Maize Genome Research Articles

An ancient origin of the naked grains of maize

Adaptation to novel environments requires genetic variation, but whether adaptation typically acts upon preexisting genetic variation or must wait for new mutations remains a fundamental question in evolutionary biology. Selection during domestication has been long used as a model to understand evolutionary processes, providing information not only on the phenotypes selected but also, in many cases, an understanding of the causal loci. For each of the causal loci that have been identified in maize, the selected allele can be found segregating in natural populations, consistent with their origin as standing genetic variation. The sole exception to this pattern is the well-characterized domestication locus tga1 (teosinte glume architecture1), which has long been thought to be an example of selection on a de novo mutation. Here, we use a large dataset of maize and teosinte genomes to reconstruct the origin and evolutionary history of tga1. We first estimated the age of tga1-maize using a genealogy-based method, finding that the allele arose approximately 42,000 to 49,000 y ago, predating the beginning of maize domestication. We also identify tga1-maize in teosinte populations, indicating that the allele can survive in the wild. Finally, we compare observed patterns of haplotype structure and mutational age distributions near tga1 with simulations, finding that patterns near tga1 in maize better resemble those generated under simulated selective sweeps on standing variation. These multiple lines of evidence suggest that maize domestication likely drew upon standing genetic variation at tga1 and cement the importance of standing variation in driving adaptation during domestication.

Pan-Genome-Wide Investigation and Expression Analysis of GATA Gene Family in Maize.

GATA is a crucial transcription factor involved in plant growth, development, and responses to abiotic stress. Therefore, identifying and exploring GATA transcription factors in maize is of significant importance. In this study, we identified 75 ZmGATA genes based on the pan-genome of maize, which includes 26 high-quality maize genomes. These consist of 58 core genes (present in all 26 lines), 12 non-essential genes (present in 2 to 23 lines), 2 near-core genes (present in 24 to 25 lines), and 3 private genes (present in only 1 line). By evaluating the Ka/Ks ratio of the ZmGATA genes in 26 maize varieties, we found that the Ka/Ks ratios of ZmGATA31, ZmGATA32, ZmGATA36, and ZmGATA9 were greater than 1, which may indicate that these four genes are under positive selection. In contrast, the Ka/Ks ratios of other ZmGATA genes were less than 1, suggesting that these genes may be under purifying selection. In the 26 maize genomes, we observed a significant difference in the expression of ZmGATA8 between varieties affected by structural variations (SVs) and those not affected. In certain varieties, SVs altered conserved structures. Additionally, we analyzed the expression levels of ZmGATA genes in different maize tissues and under abiotic stress. ZmGATA38 and ZmGATA39 were highly expressed in the endosperm, thereby influencing starch synthesis, while ZmGATA7, ZmGATA10, ZmGATA19, ZmGATA28, and ZmGATA40 were found to be associated with abiotic stress responses. These findings provide valuable new resources for functional research on ZmGATA.

Comparative evaluation of maize chromosome pretreatment using cold water and 8-hydroxyquinoline.

In this study, a more efficient and time-saving method for chromosome preparation in maize is proposed. Studying chromosomes is crucial for understanding their organization, abnormalities (such as translocations, bridges, and aneuploidy), structure, and the evolution of maize genes and genomes. While there are several valuable protocols available for chromosome preparation-for purposes like counting chromosomes and performing karyotype analysis-these methods are often time-consuming, and the proportion of metaphase cells can be low. Therefore, it is important to explore more efficient methods for preparing maize chromosomes. Pretreatment plays a crucial role in chromosome preparation. This study compared the effects of different pretreatment methods (cold pretreatment and 8-hydroxyquinoline pretreatment), varying durations of pretreatment (cold pretreatment: 6, 12, 24, and 36h; 8-hydroxyquinoline pretreatment: 0.5, 1, 2, 3, 4, and 5h), and different fixation durations (1, 2, 3, 6, 12, 16, 20, 24, and 28h) on maize chromosome preparations (Zea mays L.). The results indicated that cold pretreatment lasting over 12h yielded the most countable chromosome figures. Additionally, pretreatment with 0.006M 8-hydroxyquinoline for 2-3h showed no significant difference in the number of countable chromosome figures. However, the proportion of mitotic cells significantly decreased when treated for four or five h with 0.006M 8-hydroxyquinoline. Furthermore, there was no significant difference in the proportion of metaphase cells when fixed with Carnoy's fixative, regardless of the fixation time used. Based on these findings, a more efficient and time-saving method for chromosome preparation in maize is proposed: the root tips of maize should be pretreated with a mixture of ice and water at 4°C for 12h or with a 0.006M 8-hydroxyquinoline solution at room temperature for 3h. The root tips should then be fixed with Carnoy's fixative (composed of glacial acetic acid and absolute ethanol in a 1:3 ratio) for 1h.

