C4/CAM photosynthesis

Previously regarded as an intriguing photosynthetic curiosity, the occurrence of C4 and Crassulacean acid metabolism (CAM) photosynthesis within a single organism has recently emerged as a source of information for future biotechnological use. Among C4/CAM facultative species, Portulaca oleracea L. has been used as a model for biochemical and gene expression analysis of C4/CAM under field and laboratory conditions. In the present work, we focussed on developing molecular tools to facilitate functional genomics studies in this species, from the optimisation of RNA isolation protocols to a method for stable genetic transformation. Eleven variations of RNA extraction procedures were tested and compared for RNA quantity and quality. Also, 7 sample sets comprising total RNA from hormonal and abiotic stress treatments, distinct plant organs, leaf developmental stages, and subspecies were used to select, among 12 reference genes, the most stable reference genes for RT-qPCR analysis of each experimental condition. Furthermore, different explant sources, Agrobacterium tumefaciens strains, and regeneration and antibiotic selection media were tested in various combinations to optimise a protocol for stable genetic transformation of P. oleracea. Altogether, we provide essential tools for functional gene analysis in the context of C4/CAM photosynthesis, including an efficient RNA isolation method, preferred reference genes for RT-qPCR normalisation for a range of experimental conditions, and a protocol to produce P. oleracea stable transformants using A. tumefaciens.

Maize specialized metabolome networks reveal organ-preferential mixed glycosides

Despite the scientific and economic importance of maize, little is known about its specialized metabolism. Here, five maize organs were profiled using different reversed-phase liquid chromatography-mass spectrometry methods. The resulting spectral metadata, combined with candidate substrate-product pair (CSPP) networks, allowed the structural characterization of 427 of the 5,420 profiled compounds, including phenylpropanoids, flavonoids, benzoxazinoids, and auxin-related compounds, among others. Only 75 of the 427 compounds were already described in maize. Analysis of the CSPP networks showed that phenylpropanoids are present in all organs, whereas other metabolic classes are rather organ-enriched. Frequently occurring CSPP mass differences often corresponded with glycosyl- and acyltransferase reactions. The interplay of glycosylations and acylations yields a wide variety of mixed glycosides, bearing substructures corresponding to the different biochemical classes. For example, in the tassel, many phenylpropanoid and flavonoid-bearing glycosides also contain auxin-derived moieties. The characterized compounds and mass differences are an important step forward in metabolic pathway discovery and systems biology research. The spectral metadata of the 5,420 compounds is publicly available (DynLib spectral database, https://bioit3.irc.ugent.be/dynlib/).

Identification, Association of Natural Variation and Expression Analysis of ZmNAC9 Gene Response to Low Phosphorus in Maize Seedling Stage

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.

Interplay between hydrogen sulfide and methylglyoxal initiates thermotolerance in maize seedlings by modulating reactive oxidative species and osmolyte metabolism

Hydrogen sulfide (H₂S) and methylglyoxal (MG) were supposed to be novel signaling molecules in plants. However, whether interplay between H₂S and MG can initiate thermotolerance in maize seedlings and in relation to metabolism of reactive oxygen species (ROS) and osmolytes is little known. In this study, watering with MG and NaHS (H₂S donor) alone or in combination elevated survival and tissue vigor of maize seedlings under heat stress and coped with an increase in the biomembrane injury (as indicated in membrane lipid peroxidation and electrolyte leakage). The above-mentioned effects were separately weakened by MG scavengers (N-acetyl cysteine: NAC; aminoguanidine: AG) and H₂S inhibitor (DL-propargylglycine, PAG) and scavenger (hypotaurine, HT). These suggested that the interplay between H₂S and MG initiated the thermotolerance in maize seedlings. The further data indicated that, under non-heat stress and heat stress conditions, MG and NaHS alone or in combination modulated ROS metabolism by regulating the activities of antioxidant enzymes (catalase, ascorbate peroxidase, guaiacol peroxidase, glutathione reductase, monodehydroascorbate reductase, and dehydroascorbate reductase) and the contents of non-enzymatic antioxidants (ascorbic acid, glutathione, flavonoids, and carotenoids) in maize seedlings. In addition, MG and NaHS alone or in combination also separately modulated the metabolism of osmolytes (proline, trehalose, glycine betaine, and total soluble sugar), H₂S (L-cysteine desulfhydrase and O-acetylserine (thione) lyase), and MG (glyoxalase I, glyoxalase II, and MG reductase). These physiological effects also were separately impaired by NAC, AG, PAG, and HT. The current data illustrated that the interplay between H₂S and MG initiated the thermotolerance in maize seedlings by modulating ROS, osmolyte, H₂S, and MG metabolism.

