Search Results (36)

Background: Acyl-CoA oxidase (ACX), a ubiquitous eukaryotic enzyme, catalyzes the initial steps of fatty acid β oxidation and plays an important role in the biosynthesis of jasmonic acid (JA). At present, no studies have been reported on ACX family members of maize and their function in disease resistance. Objectives: This study aims to lay a foundation for clarifying the functions of ACX family genes in maize growth, development, and stress response by conducting a genome-wide identification of ACX family genes in maize, analyzing the expression characteristics of these genes in maize growth and development, hormone treatment and response to biotic and abiotic stresses, and exploring the functions of key genes in the maize disease resistance process through the use of mutants. Methods: ProtParam, TBtools, MEME, MEGA, and IBS tools were used to identify maize ACX family genes and analyze the physicochemical properties of their proteins, chromosome location, phylogenetic relationships among family members, conserved domains, conserved motifs, and cis-acting elements. Meanwhile, the expression patterns of maize ACX family genes in different tissues and their expression patterns under abiotic and biotic stresses were studied by using the data from the maize GDB database and qRT-PCR technology. Moreover, the mutants of ZmACX1, ZmACX3, ZmACX4, and ZmACX5 genes were obtained, and the disease resistance of the mutants was detected to further determine the functions of ACX genes in the maize disease resistance process. This study identified maize ACX family genes using bioinformatics methods. Results: We discovered that six ACX genes in the maize genome are distributed across four different chromosomes. Cluster analysis further classified these genes into three subfamilies. All maize ACX genes possess a conserved ACOX domain, and their promoter regions are enriched with cis-acting elements associated with heat stress and the plant hormone response. Under various tissue, biotic, and abiotic stress conditions, as well as treatments with methyl jasmonate (MeJA) and salicylic acid (SA), the expression levels of maize ACX family genes exhibited significant differences. Notably, the expression levels of ZmACX1, ZmACX3, ZmACX4, and ZmACX5 were significantly up-regulated following stress and pathogen infection, suggesting their involvement in maize growth, development, and disease resistance. To elucidate the function of these genes in maize disease resistance, the resistance of ZmACX1, ZmACX3, ZmACX4, and ZmACX5 mutants to Cochliobolus heterostrophus, Curvularia lunata, and Fusarium graminearum were further examined. The results revealed that compared to the wild-type B73, the lesion area of the mutants was significantly increased after inoculation with pathogens. This directly demonstrated the crucial role of these genes in maize resistance to C. heterostrophus, C. lunata, and F. graminearum. Conclusions: In summary, this study systematically identified maize ACX family genes, and thoroughly investigated their expression patterns and functions in maize disease resistance. Our findings provide valuable insights into the comprehensive understanding of the function and mechanism of maize ACX family genes. Full article

The TaVP1-B gene, located on the 3B chromosome of wheat, is a homolog of the Viviparous-1 (VP-1) gene of maize and was reported to confer resistance to pre-harvest sprouting (PHS) in wheat. In this study, the structure of the TaVP1-B gene was analyzed using the wheat pan-genome consisting of 20 released cultivars (19 wheat are from China), and 3 single nucleotide polymorphisms (SNPs), which were identified at the 496 bp, 524 bp, and 1548 bp of the TaVP1-B CDS region, respectively. Haplotypes analysis showed that these SNPs were in complete linkage disequilibrium and that only two haplotypes designated as hap1 (TGG) and hap2 (GAA) were present. Association analysis between TaVP1-B haplotypes and PHS resistance of the 20 wheat cultivars in four experiment environments revealed that the average PHS resistance of accessions with hap1 was significantly better than that of accessions with hap2, which infers the effects of TaVP1-B on wheat PHS resistance. To further investigate the impacts of alleles at the TaVP1-B locus on PHS resistance, the SNP at 1548 bp of the TaVP1-B CDS region was converted to a KASP marker, which was used for genotyping 304 Chinese wheat cultivars, whose PHS resistance was evaluated in three environments. The average sprouting rates (SRs) of 135 wheat cultivars with the hap1 were significantly lower than the 169 cultivars with the hap2, validating the impacts of TaVP1-B on PHS resistance in Chinese wheat. The present study provided the breeding-friendly marker for functional variants in the TaVP1-B gene, which can be used for genetic improvement of PHS resistance in wheat. Full article