The regulatory potential of transposable elements in maize.

The genomes of flowering plants consist largely of transposable elements (TEs), some of which modulate gene regulation and function. However, the repetitive nature of TEs and difficulty of mapping individual TEs by short-read sequencing have hindered our understanding of their regulatory potential. Here we show that long-read chromatin fibre sequencing (Fiber-seq) comprehensively identifies accessible chromatin regions (ACRs) and CpG methylation across the maize genome. We uncover stereotypical ACR patterns at young TEs that degenerate with evolutionary age, resulting in TE enhancers preferentially marked by a novel plant-specific epigenetic feature: simultaneous hyper-CpG methylation and chromatin accessibility. We show that TE ACRs are co-opted as gene promoters and that ACR-containing TEs can facilitate gene amplification. Lastly, we uncover a pervasive epigenetic signature-hypo-5mCpG methylation and diffuse chromatin accessibility-directing TEs to specific loci, including the loci that sparked McClintock's discovery of TEs.

Transcriptions of ACO and ACS genes are involved in nitrate-dependent root growth of maize seedlings.

Improving nitrogen use efficiency (NUE) is one of the major objectives for crop breeding. As nitrate signaling plays pivotal roles in nitrogen use of plants, factors in this pathway might be valuable for improving the NUE of maize. In this research, we performed Gene Set Enrichment Analysis (GSEA) of maize transcriptomes in response to nitrate and found that the ethylene action pathway might participate in nitrate signaling. Through a modified reciprocal best hit approach, we obtained 16 maize aminocyclopropane-1-carboxylic acid (ACC) oxidase (ACO) and four ACC synthase (ACS) homologs in maize genome. In silico analyses and the reverse transcription quantitative PCR assays demonstrated that ZmACCO7, ZmACCO5, ZmACCO15, ZmACCO35, and ZmACCO31 are the top five highly expressed ACO genes, and ZmACS1 is the most highly expressed ACS gene in the primary and seminal roots of maize. We discovered that ACO and ACS genes have different regulatory modes in response to nitrate provision. Some ACO genes, which are mainly expressed in root regions far from the root tip like ZmACCO7, are repressed by nitrate, while the others, which are mainly expressed in root regions near the root tip like ZmACCO5, are induced by nitrate. ZmACS1, which has more uniform expression across maize roots, is induced in root regions near the root tip and repressed in regions far from the root tip. A phenotypic analysis indicated that upregulation of ACO and ACS genes by nitrate is linked to repression of axial root elongation by nitrate while the downregulation of these genes is associated with the promotion of growth of lateral roots of the axial roots. In addition, differences in regulation of ACO and ACS genes by nitrate were observed between genotypes, which is related to the differences in the responses of their primary root growth to nitrate. These results suggested that the ethylene synthesis pathway is involved in the responses of maize roots to nitrate, which is associated with the remodeling of maize root architecture by nitrate.

A map of integrated cis-regulatory elements enhances gene-regulatory analysis in maize.

A map of integrated cis-regulatory elements enhances gene-regulatory analysis in maize.

Molecular Characterization of Acyl-CoA Oxidase (ACX) Family Genes in Maize Reveals Their Role in Disease Resistance.

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. 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. 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. 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. 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.