Detection of genetically modified maize in Jordan

This study aimed to detect genetically modified maize (GMM) in seeds of eleven imported maize hybrids grown in Jordan. We used promoter 35 S and T-nos terminator for general screening of transgenic materials. Conventional PCR detected the specific events for the screening of Bt 11, MON810, and Bt176 events. Seeds of eleven maize hybrids samples showed a positive response to the 35 S promoter; nine out of eleven showed a positive response for T-nos terminator. Bt11 event was the most used in GMM seeds, where seven out of eleven samples showed positive results. Two out of eleven hybrids showed the presence of the Bt176 event; however, MON810 not detected in any of the tested hybrids. We studied the Bt11 event in imported GMM seeds in Jordan for the first time, reinforcing the need for a mandatory labeling system and a valid simple qualitative method in routine analysis of GMCs.

MaizeGDB 2018: the maize multi-genome genetics and genomics database

Since its 2015 update, MaizeGDB, the Maize Genetics and Genomics database, has expanded to support the sequenced genomes of many maize inbred lines in addition to the B73 reference genome assembly. Curation and development efforts have targeted high quality datasets and tools to support maize trait analysis, germplasm analysis, genetic studies, and breeding. MaizeGDB hosts a wide range of data including recent support of new data types including genome metadata, RNA-seq, proteomics, synteny, and large-scale diversity. To improve access and visualization of data types several new tools have been implemented to: access large-scale maize diversity data (SNPversity), download and compare gene expression data (qTeller), visualize pedigree data (Pedigree Viewer), link genes with phenotype images (MaizeDIG), and enable flexible user-specified queries to the MaizeGDB database (MaizeMine). MaizeGDB also continues to be the community hub for maize research, coordinating activities and providing technical support to the maize research community. Here we report the changes MaizeGDB has made within the last three years to keep pace with recent software and research advances, as well as the pan-genomic landscape that cheaper and better sequencing technologies have made possible. MaizeGDB is accessible online at https://www.maizegdb.org.

MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database

MaizeMine is the data mining resource of the Maize Genetics and Genome Database (MaizeGDB; http://maizemine.maizegdb.org). It enables researchers to create and export customized annotation datasets that can be merged with their own research data for use in downstream analyses. MaizeMine uses the InterMine data warehousing system to integrate genomic sequences and gene annotations from the Zea mays B73 RefGen_v3 and B73 RefGen_v4 genome assemblies, Gene Ontology annotations, single nucleotide polymorphisms, protein annotations, homologs, pathways, and precomputed gene expression levels based on RNA-seq data from the Z. mays B73 Gene Expression Atlas. MaizeMine also provides database cross references between genes of alternative gene sets from Gramene and NCBI RefSeq. MaizeMine includes several search tools, including a keyword search, built-in template queries with intuitive search menus, and a QueryBuilder tool for creating custom queries. The Genomic Regions search tool executes queries based on lists of genome coordinates, and supports both the B73 RefGen_v3 and B73 RefGen_v4 assemblies. The List tool allows you to upload identifiers to create custom lists, perform set operations such as unions and intersections, and execute template queries with lists. When used with gene identifiers, the List tool automatically provides gene set enrichment for Gene Ontology (GO) and pathways, with a choice of statistical parameters and background gene sets. With the ability to save query outputs as lists that can be input to new queries, MaizeMine provides limitless possibilities for data integration and meta-analysis.