Tartary buckwheat is a nutrient-rich pseudo-cereal whose starch contents, including amylose and amylopectin contents, and their properties hold significant importance for enhancing yield and quality. The granule-bound starch synthase (GBSS) is a key enzyme responsible for the synthesis of amylose, directly determining the amylose content and amylose-to-amylopectin ratio in crops. Although one has already been cloned, the GBSS genes at the genome-wide level have not yet been fully assessed and thoroughly analyzed in Tartary buckwheat. This study comprehensively analyzed the FtGBSSs in Tartary buckwheat. Based on the genome data of Tartary buckwheat, five FtGBSS genes, namely FtGBSS-1 to FtGBSS-5, were identified on three chromosomes, exhibiting about 1800 bp lengths in their CDSs and numerous exons and introns in gene structures. Amino acid analyses revealed high homology in ten GBSS proteins from Tartary buckwheat, rice, maize, and Arabidopsis thaliana, with a specific starch synthase catalytic domain and ten conserved motifs. The Tartary buckwheat GBSS proteins had a closer relationship with GBSS proteins from monocot based on evolutionary relationship analysis. Expression analyses suggested that the FtGBSS genes showed distinct tissue-specific expression patterns in Tartary buckwheat and rice-Tartary buckwheat. Among them, FtGBSS-1, FtGBSS-2, and FtGBSS-4 were higher expressed in the root, stem, or flower, suggesting that they have a role in the amylose synthesis of these tissues. Notably, FtGBSS-3 and FtGBSS-5 were more highly expressed in seeds than in other tissues, suggesting that they have a pivotal role in amylose synthesis of the seeds of Tartary buckwheat. Furthermore, the cis acting elements in the promoters of FtGBSSs and their binding transcription factors (TFs) were investigated. A protein–protein interaction network was constructed and co-expression was analyzed based on the gene expression patterns of the FtGBSSs, and the identified TFs, belonging to bZIP, ERF, bHLH, and MADS-box TF families, were identified within this network, and their expression patterns were significantly correlated to the expression patterns of two seed-specific FtGBSS genes (FtGBSS-3 and FtGBSS-5). Finally, FtGBSS1-5 was successfully transformed into rice through transgenic manipulation, and the FtGBSS1-5 overexpression lines showed an increase in amylose content accompanied by a reduction in amylopectin and total starch contents compared with WT. Overall, this research not only deepens our understanding of the molecular mechanisms of amylose synthesis in Tartary buckwheat, but also provides scientific insights for enhancing crop amylose content and quality through molecular breeding. Full article

Background/Objectives: Chitinases, enzymes belonging to the glycoside hydrolase family, play a crucial role in plant growth and stress response by hydrolyzing chitin, a natural polymer found in fungal cell walls. This study aimed to identify and analyze the maize chitinase gene family, assessing their response to various biotic and abiotic stresses to understand their potential role in plant defense mechanisms and stress tolerance. Methods: We employed bioinformatics tools to identify 43 chitinase genes in the maize B73_V5 genome. These genes were characterized for their chromosomal positions, gene and protein structures, phylogenetic relationships, functional enrichment, and collinearity. Based on previous RNA-seq data, the analysis assessed the expression patterns of these genes at different developmental stages and under multiple stress conditions. Results: The identified chitinase genes were unevenly distributed across maize chromosomes with a history of tandem duplications contributing to their divergence. The ZmChi protein family was predominantly hydrophilic and localized mainly in chloroplasts. Expression analysis revealed that certain chitinase genes were highly expressed at specific developmental stages and in response to various stresses, with ZmChi31 showing significant responsiveness to 11 different abiotic and biotic stresses. Conclusions: This study provides new insights into the role of chitinase genes in maize stress response, establishing a theoretical framework for exploring the molecular basis of maize stress tolerance. The identification of stress-responsive chitinase genes, particularly ZmChi31, offers potential candidates for further study in enhancing maize resistance to environmental challenges. Full article

