The genome-wide characterization of WOX gene family in Phaseolus vulgaris L. during salt stress

Transcription factor WUSCHEL-related homeobox (WOX) underground revelations: Insights into plant root development

Plant roots are essential for nutrient and water uptake and play a crucial role in plant growth and development. The development of roots is a complex process regulated by numerous factors, among which transcription factors (TFs) like WUSCHEL-related homeobox (WOX) have an essential function. The importance of WOXs in root development cannot be overstated. They act as key regulators in maintaining the balance between cell proliferation and differentiation and ensure the proper formation and function of root tissues. This review comprehensively presents the roles of WOXs in various root development aspects across multiple plant species, including primary, lateral, adventitious, and crown root development, as well as root hair, rhizoid formation, de novo root regeneration, and root apical meristem maintenance. We also discuss how WOXs regulate root development through various mechanisms in different plant species. Overall, this review provides comprehensive insights into the complex regulatory networks governing plant root growth and the importance of WOXs therein. Understanding WOXs in root development can help improve crop root architecture and stress tolerance and provide insights into the regulatory networks of plant root growth, contributing to plant breeding and agricultural productivity.

Genome-wide identification of the WOX gene family in Populus davidiana×P.bolleana and functional analysis of PdbWOX4 in salt resistance

WOX transcription factors (TFs) are plant specific transcription regulatory factors that have a momentous role in maintaining plant growth and development and responding to abiotic stress. In this study, a total of 13 PdbWOX genes were identified. qRT-PCR analyses showed that 13 PdbWOX genes were responsive to salt stress. Notably, the expression of PdbWOX4 was significantly changed at all time points under NaCl stress, suggesting that PdbWOX4 expression may be involved in salt stress. Further, an overexpression vector of PdbWOX4 was constructed and transient transformed into Shanxin poplar. Biochemical staining and physiological parameter analysis showed that overexpression of PdbWOX4 decreased the total antioxidant capacity (T-AOC) and peroxidase (POD) activity, which in turn reduced the scavenging capacity of reactive oxygen species (ROS), and increased the cell damage and death induced by salt stress. qRT-PCR and ChIP-PCR demonstrated that PdbWOX4 can regulate the expression of PdbDREB2C by binding to its promoter. Further analyses revealed that overexpression of PdbDREB2C can reduce cellular damage by increasing ROS scavenging capacity thereby improving salt tolerance in Shanxin poplar. Taken together, we found that PdbWOX4 negatively regulated the salt tolerance of Shanxin poplar by repressing the PdbDREB2C, suggesting that PdbWOX4 may play a key role in the tolerance of Shanxin poplar to salt stress, and is an important candidate gene for molecular resistance breeding in forest trees.

Genome-wide identification of WOX family members in rose and functional analysis of RcWUS1 in embryogenic transformation

WUSCHEL-related homeobox (WOX) is a class of plant-specific transcription factors and plays vital roles in plant development and evolution. Here, we analyzed WOX family genes of three Rosa species and explored their potential functions in Rosa. A total of 351 WOX genes were identified from Rosa chinensis 'Old Blush' (208), Rosa wichuraiana 'Basye's Thornless' (21) and Rosa rugosa (122). The WOX genes were found to significantly expand in Rosa compared to Arabidopsis. Phylogenetic analysis showed that Rosa WOXs genes were classified into an ancient clade, an intermediate clade, and a WUS clade. Collinearity analysis suggested that gene duplication and purifying selection might be important driving forces in the evolution of WOXs. Expression patterns of WOXs found that higher levels of RcWUS1 expression were detected at the shoot apex somatic embryos. Furthermore, we found that RcWUS1 was a transcriptional repressor located in the nucleus. Overexpression of RcWUS1 enhanced the regeneration efficiency of somatic embryos. In summary, our results indicated the functional potential of RcWUS1 in embryogenic transformation, which can be further utilized to improve the genetic transformation efficiency in rose.

Telomere-to-telomere genome of common bean (Phaseolus vulgaris L., YP4)

BACKGROUND

Common bean is a significant grain legume in human diets. However, the lack of a complete reference genome for common beans has hindered efforts to improve agronomic cultivars.