Identification of Key Genes Involved in Embryo Development and Differential Oil Accumulation in Two Contrasting Maize Genotypes

Maize is an important oil seed crop and a major food crop in different parts of the world. Since maize has relatively lower seed oil content as compared to other oil crops, efforts are continuing to improve its oil content percentage. In this study, we analyzed two contrasting maize genotypes with differential oil accumulation percentages. High oil-content (HOC) maize had 11% oil content while low oil-content (LOC) maize had significantly lower oil content (5.4%). Transmission electron microscopy revealed a higher accumulation of oil bodies in the HOC maize embryo as compared to LOC maize. Comparative RNA-sequencing analysis at different developmental stages of the seed embryos identified 739 genes that are constantly differentially expressed (DEGs) at all the six developmental stages from 15 days after pollination (DAP) to 40 DAP. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified fatty acid metabolism and fatty acid biosynthesis as the most enriched biological pathways contributed by these DEGs. Notably, transcriptional changes are more intense at the early stages of embryo development as compared to later stages. In addition, pathways related to oil biosynthesis and their corresponding genes were more enriched at 30 DAP, which seems to be the key stage for oil accumulation. The study also identified 33 key DEGs involved in fatty acid and triacylglycerols biosynthesis, most of which were up-regulated in HOC, that may shape the differential oil contents in the two contrasting maize. Notably, we discovered that both acyl-CoA-dependent and acyl-CoA-independent processes are essential for the high oil accumulation in maize embryo.

ZmRAD51C is Essential for Double-Strand Break Repair and Homologous Recombination in Maize Meiosis

Radiation sensitive 51 (RAD51) recombinases play crucial roles in meiotic double-strand break (DSB) repair mediated by homologous recombination (HR) to ensure the correct segregation of homologous chromosomes. In this study, we identified the meiotic functions of ZmRAD51C, the maize homolog of Arabidopsis and rice RAD51C. The Zmrad51c mutants exhibited regular vegetative growth but complete sterility for both male and female inflorescence. However, the mutants showed hypersensitivity to DNA damage by mitomycin C. Cytological analysis indicated that homologous chromosome pairing and synapsis were rigorously inhibited, and meiotic chromosomes were often entangled from diplotene to metaphase I, leading to chromosome fragmentation at anaphase I. Immunofluorescence analysis showed that although the signals of the axial element absence of first division (AFD1) and asynaptic1 (ASY1) were normal, the assembly of the central element zipper1 (ZYP1) was severely disrupted. The DSB formation was normal in Zmrad51c meiocytes, symbolized by the regular occurrence of γH2AX signals. However, RAD51 and disrupted meiotic cDNA 1 (DMC1) signals were never detected at the early stage of prophase I in the mutant. Taken together, our results indicate that ZmRAD51C functions crucially for both meiotic DSB repair and homologous recombination in maize.

Genome-Wide Profiling of Polyadenylation Events in Maize Using High-Throughput Transcriptomic Sequences

Polyadenylation is an essential post-transcriptional modification of eukaryotic transcripts that plays critical role in transcript stability, localization, transport, and translational efficiency. About 70% genes in plants contain alternative polyadenylation (APA) sites. Despite availability of vast amount of sequencing data, to date, a comprehensive map of the polyadenylation events in maize is not available. Here, 9.48 billion RNA-Seq reads were analyzed to characterize 95,345 Poly(A) Clusters (PAC) in 23,705 (51%) maize genes. Of these, 76% were APA genes. However, most APA genes (55%) expressed a dominant PAC rather than favoring multiple PACs equally. The lincRNA genes with PACs were significantly longer in length than the genes without any PAC and about 48% genes had APA sites. Heterogeneity was observed in 52% of the PACs supporting the imprecise nature of the polyadenylation process. Genomic distribution revealed that the majority of the PACs (78%) were located in the genic regions. Unlike previous studies, large number of PACs were observed in the intergenic (n = 21,264), 5′-UTR (735), CDS (2,542), and the intronic regions (12,841). The CDS and introns with PACs were longer in length than without PACs, whereas intergenic PACs were more often associated with transcripts that lacked annotated 3′-UTRs. Nucleotide composition around PACs demonstrated AT-richness and the common upstream motif was AAUAAA, which is consistent with other plants. According to this study, only 2,830 genes still maintained the use of AAUAAA motif. This large-scale data provides useful insights about the gene expression regulation and could be utilized as evidence to validate the annotation of transcript ends.