Leaf angle (LA) is closely related to plant architecture, photosynthesis and density tolerance in maize. In the current study, we used a recombinant inbred line population constructed by two maize-inbred lines to detect quantitative trait loci (QTLs) controlling LA. Based on the average LA in three environments, 13 QTLs were detected, with the logarithm of odds ranging from 2.7 to 7.21, and the phenotypic variation explained by a single QTL ranged from 3.93% to 12.64%. A stable QTL, qLA2-3, on chromosome 2 was detected and was considered to be the major QTL controlling the LA. On the basis of verifying the genetic effect of qLA2-3, a fine map was used to narrow the candidate interval, and finally, the target segment was located at a physical distance of approximately 338.46 kb (B73 RefGen_v4 version), containing 16 genes. Re-sequencing and transcriptome results revealed that five candidate genes may be involved in the regulation of LA. The results enrich the information for molecular marker-assisted selection of maize LA and provide genetic resources for the breeding of dense planting varieties. Full article

Dirigent (DIR) genes play a pivotal role in plant development and stress adaptation. Manihot esculenta Crantz, commonly known as cassava, is a drought-resistant plant thriving in tropical and subtropical areas. It is extensively utilized for starch production, bioethanol, and animal feed. However, a comprehensive analysis of the DIR family genes remains unexplored in cassava, a crucial cash and forage crop in tropical and subtropical regions. In this study, we characterize a total of 26 cassava DIRs (MeDIRs) within the cassava genome, revealing their uneven distribution across 13 of the 18 chromosomes. Phylogenetic analysis classified these genes into four subfamilies: DIR-a, DIR-b/d, DIR-c, and DIR-e. Comparative synteny analysis with cassava and seven other plant species (Arabidopsis (Arabidopsis thaliana), poplar (Populus trichocarpa), soybean (Glycine max), tomato (Solanum lycopersicum), rice (Oryza sativa), maize (Zea mays), and wheat (Triticum aestivum)) provided insights into their likely evolution. We also predict protein interaction networks and identify cis-acting elements, elucidating the functional differences in MeDIR genes. Notably, MeDIR genes exhibited specific expression patterns across different tissues and in response to various abiotic and biotic stressors, such as pathogenic bacteria, cadmium chloride (CdCl₂), and atrazine. Further validation through quantitative real-time PCR (qRT-PCR) confirmed the response of DIR genes to osmotic and salt stress. These findings offer a comprehensive resource for understanding the characteristics and biological functions of MeDIR genes in cassava, enhancing our knowledge of plant stress adaptation mechanisms. Full article

Maize is one of the most successful crops with regard to the utilization of heterosis. The haploid induction technique is one of the fastest methods to obtain pure maize material at the present stage. However, the molecular mechanism of haploid doubling is rarely reported. In this study, we treated B73 and ZNC442 haploid young shoots with colchicine for 0 h, 6.2 h, and 10 h, and analyzed the differentially expressed genes (DEGs). We found that colchicine treatment for 6.2 h and 10 h compared to 0 h resulted in a total of 4868 co-DEGs. GO enrichment analysis and KEGG metabolic pathway analysis found significantly enriched 282 GO terms and 31 significantly pathways, respectively. Additionally, The GO term and KEGG pathway genes of spindle, cytoskeleton, microtubules and nuclear division were selected for analysis, and three candidate genes were screened by taking intersections. Zm00001d033112, Zm00001d010525, and Zm00001d043386 were annotated as kinesin-associated protein 13, kinesin-like protein KIN-10C, and kinesin light-chain LC6, respectively. The real-time fluorescence quantification (RT-PCR) results revealed that Zm00001d033112, Zm00001d010525, and Zm00001d043386 had the same trends as RNA-seq. Interestingly, Zm00001d033112 is homologous gene AT3G20150 in Arabidopsis, which was involved in the regulation of chromosome movement and mitotic spindle assembly. Our study suggests that kinesin genes may play an important role in doubling chromosomes, thus providing valuable information for future studies on the molecular mechanisms of chromosome doubling in maize. Full article