Identification and Expression Profiling of the Cytokinin Synthesis Gene Family IPT in Maize

Isopentyltransferase (IPT) is a key rate-limiting enzyme in cytokinin synthesis, playing a crucial role in plant growth, development, and response to adverse conditions. Although the IPT gene family has been studied in various plants, comprehensive identification and functional characterization of IPT genes in maize (Zea mays) remain underexplored. In this study, ten IPT gene family members (ZmIPT1–ZmIPT10) were identified in the maize genome, and their gene structure, physicochemical properties, evolutionary relationships, expression patterns, and stress response characteristics were systematically analyzed. The ZmIPT genes were found to be unevenly distributed across six chromosomes, with most proteins predicted to be basic and localized primarily in chloroplasts. Phylogenetic analysis grouped the ZmIPT family into four subfamilies, showing close evolutionary relationships with rice IPT genes. Conserved motif and gene structure analyses indicated that the family members were structurally conserved, with five collinear gene pairs being identified. Ka/Ks analysis revealed that these gene pairs underwent strong purifying selection during evolution.Cis-element analysis of promoter regions suggested that ZmIPT genes are widely involved in hormone signaling and abiotic stress responses. Tissue-specific expression profiling showed that ZmIPT5, ZmIPT7, and ZmIPT8 were highly expressed in roots, with ZmIPT5 exhibiting consistently high expression under multiple abiotic stresses. qRT-PCR validation confirmed that ZmIPT5 expression peaked at 24 h after stress treatment, indicating its key role in long-term stress adaptation. Protein interaction analysis further revealed potential interactions between ZmIPT5 and cytokinin oxidases (CKX1, CKX5), as well as FPP/GGPP synthase family proteins, suggesting a regulatory role in cytokinin homeostasis and stress adaptation. Overall, this study provides comprehensive insights into the structure and function of the ZmIPT gene family and identifies ZmIPT5 as a promising candidate for improving stress tolerance in maize through molecular breeding.

Computationally derived RNA polymerase III promoters enable maize genome editing.

CRISPR endonucleases require cognate non-coding RNA species for site-specific activity. These RNA species are typically expressed using endogenous RNA polymerase III (Pol III) promoters compatible with the host species. This study describes applications of novel Pol III promoters, which were computationally derived from a training set of monocot U6 and U3 promoters. These promoters enabled genome editing in maize protoplast cells and maize plants. Out of 37 novel promoters, 27 performed similarly to a control U6 promoter. Multiplexing five novel promoters in one construct enabled simultaneous editing of the maize genome at 27 unique sites in a single plant. Moreover, repeating the same CRISPR RNA (crRNA) with multiple novel promoters improved editing up to three-fold at a low-efficiency target site in maize plants. The ability to computationally derive novel Pol III promoters on-demand increases genome editing flexibility and efficiency in maize.

GWAS and transcriptome analyses unravel ZmGRAS15 regulates drought tolerance and root elongation in maize

BackgroundDrought is a major abiotic stress affecting maize development and growth. Unravelling the molecular mechanisms underlying maize drought tolerance and enhancing the drought tolerance of maize is of great importance. However, due to the complexity of the maize genome and the multiplicity of drought tolerance mechanisms, identifying the genetic effects of drought tolerance remains great challenging.ResultsUsing a mixed linear model (MLM) based on 362 maize inbred lines, we identified 40 associated loci and 150 candidate genes associated with survival rates. Concurrently, transcriptome analysis was conducted for five drought - tolerant and five drought - sensitive lines under Well-Watered (WW) and Water-Stressed (WS) conditions. Additionally, through co-expression network analysis (WGCNA), we identified five modules significantly associated with the leaf relative water content (RWC) under drought treatment. By integrating the results of GWAS, DEGs, and WGCNA, four candidate genes (Zm00001d006947, Zm00001d038753, Zm00001d003429 and Zm00001d003553) significantly associated with survival rate were successfully identified. Among them, ZmGRAS15 (Zm00001d003553), a GRAS transcription factor considered as a key hub gene, was selected for further functional validation. The overexpression of ZmGRAS15 in maize could significantly enhance drought tolerance through regulating primary root length at the seedling stage.ConclusionThis study provides valuable information for understanding the genetic basis of drought tolerance and gene resources for maize drought tolerance breeding.

A detailed comparative in silico and functional analysis of ccd1 gene in maize gives new insights of its expression and functions.