Molecular Evolution and Functional Analysis of Rubredoxin-Like Proteins in Plants

Rubredoxins are a class of iron-containing proteins that play an important role in the reduction of superoxide in some anaerobic bacteria and also act as electron carriers in many biochemical processes. Unlike the more widely studied about rubredoxin proteins in anaerobic bacteria, very few researches about the function of rubredoxins have been proceeded in plants. Previous studies indicated that rubredoxins in A. thaliana may play a critical role in responding to oxidative stress. In order to identify more rubredoxins in plants that maybe have similar functions as the rubredoxin-like protein of A. thaliana, we identified and analyzed plant rubredoxin proteins using bioinformatics-based methods. Totally, 66 candidate rubredoxin proteins were identified based on public databases, exhibiting lengths of 187-360 amino acids with molecular weights of 19.856-37.117 kDa. The results of subcellular localization showed that these candidate rubredoxins were localized to the chloroplast, which might be consistent with the fact that rubredoxins were predominantly expressed in leaves. Analyses of conserved motifs indicated that these candidate rubredoxins contained rubredoxin and PDZ domains. The expression patterns of rubredoxins in glycophyte and halophytic plant under salt/drought stress revealed that rubredoxin is one of the important stress response proteins. Finally, the coexpression network of rubredoxin in Arabidopsis thaliana under abiotic was extracted from ATTED-II to explore the function and regulation relationship of rubredoxin in Arabidopsis thaliana. Our results showed that putative rubredoxin proteins containing PDZ and rubredoxin domains, localized to the chloroplast, may act with other proteins in chloroplast to responses to abiotic stress in higher plants. These findings might provide value inference to promote the development of plant tolerance to some abiotic stresses and other economically important crops.

Analysis of the biological recovery of soils contaminated with hydrocarbons using an electrokinetic treatment

There are various treatments available for soil decontamination, including physical, chemical, thermal and biological treatments. However, when pollutants are persistent or toxic, it is often necessary to use an integrated set of techniques, to enhance decontamination effects. Integrated treatments typically include soil washing, heat treatment, stabilization processes or phytoremediation. The biological recovery of soils contaminated with hydrocarbons or heavy metals is a topic of central interest, since many treatment processes are often extremely aggressive and destroy the flora and microflora of the treated environments and can interfere with the natural properties of the soil. The objective of this work was to analyze the biological recovery of soils treated with an electrokinetic remediation (ER) method at laboratory, pilot and field-scale tests which measure the germination of seeds and growth of maize (Zea mays L.) using a 2D circular arrangement of electrodes (IrO₂-Ta₂O₅ |Ti| |Ti). The hydrocarbon removal rates obtained were greater than 80% for both the hydrocarbon's medium and heavy fractions; after this ER method was employed a phytoremediation treatment was also completed, using maize, which increased the removal rates up to 90%. A coupled electro- and phyto-remediation process was develop at the field-scale within an oil refinery property in Guanajuato, Mexico to demonstrate the successful biological recovery of soils contaminated with hydrocarbons as proved by the germination of seeds and growth of maize in the on-site fields.

Melatonin enhances thermotolerance of maize seedlings (Zea mays L.) by modulating antioxidant defense, methylglyoxal detoxification, and osmoregulation systems

Melatonin (MT), derived from tryptophan, is an amazing signaling molecule with multiple functions in plants. Heat stress (HS) induced by high temperature is a major stress factor that limits metabolism, growth, development, and productivity of plants. However, whether MT could enhance the thermotolerance of maize seedlings and the underlying mechanisms is not completely known. In this study, treatment of maize seedlings with MT enhanced the survival percentage of maize seedlings under HS conditions, mitigated an increase in malondialdehyde (MDA, product of membrane lipid peroxidation) and electrolyte leakage, and improved tissue vitality compared with the control without MT treatment, indicating that MT treatment could enhance the theromotolerance of maize seedlings. To understand the mechanisms underlying MT-enhanced thermotolerance of maize seedlings, the antioxidant defense (guaiacol peroxidease: GPX; glutathione reductase: GR; catalase: CAT; ascorbic acid: AsA; and glutathione: GSH), methylglyoxal (MG) detoxification (glyoxalase I: Gly I; and glyoxalase II: Gly II), and osmoregulation (proline: Pro; trehalose: Tre; and total soluble sugar: TSS) systems were assayed. The results showed that MT treatment stimulated the activities of antioxidant enzymes (GPX, GR, and CAT) and MG detoxification enzymes (Gly I and Gly II), increased the contents of nonenzyme antioxidants (AsA and GSH) and osmolytes (Pro, Tre, and TSS) in maize seedlings under normal culture conditions, and maintained a higher abovementioned enzyme activity and antioxidant and osmolyte contents under HS conditions compared with the control. This work reported that MT could enhance the thermotolerance of maize seedlings by modulating the antioxidant defense, MG detoxification, and osmoregulation systems.