FINDINGS

Herein, we present the first telomere-to-telomere (T2T) genome assembly of common bean (Phaseolus vulgaris L., YP4) using PacBio High-Fidelity reads, ONT ultra-long sequencing, and Hi-C technologies. The assembly resulted in a genome size of 560.30 Mb with an N50 of 55.11 Mb, exhibiting high completeness and accuracy (BUSCO score: 99.5%, quality value (QV): 54.86). The sequences were anchored into 11 chromosomes, with 20 of 22 telomeres identified, leading to the formation of 9 T2T pseudomolecules. Furthermore, we identified repetitive elements accounting for 61.20% of the genome and predicted 29,925 protein-coding genes. Phylogenetic analysis suggested an estimated divergence time of approximately 11.6 million years ago between P. vulgaris and Vigna angularis. Comparative genome analysis revealed the expanded gene families and variations between YP4 and G19833 associated with defense response.

CONCLUSIONS

The T2T reference genome and genomic insights presented here are crucial for future genetic studies not only in common bean but also in other legumes.

Global Analysis of the WOX Transcription Factor Family in Akebia trifoliata

Akebia trifoliata is an economically important, self-incompatible fruit tree in the Lardizabalaceae family. Asexual propagation is the main strategy used to maintain excellent agronomic traits. However, the generation of adventitious roots during asexual propagation is very difficult. To study the important role of the WUSCHEL-related homeobox (WOX) transcription factor in adventitious root growth and development, we characterized this transcription factor family in the whole genome of A. trifoliata. A total of 10 AktWOXs were identified, with the following characteristics: length (657~11,328 bp), exon number (2~5), isoelectric point (5.65~9.03), amino acid number (176~361 AA) and molecular weight (20.500~40.173 kDa), and their corresponding expression sequence could also be detectable in the public transcriptomic data for A. trifoliata fruit. A total of 10 AktWOXs were classified into modern (6), intermediate (2) and ancient clades (2) and all AktWOXs had undergone strong purifying selection during evolution. The expression profile of AktWOXs during A. trifoliata adventitious root formation indicated that AktWOXs play an important role in the regulation of adventitious root development. Overall, this is the first study to identify and characterize the WOX family in A. trifoliata and will be helpful for further research on A. trifoliata adventitious root formation.

Identification of WUSCHEL-related homeobox gene and truncated small peptides in transformation efficiency improvement in Eucalyptus

BACKGROUND

The WUSCHEL-related Homeobox (WOX) genes, which encode plant-specific homeobox (HB) transcription factors, play crucial roles in regulating plant growth and development. However, the functions of WOX genes are little known in Eucalyptus, one of the fastest-growing tree resources with considerable widespread cultivation worldwide.

RESULTS

A total of nine WOX genes named EgWOX1-EgWOX9 were retrieved and designated from Eucalyptus grandis. From the three divided clades marked as Modern/WUS, Intermediate and Ancient, the largest group Modern/WUS (6 EgWOXs) contains a specific domain with 8 amino acids: TLQLFPLR. The collinearity, cis-regulatory elements, protein-protein interaction network and gene expression analysis reveal that the WUS proteins in E. grandis involve in regulating meristems development and regeneration. Furthermore, by externally adding of truncated peptides isolated from WUS specific domain, the transformation efficiency in E. urophylla × E. grandis DH32-29 was significant enhanced. The transcriptomics data further reveals that the use of small peptides activates metabolism pathways such as starch and sucrose metabolism, phenylpropanoid biosynthesis and flavonoid biosynthesis.

CONCLUSIONS

Peptides isolated from WUS protein can be utilized to enhance the transformation efficiency in Eucalyptus, thereby contributing to the high-efficiency breeding of Eucalyptus.