Tassel weight (TW) is a crucial agronomic trait that significantly affects pollen supply and grain yield development in maize breeding. To improve maize yield and develop new varieties, a comprehensive understanding of the genetic mechanisms underlying tassel weight is essential. In this study, tropical maize inbred lines, namely CML312, CML373, CML444, and YML46, were selected as female parents and crossed with the elite maize inbred line Ye107, which served as the common male parent, to develop a multi-parent population comprising four F8 recombinant inbred line (RIL) subpopulations. Using 6616 high-quality single nucleotide polymorphism (SNP) markers, we conducted genome-wide association analysis (GWAS) and genomic selection (GS) on 642 F8 RILs in four subpopulations across three different environments. Through GWAS, we identified 16 SNPs that were significantly associated with TW, encompassing two stable loci expressed across multiple environments. Furthermore, within the candidate regions of these SNPs, we discovered four novel candidate genes related to TW, namely Zm00001d044362, Zm00001d011048, Zm00001d011049, and Zm00001d031173 distributed on chromosomes 1, 3, and 8, which have not been previously reported. These genes are involved in processes such as signal transduction, growth and development, protein splicing, and pollen development, all of which play crucial roles in inflorescence meristem development, directly affecting TW. The co-localized SNP, S8_137379725, on chromosome 8 was situated within a 16.569 kb long terminal repeat retrotransposon (LTR-RT), located 22.819 kb upstream and 26.428 kb downstream of the candidate genes (Zm00001d011048 and Zm00001d011049). When comparing three distinct GS models, the BayesB model demonstrated the highest accuracy in predicting TW. This study establishes the theoretical foundation for future research into the genetic mechanisms underlying maize TW and the efficient breeding of high-yielding varieties with desired tassel weight through GS. Full article

As transcription factors derived from transposase, FAR-RED IMPAIRED RESPONSE1 (FAR1) and its homolog FHY3 play crucial roles in the regulation of light signaling and various stress responses by coordinating the expression of downstream target genes. Despite the extensive investigation of the FAR1/FHY3 family in Arabidopsis thaliana and other species, a comprehensive examination of these genes in maize has not been conducted thus far. In this study, we employed a genomic mining approach to identify 16 ZmFAR1 genes in the maize inbred line B73, which were further classified into five subgroups based on their phylogenetic relationships. The present study characterized the predicted polypeptide sequences, molecular weights, isoelectric points, chromosomal distribution, gene structure, conserved motifs, subcellular localizations, phylogenetic relationships, and cis-regulatory elements of all members belonging to the ZmFAR1 family. Furthermore, the tissue-specific expression of the 16 ZmFAR1 genes was analyzed using RNA-seq, and their expression patterns under far-red light conditions were validated in the ear and tassel through qRT-qPCR. The observed highly temporal and spatial expression patterns of these ZmFAR1 genes were likely associated with their specific functional capabilities under different light conditions. Further analysis revealed that six ZmFAR1 genes (ZmFAR1-1, ZmFAR1-10, ZmFAR1-11, ZmFAR1-12, ZmFAR1-14, and ZmFAR1-15) exhibited a response to simulated shading treatment and actively contributed to the development of maize ears. Through the integration of expression quantitative trait loci (eQTL) analyses and population genetics, we identified the presence of potential causal variations in ZmFAR1-14 and ZmFAR1-9, which play a crucial role in regulating the kernel row number and kernel volume weight, respectively. In summary, this study represents the initial identification and characterization of ZmFAR1 family members in maize, uncovering the functional variation in candidate regulatory genes associated with the improvement of significant agronomic traits during modern maize breeding. Full article