Responses of seed germination and shoot metabolic profiles of maize (Zea maysL.) to Y2O3nanoparticle stress

The potential risks of rare-earth nanoparticles (RENPs) to plants in the environment are attracting increasing attention due to their wide-spread application. In this regard, little is known about the effects of Y₂O₃ NPs as an important member of RENPs on crop plants. Seed germination is vulnerable to environmental stress, which determines the growth and yield of crops. Here, maize seeds were exposed to a Y₂O₃ NP suspension (0–500 mg L⁻¹) in the dark for 6 days. It was found that the Y₂O₃ NPs had no significant effect on the germination rates (>93%) in all treatments, but they could reduce seed vitality, delay germination, and inhibit seedling growth in a dose-dependent manner. Further, the inhibition effect of Y₂O₃ NPs on root elongation was much stronger than that on shoot elongation. Meanwhile, the activities of peroxidase (POD) and catalase (CAT) in shoots were enhanced with the increase in the Y₂O₃ NP concentration. A high-concentration (≥300 mg L⁻¹) of Y₂O₃ NPs induced a significant increase in the malondialdehyde (MDA) level in shoots compared to the control, indicating that the membrane lipid peroxidation and permeability were enhanced. ¹H NMR-based analysis showed that the polar metabolic profiles were altered significantly after treatment with 0, 10, and 500 mg L⁻¹ of Y₂O₃ NPs, but there was no marked alteration observed for the non-polar metabolic profiles. The polar metabolites (e.g., sugars, amino acids, and most organic acids) showed a dose-dependent increase to Y₂O₃ NP stress, indicating that the metabolic pathways of carbohydrate metabolism, the tricarboxylic acid cycle (TCA), and amino acid synthesis were disturbed. There were significantly positive correlations found among the metabolites related with the antioxidant response and osmotic adjustment. The simultaneous accumulation of these metabolites possibly indicated the adaptation of the seedlings to stress at the cost of retarding glycolysis, TCA, and protein synthesis. The retarded effects finally inhibited the apparent growth of the seedlings. These findings reveal the phytotoxicity of Y₂O₃ NPs and provide physiological and biochemical and molecular-scale perspectives on the response of seedlings to stress.

A hypothetic model for the adaptation of maize to Y₂O₃ NPs stress during seed germination.

Maize domestication and gene interaction

Contents Summary 395 I. Introduction 395 II. The genetic basis of maize domestication 396 III. The tempo of maize domestication 401 IV. Genetic interactions and selection during maize domestication 401 V. Gene networks of maize domestication alleles 404 VI. Implications of gene interactions on evolution and selection404 VII. Conclusions 405 Acknowledgements 405 References 405 SUMMARY: Domestication is a tractable system for following evolutionary change. Under domestication, wild populations respond to shifting selective pressures, resulting in adaptation to the new ecological niche of cultivation. Owing to the important role of domesticated crops in human nutrition and agriculture, the ancestry and selection pressures transforming a wild plant into a domesticate have been extensively studied. In Zea mays, morphological, genetic and genomic studies have elucidated how a wild plant, the teosinte Z. mays subsp. parviglumis, was transformed into the domesticate Z. mays subsp. mays. Five major morphological differences distinguish these two subspecies, and careful genetic dissection has pinpointed the molecular changes responsible for several of these traits. But maize domestication was a consequence of more than just five genes, and regions throughout the genome contribute. The impacts of these additional regions are contingent on genetic background, both the interactions between alleles of a single gene and among alleles of the multiple genes that modulate phenotypes. Key genetic interactions include dominance relationships, epistatic interactions and pleiotropic constraint, including how these variants are connected in gene networks. Here, we review the role of gene interactions in generating the dramatic phenotypic evolution seen in the transition from teosinte to maize.