Comprehensive in silico analysis of the underutilized crop tef (Eragrostis tef (Zucc.) Trotter) genome reveals drought tolerance signatures

BACKGROUND

Tef (Eragrostis tef) is a C4 plant known for its tiny, nutritious, and gluten-free grains. It contains higher levels of protein, vitamins, and essential minerals like calcium (Ca), iron (Fe), copper (Cu), and zinc (Zn) than common cereals. Tef is cultivated in diverse ecological zones under diverse climatic conditions. Studies have shown that tef has great diversity in withstanding environmental challenges such as drought. Drought is a major abiotic stress severely affecting crop productivity and becoming a bottleneck to global food security. Here, we used in silico-based functional genomic analysis to identify drought-responsive genes in tef and validated their expression using quantitative RT-PCR.

RESULTS

We identified about 729 drought-responsive genes so far reported in six crop plants, including rice, wheat, maize, barley, sorghum, pearl millet, and the model plant Arabidopsis, and reported 20 genes having high-level of GO terms related to drought, and significantly enriched in several biological and molecular function categories. These genes were found to play diverse roles, including water and fluid transport, resistance to high salt, cold, and drought stress, abscisic acid (ABA) signaling, de novo DNA methylation, and transcriptional regulation in tef and other crops. Our analysis revealed substantial differences in the conserved domains of some tef genes from well-studied rice orthologs. We further analyzed the expression of sixteen tef orthologs using quantitative RT-PCR in response to PEG-induced osmotic stress.

CONCLUSIONS

The findings showed differential regulation of some drought-responsive genes in shoots, roots, or both tissues. Hence, the genes identified in this study may be promising candidates for trait improvement in crops via transgenic or gene-editing technologies.

Genome-Wide Identification and Characterization Analysis of WUSCHEL-Related Homeobox Family in Melon (Cucumis melo L.)

WUSCHEL-related homeobox (WOX) proteins are very important in controlling plant development and stress responses. However, the WOX family members and their role in response to abiotic stresses are largely unknown in melon (Cucumis melo L.). In this study, 11 WOX (CmWOX) transcript factors with conserved WUS and homeobox motif were identified and characterized, and subdivided into modern clade, ancient clade and intermediate clade based on bioinformatic and phylogenetic analysis. Evolutionary analysis revealed that the CmWOX family showed protein variations in Arabidopsis, tomato, cucumber, melon and rice. Alignment of protein sequences uncovered that all CmWOXs had the typical homeodomain, which consisted of conserved amino acids. Cis-element analysis showed that CmWOX genes may response to abiotic stress. RNA-seq and qRT-PCR results further revealed that the expression of partially CmWOX genes are associated with cold and drought. CmWOX13a and CmWOX13b were constitutively expressed under abiotic stresses, CmWOX4 may play a role in abiotic processes during plant development. Taken together, this study offers new perspectives on the CmWOX family's interaction and provides the framework for research on the molecular functions of CmWOX genes.

Induction of Somatic Embryogenesis in Plants: Different Players and Focus on WUSCHEL and WUS-RELATED HOMEOBOX (WOX) Transcription Factors

In plants, other cells can express totipotency in addition to the zygote, thus resulting in embryo differentiation; this appears evident in apomictic and epiphyllous plants. According to Haberlandt's theory, all plant cells can regenerate a complete plant if the nucleus and the membrane system are intact. In fact, under in vitro conditions, ectopic embryos and adventitious shoots can develop from many organs of the mature plant body. We are beginning to understand how determination processes are regulated and how cell specialization occurs. However, we still need to unravel the mechanisms whereby a cell interprets its position, decides its fate, and communicates it to others. The induction of somatic embryogenesis might be based on a plant growth regulator signal (auxin) to determine an appropriate cellular environment and other factors, including stress and ectopic expression of embryo or meristem identity transcription factors (TFs). Still, we are far from having a complete view of the regulatory genes, their target genes, and their action hierarchy. As in animals, epigenetic reprogramming also plays an essential role in re-establishing the competence of differentiated cells to undergo somatic embryogenesis. Herein, we describe the functions of WUSCHEL-RELATED HOMEOBOX (WOX) transcription factors in regulating the differentiation-dedifferentiation cell process and in the developmental phase of in vitro regenerated adventitious structures.