Weiguang Yang

Background: Dirigent genes play crucial roles in regulating plant architecture development and responses to environmental stress. However, the pan-genomic attributes of these genes remain poorly characterized. Method: The dirigent pan-gene family was reconstructed using the public genome assemblies from the 26 maize Nested Association Mapping project founder lines. Orthogroup classification based on multiple sequence alignment revealed both core and variable family members. Evolutionary pressures were assessed through Ka/Ks ratio analysis, and promoter regions were examined for cis-acting regulatory elements. Haplotype, transcriptomic and genome-wide association study (GWAS) analyses were integrated to explore genetic diversity and functional relevance. Results: Most dirigent members were under purifying selection, whereas a subset may have undergone positive selection. Promoter analysis demonstrated enrichment of stress- and phytohormone-responsive cis-acting regulatory elements, suggesting that regulatory divergence was associated with environmental adaptation. Haplotype analysis revealed allelic diversity among heterotic clusters, potentially contributing to heterosis. Integration with public genome-wide association study datasets identified candidate genes significantly associated with plant architecture and kernel-quality-related traits. Transcriptome profiles indicated that several dirigent genes were preferentially expressed in the roots, suggesting their involvement in root development and nutrient uptake. In addition, public gene expression data showed that certain dirigent genes are induced in response to salt stress, supporting their putative roles in abiotic stress tolerance. Conclusions: These findings provide insights into the molecular mechanisms underlying dirigent gene functions and reveal candidate genes with potential utility for improving maize performance and stress resilience through molecular breeding.

Maize (Zea mays L.) is one of the most important food crops. Salt stress can hinder crop growth and development, but the molecular mechanisms underlying maize’s response to salt tolerance remain unclear. In this study, we conducted comparative transcriptome, metabolome, and physiological analyses of a salt-tolerant maize inbred line (J1285) subjected to different NaCl concentrations during the seedling stage. The results demonstrated that, with increasing salt concentration, seedling growth parameters and antioxidant enzyme activities (SOD, POD, CAT) exhibited initially increases before subsequently decreasing, peaking at 50–150 mmol/L. Transcriptome data analysis revealed that the experimental groups subjected to 50, 100, 150, and 200 mmol/L treatments had 375, 1043, 2504, and 2328 differentially expressed genes (DEGs) compared to the control group, respectively. Additionally, through GO and KEGG analysis, we found that the DEGs were primarily enriched in the MAPK signaling pathway and plant hormone signal transduction, especially the abscisic acid (ABA) signaling pathway, both of which play instrumental roles in orchestrating the maize response to salt-induced stress. Transcription factors involved in the salt stress response, including WRKY, TIFY, bZIP, and bHLH, were identified. Metabolomic data analysis revealed that the experimental groups subjected to 50, 100, 150 and 200 mmol/L treatments had 44, 335, 278, and 550 differentially expressed metabolites (DEMs) compared to the control group, respectively. The DEMs were mainly enriched in metabolic pathways and the biosynthesis of secondary metabolites. Transcriptomics and metabolomics combined analysis were performed on J1285 seedling leaves, and it was found that the co-enrichment pathways included starch and sucrose metabolism, linoleic acid metabolism, α-linolenic acid metabolism, phenylpropanoid biosynthesis pathway, etc. Collectively, these results will aid in identifying resistance genes and elucidating the molecular mechanisms underlying salt tolerance for maize.

Soil salinization, recognized globally as a significant environmental issue, can directly impact the sustainable development of agriculture worldwide. As a key crop driving the global agricultural economy, maize is particularly vulnerable to the detrimental effects of salt–alkali stress, which can impede its growth and development from germination through the seedling stages. In this study, 32 maize inbred lines were screened for saline–alkali resistance identification. We performed four treatments—200 mmol/L NaCl, 100 mmol/L Na₂CO₃, 200 mmol/L NaCl with 25 mmol/L Na₂CO₃—and distilled water (CK) served as a control with a complete randomized design. Principal component analysis and the membership function value method were employed to evaluate the salt–alkali tolerance of these lines. The results indicate complex correlations among various traits at different growth stages. The relative correlation of each index was established by measuring the key physiological indexes (germination rate, root length and seedling height) of different maize inbred lines at the germination stage and seedling stage and standardizing them via the membership function value method. Subsequently, the principal component analysis method was used to reduce the dimensions of the standardized data, and the main factors affecting maize germination and seedling growth were extracted. The salt–alkali tolerance of maize inbred lines was comprehensively evaluated, and the salt–alkali tolerance and sensitive materials of maize germination and seedling stage were identified. This study found that the coefficient of variation of each trait is relatively rich. Therefore, in the preliminary screening of breeding germplasm resources, different reference indexes can be selected according to different periods and stress conditions. The enzyme activity results revealed significant variations in enzyme activity across different treatments and materials, with changes in superoxide dismutase (SOD) and peroxidase (POD) exhibiting relative stability, thereby reflecting the physiological response mechanisms of maize under salt–alkali stress. In this study, through principal component analysis, it was found that the germ and germination factors at the germination stage of maize and the root weight, root length, and seedling development factors at the seedling stage affected its saline–alkali resistance. The root weight factor, seedling development factor, and root length factor may affect the growth and development of maize at the seedling stage. Through the comprehensive analysis of the data of the germination stage and seedling stage, it can be seen that the materials with better salt resistance are Zm4 and Zm32; the material with better alkali resistance is Zm30; the material with better salt and alkali resistance is Zm2. Through the application of comprehensive evaluation system, researchers can more effectively screen out maize germplasm resources with excellent genetic characteristics to promote maize variety improvement and genetic diversity protection.

