Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) plays pivotal roles in regulating plant growth and development, mediating intercellular signal transduction, and modulating responses to environmental stresses. However, a comprehensive genome-wide identification and analysis of the CrRLK1L gene family in maize remains elusive. In this study, a total of 24 CrRLK1L genes were identified in the maize whole genome. A phylogenetic analysis further revealed that CrRLK1L proteins from Arabidopsis, rice, and maize were grouped into nine distinct subgroups, with subgroup IV being unique to maize. Gene structure analysis demonstrated that the number of introns varied greatly among ZmCrRLK1L genes. Notably, the genome-wide duplication (WGD) events promoted the expansion of the ZmCrRLK1L gene family. Compared with Arabidopsis, there were more collinear gene pairs between maize and rice. Tissue expression patterns indicated that ZmCrRLK1L genes are widely expressed in various tissues, with ZmCrRLK1L5/9 specifically highly expressed in roots, and ZmCrRLK1L8/14/16/21/22 expressed in anthers. Additionally, RNA-seq and RT-qPCR analyses revealed that the expression of ZmCrRLK1L1/2/20/22 genes exhibited different expression patterns under drought and salt stresses. In summary, our study lays a foundation for elucidating the biological roles of ZmCrRLK1L genes in maize growth and development, reproductive development, and stress responses.

Plant growth and crop yield are essentially determined by photosynthesis when considering carbon dioxide (CO₂) availability. CO₂ diffusion inside a leaf is one of the factors that dictate the CO₂ concentrations in chloroplasts. Carbonic anhydrases (CAs) are zinc-containing enzymes that interconvert CO₂ and bicarbonate ions (HCO₃⁻), which, consequently, affect CO₂ diffusion and thus play a fundamental role in all photosynthetic organisms. Recently, the great progress in the research in this field has immensely contributed to our understanding of the function of the β-type CAs; however, the analysis of α-type CAs in plants is still in its infancy. In this study, we identified and characterized the OsαCA1 gene in rice via the analysis of OsαCAs expression in flag leaves and the subcellular localization of its encoding protein. OsαCA1 encodes an α-type CA, whose protein is located in chloroplasts with a high abundance in photosynthetic tissues, including flag leaves, mature leaves, and panicles. OsαCA1 deficiency caused a significant reduction in assimilation rate, biomass accumulation, and grain yield. The growth and photosynthetic defects of the OsαCA1 mutant were attributable to the restricted CO₂ supply at the chloroplast carboxylation sites, which could be partially rescued by the application of an elevated concentration of CO₂ but not that of HCO₃⁻. Furthermore, we have provided evidence that OsαCA1 positively regulates water use efficiency (WUE) in rice. In summary, our results reveal that the function of OsαCA1 is integral to rice photosynthesis and yield potential, underscoring the importance of α-type CAs in determining plant physiology and crop yield and providing genetic resources and new ideas for breeding high-yielding rice varieties.

Dirigent (DIR) proteins play essential roles in regulating plant growth and development, as well as enhancing resistance to abiotic and biotic stresses. However, the whole-genome identification and expression profiling analysis of DIR gene family in millet (Setaria italica (Si)) have not been systematically understood. In this study, we conducted genome-wide identification and expression analysis of the S. italica DIR gene family, including gene structures, conserved domains, evolutionary relationship, chromosomal locations, cis-elements, duplication events, gene collinearity and expression patterns. A total of 38 SiDIR members distributed on nine chromosomes were screened and identified. SiDIR family members in the same group showed higher sequence similarity. The phylogenetic tree divided the SiDIR proteins into six subfamilies: DIR-a, DIR-b/d, DIR-c, DIR-e, DIR-f, and DIR-g. According to the tertiary structure prediction, DIR proteins (like SiDIR7/8/9) themselves may form a trimer to exert function. The result of the syntenic analysis showed that tandem duplication may play the major driving force during the evolution of SiDIRs. RNA-seq data displayed higher expression of 16 SiDIR genes in root tissues, and this implied their potential functions during root development. The results of quantitative real-time PCR (RT-qPCR) assays revealed that SiDIR genes could respond to the stress of CaCl₂, CdCl, NaCl, and PEG6000. This research shed light on the functions of SiDIRs in responding to abiotic stress and demonstrated their modulational potential during root development. In addition, the membrane localization of SiDIR7/19/22 was confirmed to be consistent with the forecast. The results above will provide a foundation for further and deeper investigation of DIRs.