Changes in Cytomorphology, Expression of Retinoblastoma Related Gene, and Superoxide Dismutase Enzyme Activity in Maize Cell Culture Exposed to Silver Nanoparticles

The ever-increasing use of silver nanoparticles (nAg) in various products necessitates investigation of the behavior of biological systems encountering these particles. In this paper, considering maize as a biological model, the effects of colloidal nAg (<80nm) on its cell culture were investigated. For comparison purposes, silver nitrate was used as a representative of silver ion (Ag⁺). After stabilization of cell suspensions, they were treated with nAg and Ag⁺ (1 mg/l), then cell suspension growth was measured and the microscopic analysis and a cell viability test were performed. In addition, the activity of superoxide dismutase (SOD) enzyme was explored. Owing to the key role of retinoblastoma-related protein (RBR) in cell cycle as well as in development and differentiation processes, the relative expression of ZmRBR1 was studied in nAg and Ag⁺ exposure. Microscopic analyses revealed that cells in suspensions treated by nAg and Ag⁺ were morphologically classified into five types: embryogenic; larvae-like; long; swollen; and polarized. The results showed an increase in percentages of large and live cells in the treated suspensions. Remarkably, we observed some cells which were differentiated into trichomes along with some stages of trichome development in the treated cell suspensions. Moreover, exposure to nAg and Ag⁺ did not elevate the activity of SOD enzyme in the treated cells. Also, the relative expression of ZmRBR1 was slightly reduced in the treated cells. The findings of these experimentations indicated that nAg affected maize suspension-cultured cells in the same manner as Ag⁺.

Comparative Metabolic Response between Cucumber ( Cucumis sativus) and Corn ( Zea mays) to a Cu(OH)2 Nanopesticide

Due to their unique properties, copper-based nanopesticides are emerging in the market. Thus, understanding their effect on crop plants is very important. Metabolomics can capture a snapshot of cellular metabolic responses to a stressor. We selected maize and cucumber as model plants for exposure to different doses of Cu(OH)₂ nanopesticide. GC-TOF-MS-based metabolomics was employed to determine the metabolic responses of these two species. Results revealed significant differences in metabolite profile changes between maize and cucumber. Furthermore, the Cu(OH)₂ nanopesticide induced metabolic reprogramming in both species, but in different manners. In maize, several intermediate metabolites of the glycolysis pathway and tricarboxylic acid cycle (TCA) were up-regulated, indicating the energy metabolism was activated. In addition, the levels of aromatic compounds (4-hydroxycinnamic acid and 1,2,4-benzenetriol) and their precursors (phenylalanine, tyrosine) were enhanced, indicating the activation of shikimate-phenylpropanoid biosynthesis in maize leaves, which is an antioxidant defense-related pathway. In cucumber, arginine and proline metabolic pathways were the most significantly altered pathway. Both species exhibited altered levels of fatty acids and polysaccharides, suggesting the cell membrane and cell wall composition may change in response to Cu(OH)₂ nanopesticide. Thus, metabolomics helps to deeply understand the differential response of these plants to the same nanopesticide stressor.

Changes in maize transcriptome in response to maize Iranian mosaic virus infection

Background

Maize Iranian mosaic virus (MIMV, genus Nucleorhabdovirus, family Rhabdoviridae) causes an economically important disease in maize and other gramineous crops in Iran. MIMV negative-sense RNA genome sequence of 12,426 nucleotides has recently been completed. Maize Genetics and Genomics database shows that 39,498 coding genes and 4,976 non-coding genes of maize have been determined, but still some transcripts could not be annotated. The molecular host cell responses of maize to MIMV infection including differential gene expression have so far not been elucidated.

Methodology/Principal findings

Complementary DNA libraries were prepared from total RNA of MIMV-infected and mock-inoculated maize leaves and sequenced using Illumina HiSeq 2500. Cleaned raw transcript reads from MIMV-infected maize were mapped to reads from uninfected maize and to a maize reference genome. Differentially expressed transcripts were characterized by gene ontology and biochemical pathway analyses. Transcriptome data for selected genes were validated by real-time quantitative PCR.