Biofortified maize with enhanced carotenoid content was developed to combat vitamin A deficiency. However, it was observed that during storage, carotenoids present in maize grain get degraded and it has been reported that carotenoid cleavage dioxygenase1 (ccd1) is responsible for this degradation. In our current study, comprehensive in-silico analysis deciphered a complete overview of the ccd1 gene in maize including the gene structures, phylogeny, chromosomal locations, promoter analysis, conserved motifs and interacting protein partners. In addition to these, a comparative in-silico analysis of the ccd1 gene in maize, rice and Arabidopsis was performed. An intronic region of ccd1, unique to the maize genome, was matched significantly with a lot of long non-coding RNA and was identified. Also, growth stage-specific ccd1 expression analysis was performed in two maize inbred lines, V335PV and HKI161PV. The results indicate that both inbred lines displayed higher ccd1 expression during reproductive stages compared to vegetative stages, with the highest expression level observed at the milking stage in both inbreds. This detailed in-silico characterisation and expression analysis of the ccd1 gene contributes to our understanding of its activity and expression pattern in maize in stage and tissue-specific manner. This study will further provide an effective strategy for manipulating the ccd1 gene to enhance the carotenoid content of maize grain, thereby aiding in the combat against vitamin A deficiency.

Genome-wide identification and expression profile analysis of TALE superfamily genes under hormone and abiotic stress in maize (Zea may L.).

The three-amino-acid-loop-extension (TALE) of the homeobox superfamily genes plays important roles in plant growth, development, and responses to environmental stress. Although TALE members have been identified in various species, they have not been systematically characterized in maize and their expression profiles under ABA hormone and abiotic stress are unknown. Bioinformatics methods were employed to identify the TALE family genes in the maize genome. The expression levels of ZmTALEs under ABA, salt, drought, and high temperature conditions was detected by qRT-PCR. The subcellular localization of ZmKNOX05 and ZmBELL11 proteins was observed in maize protoplasts. In this study, we identified 52 TALE members in maize, which can be divided into two subfamilies, KNOX and BELL. ZmKNOXs and ZmBELLs can be further divided into two subclasses based on the domains they contain. The protein characterizations and gene structures in the same subclass were similar, whereas they were distinct across different subclasses. There were 18 collinear gene pairs in maize genome. Inter-species evolutionary analyses showed that TALE family genes of maize were more homologous to monocotyledons than to dicotyledons. The promoter regions of ZmTALE contained abundant stress-responsive, hormone-responsive, light-responsive, and plant growth and development cis-elements. Specific spatiotemporal expression patterns analysis showed that ZmBELLs were highly expressed in root and mature leaf, whereas the ZmKNOX1 subfamily genes were more expressed in the primordium, internode, vegetative meristem, and root during developmental stages. It was found that most ZmTALEs could respond to ABA, drought, high temperature, and salt stress, indicating their roles in hormone and abiotic stress responsive. ZmKNOX05 and ZmBELL11 were cloned from B73 maize. Unexpectedly, a novel alternative transcript with a 99-base deletion for ZmKNOX05 were found, named ZmKNOX05.2, which exhibited alternative splicing event at the noncanonical site. Subcellular localization analysis revealed that ZmKNOX05.1-eGFP and ZmKNOX05.2-eGFP were localized in both the nucleus and cytoplasm, while ZmBELL11-eGFP was localized in perinuclear cytoplasm (perinuclear region of the cytoplasm). We identified TALE superfamily members in maize and conducted a comprehensive and systematic analysis. These results can lay the foundation for analysis of the functions of ZmTALE genes under ABA and abiotic stresses.

The evolution, variation and expression patterns of the annexin gene family in the maize pan-genome