Calmodulin (CaM) and Calmodulin-like (CML) genes are the primary families of Calcium (Ca²⁺) sensors which are found to be involved in response to various stresses. Some genes involved in Ca²⁺ signal transduction have been genome-wide characterized in various species. However, the detailed identification, characterization, and expression profilings of ZmCaM and ZmCML genes in maize remain poorly understood, especially in the response to drought stress. In this study, a total of 7 ZmCaMs and 46 ZmCMLs are identified in maize and unevenly located on 10 chromosomes. ZmCaM and ZmCML proteins are divided into 9 groups. Protein structures analysis shows that the EF-hand motif number of ZmCaMs/ZmCMLs ranges from 3 to 4 and 2 to 4, respectively. A large number of cis-regulatory elements are found in the promoter regions of ZmCaM and ZmCML genes. ZmCaM and ZmCML genes display highly diversified tissue-specific expression patterns. Furthermore, ZmCaM2, ZmCML3, ZmCML6, ZmCML8, ZmCML19, ZmCML24, ZmCML27, ZmCML28, ZmCML36, ZmCML39, and ZmCML40 are induced significantly under drought stress through RNA-seq data and RT-qPCR. Taken together, these results will help to understand the critical roles of ZmCaM and ZmCML genes played in drought resistance and provide valuable candidate genes that could be used to develop drought-resistant maize.

Key message Developing embryo and endosperm of sorghum show substantial and multifaceted differences in gene expression and alternative splicing, which are potentially relevant to heterosis. Abstract Differential regulation of gene expression and alternative splicing (AS) are major molecular mechanisms dictating plant growth and development, as well as underpinning heterosis in F1 hybrids. Here, using deep RNA-sequencing we analyzed differences in genome-wide gene expression and AS between developing embryo and endosperm, and between F1 hybrids and their pure-line parents in sorghum. We uncover dramatic differences in both gene expression and AS between embryo and endosperm with respect to gene features and functions, which are consistent with the fundamentally different biological roles of the two tissues. Accordingly, F1 hybrids showed substantial and multifaceted differences in gene expression and AS compared with their pure-line parents, again with clear tissue specificities including extents of difference, genes involved and functional enrichments. Our results provide useful transcriptome resources as well as novel insights for further elucidation of seed yield heterosis in sorghum and related crops.

Plants have evolved a series of sophisticated defense mechanisms to help them from harm. Ethylene Response Factor (ERF) plays pivotal roles in plant immune reactions, however, its underlying mechanism in maize with a defensive function to Exserohilum turcicum (E. turcicum) remains poorly understood. Here, we isolated and characterized a novel ERF transcription factor, designated ZmERF061, from maize. Phylogenetic analysis revealed that ZmERF061 is a member of B3 group in the ERF family. qRT-PCR assays showed that the expression of ZmERF061 is significantly induced by E. turcicum inoculation and hormone treatments with salicylic acid (SA) and methyl jasmonate (MeJA). ZmERF061 was proved to function as a nucleus-localized transcription activator and specifically bind to the GCC-box element. zmerf061 mutant lines resulted in enhanced susceptibility to E. turcicum via decreasing the expression of ZmPR10.1 and ZmPR10.2 and the activity of antioxidant defense system. zmerf061 mutant lines increased the expression of the SA signaling-related gene ZmPR1a and decreased the expression of the jasmonic acid (JA) signaling-related gene ZmLox1 after infection with E. turcicum. In addition, ZmERF061 could interact with ZmMPK6-1. These results suggested that ZmERF061 plays an important role in response to E. turcicum and may be useful in genetic engineering breeding.

The ethylene response factor (ERF) plays a crucial role in plant innate immunity. However, the molecular function of ERF in response to Exserohilum turcicum (E. turcicum) remains unknown in maize. In this study, a novel ERF gene, designated as ZmERF105, was firstly isolated and characterized. The ZmERF105 protein contains an APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) domain and a conserved LSPLSPHP motif in its C-terminal region. ZmERF105 protein was exclusively localized to the nucleus. ZmERF105 expression responded to E. turcicum treatment. Yeast one-hybrid and transcription activity assays revealed that ZmERF105 is an activator of transcription and binds to GCC-box elements. Over-expression of ZmERF105 was shown to increase maize resistance against E. turcicum, and erf105 mutant lines displayed opposite phenotype. Moreover, the activities of superoxide dismutase (SOD) and peroxidase (POD) in the ZmERF105 over-expression lines were markedly higher than in the wild-type maize lines (WT) after infection with E. turcicum, and were compromised in the erf105 mutant lines. Simultaneously, ZmERF105 over-expression lines enhanced the expression of several pathogenesis-related (PR) genes, including ZmPR1a, ZmPR2, ZmPR5, ZmPR10.1, and ZmPR10.2 after infection with E. turcicum. In contrast, the expression of PR genes was reduced in erf105 mutant lines. Our work reveals that ZmERF105 as a novel player of the ERF network and positively regulates the maize resistance response to E. turcicum.