Dirigent (DIR) members have been shown to play essential roles in plant growth, development and adaptation to environmental changes. However, to date, there has been no systematic analysis of the DIR members in the genus Oryza. Here, 420 genes were identified from nine rice species to have the conserved DIR domain. Importantly, the cultivated rice species Oryza sativa has more DIR family members than the wild rice species. DIR proteins in rice could be classified into six subfamilies based on phylogeny analysis. Gene duplication event analysis suggests that whole genome/segmental duplication and tandem duplication are the primary drivers for DIR genes’ evolution in Oryza, while tandem duplication is the main mechanism of gene family expansion in the DIR-b/d and DIR-c subfamilies. Analysis of the RNA sequencing data indicates that OsjDIR genes respond to a wide range of environmental factors, and most OsjDIR genes have a high expression level in roots. Qualitative reverse transcription PCR assays confirmed the responsiveness of OsjDIR genes to the undersupply of mineral elements, the excess of heavy metals and the infection of Rhizoctonia solani. Furthermore, there exist extensive interactions between DIR family members. Taken together, our results shed light on and provide a research foundation for the further exploration of DIR genes in rice.

Rapid Alkalization Factor (RALF) is a signaling molecule in plants that plays a crucial role in growth and development, reproductive processes, and responses to both biotic and abiotic stresses. Although RALF peptides have been characterized in Arabidopsis and rice, a comprehensive bioinformatics analysis of the ZmRALF gene family in maize is still lacking. In this study, we identified 20 RALF genes in the maize genome. Sequence alignment revealed significant structural variation among the ZmRALF family genes. Phylogenetic analysis indicates that RALF proteins from Arabidopsis, rice, and maize can be classified into four distinct clades. Duplication events suggest that the expansion of the RALF gene family in maize primarily relies on whole-genome duplication. ZmRALF genes are widely expressed across various tissues; ZmRALF1/15/18/19 are highly expressed in roots, while ZmRALF6/11/14/16 are predominantly expressed in anthers. RNA-seq and RT-qPCR demonstrated that the expression levels of ZmRALF7, ZmRALF9, and ZmRALF13 were significantly up-regulated and down-regulated in response to PEG and NaCl stresses, respectively. Overall, our study provides new insights into the role of the RALF gene family in abiotic stress.

BIG, a regulator of polar auxin transport, is necessary to regulate the growth and development of Arabidopsis. Although mutations in the BIG gene cause severe root developmental defects, the exact mechanism remains unclear. Here, we report that disruption of the BIG gene resulted in decreased quiescent center (QC) activity and columella cell numbers, which was accompanied by the downregulation of WUSCHEL-RELATED HOMEOBOX5 (WOX5) gene expression. BIG affected auxin distribution by regulating the expression of PIN-FORMED proteins (PINs), but the root morphological defects of big mutants could not be rescued solely by increasing auxin transport. Although the loss of BIG gene function resulted in decreased expression of the PLT1 and PLT2 genes, genetic interaction assays indicate that this is not the main reason for the root morphological defects of big mutants. Furthermore, genetic interaction assays suggest that BIG affects the stem cell niche (SCN) activity through the SCRSCARECROW (SCR)/SHORT ROOT (SHR) pathway and BIG disruption reduces the expression of SCR and SHR genes. In conclusion, our findings reveal that the BIG gene maintains root meristem activity and SCN integrity mainly through the SCR/SHR pathway.