Annexins (Anns) are a family of evolutionarily conserved, calcium-dependent, phospholipid-binding proteins that play critical roles in plant growth, development, and stress responses. Utilizing the pan-genome of 26 high-quality maize genomes, we identified 12 Ann genes, comprising 9 core genes (present in all 26 lines) and 3 near-core genes (present in 24–25 lines). This highlights the limitations of studying ZmAnn genes based on a single reference genome. Evaluating the Ka/Ks values of Ann genes in 26 varieties revealed that ZmAnn10 was under positive selection in certain varieties, while the remaining genes had Ka/Ks values less than 1, indicating purifying selection. Phylogenetic analysis divided ZmAnn proteins into six groups, with group VI containing only ZmAnn12. Structural variation in certain varieties altered the conserved domains, generating many atypical genes. Transcriptome analysis showed that different Ann members have distinct expression patterns in various tissues and under different abiotic and biotic stress treatments. Weighted gene co-expression network analysis of transcriptome data from various maize tissues under cold stress identified four Ann genes (ZmAnn2, ZmAnn6, ZmAnn7, ZmAnn9) involved in co-expression modules. Overall, this study utilized high-quality maize pangenomes to perform a bioinformatic analysis of ZmAnn genes, providing a foundation for further research on ZmAnn genes.

Benchmarking, detection, and genotyping of structural variants in a population of whole-genome assemblies using the SVGAP pipeline.

Comparisons of complete genome assemblies offer a direct procedure for characterizing all genetic differences among them. However, existing tools are often limited to specific aligners or optimized for specific organisms, narrowing their applicability, particularly for large and repetitive plant genomes. Here, we introduce SVGAP, a pipeline for structural variant (SV) discovery, genotyping, and annotation from high-quality genome assemblies at the population level. Through extensive benchmarks using simulated SV datasets at individual, population, and phylogenetic contexts, we demonstrate that SVGAP performs favorably relative to existing tools in SV discovery. Additionally, SVGAP is one of the few tools to address the challenge of genotyping SVs within large assembled genome samples, and it generates fully genotyped VCF files. Applying SVGAP to 26 maize genomes revealed hidden genomic diversity in centromeres, driven by abundant insertions of centromere-specific LTR-retrotransposons. The output of SVGAP is well-suited for pan-genome construction and facilitates the interpretation of previously unexplored genomic regions.

The regulatory potential of transposable elements in maize

The genomes of flowering plants consist largely of transposable elements (TEs), some of which modulate gene regulation and function. However, the repetitive nature of TEs and difficulty of mapping individual TEs by short-read-sequencing have hindered our understanding of their regulatory potential. We demonstrate that long-read chromatin fiber sequencing (Fiber-seq) comprehensively identifies accessible chromatin regions (ACRs) and CpG methylation across the maize genome. We uncover stereotypical ACR patterns at young TEs that degenerate with evolutionary age, resulting in TE-enhancers preferentially marked by a novel plant-specific epigenetic feature: simultaneous hyper-CpG methylation and chromatin accessibility. We show that TE ACRs are co-opted as gene promoters and that ACR-containing TEs can facilitate gene amplification. Lastly, we uncover a pervasive epigenetic signature – hypo-5mCpG methylation and diffuse chromatin accessibility – directing TEs to specific loci, including the loci that sparked McClintock’s discovery of TEs.

Expression divergence of BAG gene family in maize under heat stress

Heat stress poses a significant challenge for maize production, especially during the spring when high temperatures disrupt cellular processes, impeding plant growth and development. The B-cell lymphoma-2 (Bcl-2) associated athanogene (BAG) gene family is known to be relatively conserved across various species. It plays a crucial role as molecular chaperone cofactors that are responsible for programmed cell death and tumorigenesis. Once the plant is under heat stress, the BAG genes act as co-chaperones and modulate the molecular functions of HSP70/HSC70 saving the plant from the damage of high temperature stress. The study was planned to identify and characterize the BAG genes for heat stress responsiveness in maize. Twenty-one (21) BAG genes were identified in the latest maize genome. The evolutionary relationship of Zea mays BAGs (ZmBAGs) with Arabidopsis thaliana, Solanum lycopersicum, Theobroma cacao, Sorghum bicolor, Ananas comosus, Physcomitrium patens, Oryza sativa and Populus trichocarpa were represented by the phylogenetic analysis. Differential expressions of BAG gene family in leaf, endosperm, anther, silk, seed and developing embryo depict their contribution to the growth and development. The in-silico gene expression analysis indicated ZmBAG-8 (Zm00001eb170080), and ZmBAG-11 (Zm00001eb237960) showed higher expression under abiotic stresses (cold, heat and salinity). The RT-qPCR further confirmed the expression of ZmBAG-8 and ZmBAG-11 in plant leaf tissue across the contrasting inbred lines and their F1 hybrid (DR-139, UML-1 and DR-139 × UML-1) when exposed to heat stress. Furthermore, the protein-protein interaction networks of ZmBAG-8 and ZmBAG-11 further elucidated their role in stress tolerance related pathways. This research offers a roadmap to plan functional research and utilize ZmBAG genes to enhance heat tolerance in grasses.

Meta-QTL analysis for mining of candidate genes and constitutive gene network development for viral disease resistance in maize (Zea mays L.).

Meta-QTL analysis for mining of candidate genes and constitutive gene network development for viral disease resistance in maize (Zea mays L.).

MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.

Modern maize (Zea mays ssp. mays) was domesticated from Teosinte parviglumis (Zea mays ssp. parviglumis), with subsequent introgressions from Teosinte mexicana (Zea mays ssp. mexicana), yielding increased kernel row number, loss of the hard fruit case and dissociation from the cob upon maturity, as well as fewer tillers. Molecular approaches have identified transcription factors controlling these traits, yet revealed that a complex regulatory network is at play. MaizeCODE deploys ENCODE strategies to catalog regulatory regions in the maize genome, generating histone modification and transcription factor ChIP-seq in parallel with transcriptomics datasets in 5 tissues of 3 inbred lines which span the phenotypic diversity of maize, as well as the teosinte inbred TIL11. Transcriptomic analysis reveals that pollen grains share features with endosperm, and express dozens of "proto-miRNAs" potential vestiges of gene drive and hybrid incompatibility. Integrated analysis with chromatin modifications results in the identification of a comprehensive set of regulatory regions in each tissue of each inbred, and notably of distal enhancers expressing non-coding enhancer RNAs bi-directionally, reminiscent of "super enhancers" in animal genomes. Furthermore, the morphological traits selected during domestication are recapitulated, both in gene expression and within regulatory regions containing enhancer RNAs, while highlighting the conflict between enhancer activity and silencing of the neighboring transposable elements.

Genome-Wide Association Analysis Identifies Loci and Candidate Genes for 100-Kernel Weight in Maize

Maize is an important food crop, and 100-kernel weight (HKW) is one of the three key components of yield. In this study, 200 maize inbred lines were used as the material, and HKW was evaluated over three consecutive years in two environments. A genome-wide association study (GWAS) was conducted using the Blink and FarmCPU models with 44,935 SNP markers evenly distributed across the maize genome. A total of 25 SNPs significantly associated with HKW were identified, with three SNPs detected in both models. Six significant SNPs were located within previously mapped QTL bins associated with grain weight. In the linkage disequilibrium (LD) regions of the significant SNP loci, 198 candidate genes were identified, of which 74 had annotation information. Further analysis revealed 21 candidate genes related to HKW, such as GRMZM2G010555 (alternative oxidase), GRMZM2G102471 (ubiquitin-conjugating enzyme), GRMZM2G060669 (histone deacetylase), GRMZM2G090156 (methyltransferase), GRMZM2G002075 (BZIP transcription factor), and GRMZM2G138454 (bHLH transcription factor). The SNP loci and candidate genes identified in this study provide important references for marker-assisted selection, fine mapping, and gene cloning related to HKW in maize.

Research on the Application of Maize Genome Editing Technology in High-yield Breeding

With the continuous growth of global population, there is an increasing demand for high-yield crops, and how to improve the yield of maize, as an important food and feed crop, has become one of the important directions of agricultural research. Although traditional breeding techniques have made progress in improving high-yield traits in maize, their long cycle time and low efficiency make it difficult to meet the rapidly growing production demand. The emergence of genome editing technologies, especially the CRISPR/Cas9 system, has brought new opportunities for maize high-yield breeding. This paper systematically reviews the application of genome editing technology in maize breeding, focusing on the methods of target gene screening, optimization of editing tools and evaluation of high-yield traits, and describes the research results of the current technology in enhancing maize yield. The potential application value of novel editing tools in the maize genome editing process in future efficient breeding was analyzed. This study provides theoretical support and technical guidance for the use of genome editing technology to realize the precise improvement of high-yield traits in maize.