Conclusion/Significance

Approximately 42 million clean reads for each treatment were obtained. In MIMV-infected maize compared to uninfected plants, 1689 transcripts were up-regulated and 213 transcripts were down-regulated. In response to MIMV infection, several pathways were activated in maize including immune receptor signaling, metabolic pathways, RNA silencing, hormone-mediated pathways, protein degradation, protein kinase and ATP binding activity, and fatty acid metabolism. Also, several transcripts including those encoding hydrophobic protein RCI2B, adenosylmethionine decarboxylase NAC transcription factor and nucleic acid binding, leucine-rich repeat, heat shock protein, 26S proteasome, oxidoreductases and endonuclease activity protein were up-regulated. These data will contribute to the identification of genes and pathways involved in plant-virus interactions that may serve as future targets for improved disease control.

Evolution of intron-poor clades and expression patterns of the glycosyltransferase family 47

A large-scale bioinformatics analysis revealed the origin and evolution of GT47 gene family, and identified two clades of intron-poor genes with putative functions in drought stress responses and seed development in maize. Glycosyltransferase family 47 (GT47) genes encode β-galactosyltransferases and β-glucuronyltransferases that synthesize pectin, xyloglucans and xylan, which are important components of the plant cell wall. In this study, we performed a systematic and large-scale bioinformatics analysis of GT47 gene family using 352 GT47 proteins from 15 species ranging from cyanobacteria to seed plants. The analysis results showed that GT47 family may originate in cyanobacteria and expand along the evolutionary trajectory to moss. Further analysis of 47 GT47 genes in maize revealed that they can divide into five clades with diverse exon-intron structures. Among these five clades, two were mainly composed with intron-poor genes, which may originate in the moss. Gene duplication analysis revealed that the expansion of GT47 gene family in maize was significantly driven from tandem duplication events and segmental duplication events. Significantly, almost all duplicated genes are intron-poor genes. Expression analysis indicated that several intron-poor GT47 genes may be involved in the drought stress response and seed development in maize. This work provides insight into the origin and evolutionary process, expansion mechanisms and expression patterns of GT47 genes, thus facilitating their functional investigations in the future.

The Maize ABA Receptors ZmPYL8, 9, and 12 Facilitate Plant Drought Resistance

Drought is one of the major abiotic stresses affecting world agriculture. Breeding drought-resistant crops is one of the most important challenges for plant biologists. PYR1/PYL/RCARs, which encode the abscisic acid (ABA) receptors, play pivotal roles in ABA signaling, but how these genes function in crop drought response remains largely unknown. Here we identified 13 PYL family members in maize (ZmPYL1-13). Changes in expression of these genes under different stresses indicated that ZmPYLs played important roles in responding to multiple abiotic stresses. Transgenic analyses of ZmPYL genes in Arabidopsis showed that overexpression of ZmPYL3, ZmPYL9, ZmPYL10, and ZmPYL13 significantly enhanced the sensitivity of transgenic plants to ABA. Additionally, transgenic lines overexpressing ZmPYL8, ZmPYL9, and ZmPYL12 were more resistant to drought. Accumulation of proline and enhanced expression of drought-related marker genes in transgenic lines further confirmed the positive roles of ZmPYL genes in plant drought resistance. Association analyses with a panel of 368 maize inbred lines identified natural variants in ZmPYL8 and ZmPYL12 that were significantly associated with maize drought resistance. Our results deepen the knowledge of the function of maize PYL genes in responses to abiotic stresses, and the natural variants identified in ZmPYL genes may serve as potential molecular markers for breeding drought-resistant maize cultivars.

Evolutionary conservation and functional divergence of the LFK gene family play important roles in the photoperiodic flowering pathway of land plants