Maize is an important food and cash crop worldwide. The WUSCHEL (WUS)-related homeobox (WOX) transcription factor (TF) family plays a significant role in the development process and the response to abiotic stress of plants. However, few studies have been reported on the function of WOX genes in maize. This work, utilizing the latest maize B73 reference genome, results in the identification of 22 putative ZmWOX gene family members. Except for chromosome 5, the 22 ZmWOX genes were homogeneously distributed on the other nine chromosomes and showed three tandem duplication and 10 segmental duplication events. Based on phylogenetic characteristics, ZmWOXs are divided into three clades (e.g., WUS, intermediate, and ancient groups), and the majority of ZmWOXs in same group display similar gene and protein structures. Cross-species collinearity results indicated that some WOX genes might be evolutionarily conservative. The promoter region of ZmWOX family members is enriched in light, plant growth/hormone, and abiotic stress-responsive elements. Tissue-specific expression evaluation showed that ZmWOX genes might play a significant role in the occurrence of maize reproductive organs. Transcriptome data and RT-qPCR analysis further showed that six ZmWOX genes (e.g., ZmWOX1, 4, 6, 13, 16, and 18) were positively or negatively modulated by temperature, salt, and waterlogging stresses. Moreover, two ZmWOXs, ZmWOX1 and ZmWOX18, both were upregulated by abiotic stress. ZmWOX18 was localized in the nucleus and had transactivation activities, while ZmWOX1 was localized in both the cytoplasm and nucleus, without transactivation activity. Overall, this work offers new perspectives on the evolutionary relationships of ZmWOX genes and might provide a resource for further detecting the biological functions of ZmWOXs. Full article

Members of the WRKY transcription factor (TF) family are unique to plants and serve as important regulators of diverse physiological processes, including the ability of plants to manage biotic and abiotic stressors. However, the functions of specific WRKY family members in the context of maize responses to fungal pathogens remain poorly understood, particularly in response to Ustilago maydis (DC.) Corda (U. maydis), which is responsible for the devastating disease known as corn smut. A systematic bioinformatic approach was herein employed for the characterization of the maize WRKY TF family, leading to the identification of 120 ZmWRKY genes encoded on 10 chromosomes. Further structural and phylogenetic analyses of these TFs enabled their classification into seven different subgroups. Segmental duplication was established as a major driver of ZmWRKY family expansion in gene duplication analyses, while the Ka/Ks ratio suggested that these ZmWRKY genes had experienced strong purifying selection. When the transcriptional responses of these genes to pathogen inoculation were evaluated, seven U. maydis-inducible ZmWRKY genes were identified, as validated using a quantitative real-time PCR approach. All seven of these WKRY proteins were subsequently tested using a yeast one-hybrid assay approach, which revealed their ability to directly bind the ZmSWEET4b W-box element, thereby controlling the U. maydis-inducible upregulation of ZmSWEET4b. These results suggest that these WRKY TFs can control sugar transport in the context of fungal infection. Overall, these data offer novel insight into the evolution, transcriptional regulation, and functional characteristics of the maize WRKY family, providing a basis for future research aimed at exploring the mechanisms through which these TFs control host plant responses to common smut and other fungal pathogens. Full article

Ear diameter (ED) is a critical component of grain yield (GY) in maize (Zea mays L.). Studying the genetic basis of ED in maize is of great significance in enhancing maize GY. Against this backdrop, this study was framed to (1) map the ED-related quantitative trait locus (QTL) and SNPs associated with ED; and (2) identify putative functional genes that may affect ED in maize. To accomplish this, an elite maize inbred line, Ye107, which belongs to the Reid heterotic group, was used as a common parent and crossed with seven elite inbred lines from three different heterotic groups (Suwan1, Reid, and nonReid) that exhibited abundant genetic variation in ED. This led to the construction of a multi-parent population consisting of 1215 F₇ recombinant inbred lines (F₇RILs). A genome-wide association study (GWAS) and linkage analysis were then conducted for the multi-parent population using 264,694 high-quality SNPs generated via the genotyping-by-sequencing method. Our study identified a total of 11 SNPs that were significantly associated with ED through the GWAS, and three QTLs were revealed by the linkage analysis for ED. The major QTL on chromosome 1 was co-identified in the region by the GWAS at SNP_143985532. SNP_143985532, located upstream of the Zm00001d030559 gene, encodes a callose synthase that is expressed in various tissues, with the highest expression level in the maize ear primordium. Haplotype analysis indicated that the haplotype B (allele AA) of Zm00001d030559 was positively correlated with ED. The candidate genes and SNPs identified in this study provide crucial insights for future studies on the genetic mechanism of maize ED formation, cloning of ED-related genes, and genetic improvement of ED. These results may help develop important genetic resources for enhancing maize yield through marker-assisted breeding. Full article

In maize (Zea mays), fungal-elicited immune responses include the accumulation of terpene synthase (TPS) and cytochrome P450 monooxygenases (CYP) enzymes resulting in complex antibiotic arrays of sesquiterpenoids and diterpenoids, including α/β-selinene derivatives, zealexins, kauralexins and dolabralexins. To uncover additional antibiotic families, we conducted metabolic profiling of elicited stem tissues in mapping populations, which included B73 × M162W recombinant inbred lines and the Goodman diversity panel. Five candidate sesquiterpenoids associated with a chromosome 1 locus spanning the location of ZmTPS27 and ZmTPS8. Heterologous enzyme co-expression studies of ZmTPS27 in Nicotiana benthamiana resulted in geraniol production while ZmTPS8 yielded α-copaene, δ-cadinene and sesquiterpene alcohols consistent with epi-cubebol, cubebol, copan-3-ol and copaborneol matching the association mapping efforts. ZmTPS8 is an established multiproduct α-copaene synthase; however, ZmTPS8-derived sesquiterpene alcohols are rarely encountered in maize tissues. A genome wide association study further linked an unknown sesquiterpene acid to ZmTPS8 and combined ZmTPS8-ZmCYP71Z19 heterologous enzyme co-expression studies yielded the same product. To consider defensive roles for ZmTPS8, in vitro bioassays with cubebol demonstrated significant antifungal activity against both Fusarium graminearum and Aspergillus parasiticus. As a genetically variable biochemical trait, ZmTPS8 contributes to the cocktail of terpenoid antibiotics present following complex interactions between wounding and fungal elicitation. Full article

The ontogenesis and yield formation in crop plants are modified by environmental conditions. Due to climatic change detected over two decades, the harmful influence of abiotic factors is increasing. One of the most threatening issues reducing plant productivity is drought stress. The strength of plant response to water shortages could differ depending on the strength of the drought stress, type of crop, genetic background, presence of additional stresses, and stage of plant development. There are examples of sexual hybridization between crop plants like oat (Avena sativa L.) and maize (Zea mays L.) with which stable fertile hybrids were generated. Additional maize chromosomes in oat plants (oat × maize addition, OMA) often infer morphological and physiological (e.g., PS II photosystem activity and chlorophyll production) changes modulated by the interaction of certain maize chromosomes added to the oat genome. The aim of the research was to evaluate the chosen physiological, biochemical, and agronomic parameters of OMA plants subjected to soil drought. Analysis of variance indicated that the main effects of genotype as well as treatment × genotype interaction were significant for all the traits studied (photosynthetic pigment content, selected PSII indices, mass of stem, number of grains/plant, mass of grains/plant). Most of the examined lines severely reduced PSII photosystem parameters, pigment content, and yield-related traits under drought stress. The results indicated that two lines (9 and 78b) retained high yielding potential under drought stress compared to commercial cv. Bingo. Full article

Subtilisin-like proteases (subtilases) are found in almost all plant species and are involved in regulating various biotic and abiotic stresses. Although the literature on subtilases in different plant species is vast, the gene function of the serine peptidase S8 family and its maize subfamily is still unknown. Here, a bioinformatics analysis of this gene family was conducted by describing gene structure, conserved motifs, phylogenetic relationships, chromosomal distributions, gene duplications, and promoter cis-elements. In total, we identified 18 ZmSPS8 genes in maize, distributed on 7 chromosomes, and half of them were hydrophilic. Most of these proteins were located at the cell wall and had similar secondary and tertiary structures. Prediction of cis-regulatory elements in promoters illustrated that they were mainly associated with hormones and abiotic stress. Maize inbred lines B73, Zheng58, and Qi319 were used to analyze the spatial-temporal expression patterns of ZmSPS8 genes under drought treatment. Seedling drought results showed that Qi319 had the highest percent survival after 14 d of withholding irrigation, while B73 was the lowest. Leaf relative water content (LRWC) declined more rapidly in B73 and to lower values, and the nitrotetrazolium blue chloride (NBT) contents of leaves were higher in Qi319 than in the other inbreds. The qPCR results indicated that 6 serine peptidase S8 family genes were positively or negatively correlated with plant tolerance to drought stress. Our study provides a detailed analysis of the ZmSPS8s in the maize genome and finds a link between drought tolerance and the family gene expression, which was established by using different maize inbred lines. Full article