ZEITLUPE (ZTL), LOV KELCH PROTEIN 2 (LKP2), and FLAVIN-BINDING KELCH REPEAT F-BOX 1 (FKF1)-blue-light photoreceptors-play important roles in regulating the circadian clock and photoperiodic flowering pathway in plants. In this study, phylogenetic analysis revealed that the LOV (Light, Oxygen, or Voltage) and Kelch repeat-containing F-box (LFK) gene family can be classified into two clades, ZTL/LKP2 and FKF1, with clear differentiation between monocots and dicots within each clade. The LFK family genes underwent strong purifying selection; however, signatures of positive selection to adapt to local conditions still existed in 18 specific codons. In 87 diverse maize inbred lines, significant differences were identified (P ≤ 0.01) for days to female flowering between the haplotypes consisting of eight positive selection sites at ZmFKF1b corresponding to tropical and temperate maize groups of the phylogenetic tree, indicating a key role of ZmFKF1b in maize adaptive evolution. In addition, positive coevolution was detected in the domains of the LFK family for long-term cooperation to targets. The Type-I and Type-II functional divergence analysis revealed subfunctionalization or neofunctionalization of the LFKs, and the ZTL subfamily is most likely to maintain the ancestral function of LFKs. Over 50% of critical amino acid sites involved in the functional divergence were identified in the Kelch repeat domain, resulting in the distinction of substrates for ubiquitination and degradation. These results suggest that evolutionary conservation contributes to the maintenance of critical physiological functions, whereas functional divergence after duplication helps to generate diverse molecular regulation mechanisms.

Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels

BACKGROUND

Dissecting the genetic basis and regulatory mechanisms for the biosynthesis and accumulation of nutrients in maize could lead to the improved nutritional quality of this crop. Gene expression is regulated at the genomic, transcriptional, and post-transcriptional levels, all of which can produce diversity among traits. However, the expression of most genes connected with a particular trait usually does not have a direct association with the variation of that trait. In addition, expression profiles of genes involved in a single pathway may vary as the intrinsic cellular state changes. To work around these issues, we utilized a statistical method, liquid association (LA) to investigate the complex pattern of gene regulation in maize kernels.

RESULTS

We applied LA to the expression profiles of 28,769 genes to dissect dynamic trait-trait correlation patterns in maize kernels. Among the 1000 LA pairs (LAPs) with the largest LA scores, 686 LAPs were identified conditional correlation. We also identified 830 and 215 LA-scouting leaders based on the positive and negative LA scores, which were significantly enriched for some biological processes and molecular functions. Our analysis of the dynamic co-expression patterns in the carotene biosynthetic pathway clearly indicated the important role of lcyE, CYP97A, ZEP1, and VDE in this pathway, which may change the direction of carotene biosynthesis by controlling the influx and efflux of the substrate. The dynamic trait-trait correlation patterns between gene expression and oil concentration in the fatty acid metabolic pathway and its complex regulatory network were also assessed. 23 of 26 oil-associated genes were correlated with oil concentration conditioning on 580 LA-scoutinggenes, and 5% of these LA-scouting genes were annotated as enzymes in the oil metabolic pathway.

CONCLUSIONS

By focusing on the carotenoid and oil biosynthetic pathways in maize, we showed that a genome-wide LA analysis provides a novel and effective way to detect transcriptional regulatory relationships. This method will help us understand the biological role of maize kernel genes and will benefit maize breeding programs.

Identification of differentially regulated maize proteins conditioning Sugarcane mosaic virus systemic infection

Sugarcane mosaic virus (SCMV) is the most important cause of maize dwarf mosaic disease. To identify maize genes responsive to SCMV infection and that may be involved in pathogenesis, a comparative proteomic analysis was performed using the first and second systemically infected leaves (termed 1 SL and 2 SL, respectively). Seventy-one differentially expressed proteins were identified in 1 SL and 2 SL upon SCMV infection. Among them, eight proteins showed the same changing patterns in both 1 SL and 2 SL. Functional annotations of regulated proteins and measurement of photosynthetic activity revealed that photosynthesis was more inhibited and defensive gene expression more pronounced in 1 SL than in 2 SL. Knockdown of regulated proteins in both 1 SL and 2 SL by a brome mosaic virus-based gene silencing vector in maize indicated that protein disulfide isomerase-like and phosphoglycerate kinase were required for optimal SCMV replication. By contrast, knockdown of polyamine oxidase (ZmPAO) significantly increased SCMV accumulation, implying that ZmPAO activity might contribute to resistance or tolerance. The results suggest that combining comparative proteomic analyses of different tissues and virus-induced gene silencing is an efficient way to identify host proteins supporting virus replication or enhancing resistance to virus infection.

Improved maize reference genome with single-molecule technologies

Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and notable improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed more than 130,000 intact transposable elements, allowing us to identify transposable element lineage expansions that are unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by single-molecule real-time sequencing. In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes.