WUSCHEL-related Homeobox Research Articles

Plant Growth Regulators: An Overview of WOX Gene Family

The adaptation of plants to land requires sophisticated biological processes and signaling. Transcription factors (TFs) regulate several cellular and metabolic activities, as well as signaling pathways in plants during stress and growth and development. The WUSCHEL-RELATED HOMEOBOX (WOX) genes are TFs that are part of the homeodomain (HD) family, which is important for the maintenance of apical meristem, stem cell niche, and other cellular processes. The WOX gene family is divided into three clades: ancient, intermediate, and modern (WUS) based on historical evolution linkage. The number of WOX genes in the plant body increases as plants grow more complex and varies in different species. Numerous research studies have discovered that the WOX gene family play a role in the whole plant’s growth and development, such as in the stem, embryo, root, flower, and leaf. This review comprehensively analyzes roles of the WOX gene family across various plant species, highlighting the evolutionary significance and potential biotechnological applications in stress resistance and crop improvement.

A WUSCHEL-related homeobox transcription factor, SlWOX4, negatively regulates drought tolerance in tomato.

CRISPR/Cas9-mediated knockout of SlWOX4 gene in tomato enhances tolerance to drought stress. Drought stress is one of the major abiotic factors that seriously affects plant growth and crop yield. WUSCHEL-related homeobox (WOX) transcription factors are involved in plant growth, development and stress response. However, little is known about the role of WOX genes in drought tolerance in tomato. Here, SlWOX4, a member of the WOX family in tomato, was functionally characterized in mediating drought tolerance. SlWOX4 was homologous to Nicotiana tabacum NtWOX4 with a conserved HD domain, and was localized in the nucleus. SlWOX4 was significantly down-regulated by drought and abscisic acid (ABA) treatments. The loss-of-functionmutations of SlWOX4 produced using the CRISPR-Cas9 system in tomato improved drought tolerance by reducing water loss rate and enhancing stomatal closure. In addition, the wox4 lines exhibited reduced accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA), increased antioxidant enzyme activity, proline contents and ABA contents under drought stress. Moreover, gene editing of SlWOX4 in tomato enhanced drought tolerance by regulating the expression of genes encoding antioxidants and ABA signaling molecules. In summary, SlWOX4 gene might negatively regulate drought stress tolerance in tomato and has great potential as a drought-resistant crop-breeding target genes.

The cleavage of WOX5 by the peptidase DA1 connects cytokinin signaling and root stem cell regulation.

The root system of a plant is essential for plant growth and development because it absorbs nutrients and water from the soil. The root stem cells are maintained and replenished by the quiescent center and are essential for the formation of the specific root structure. In Arabidopsis, the WUSCHEL-RELATED HOMEOBOX 5 (WOX5) plays a key role in regulating root stem cell fate. However, which factor can directly modulate the stability of WOX5 protein remains totally unknown. Here, we report that the peptidase DA1 (LARGE IN CHINESE) interacts with and cleaves WOX5, resulting in the destabilization of WOX5. Genetic analyses support that DA1 acts through WOX5 to regulate root stem cell function. We further demonstrate that cytokinin (CK) signaling induces the accumulation of DA1 protein, thereby decreasing the abundance of WOX5 protein in the root. Consistent with these results, the mutation in DA1 increases the layers of columella stem cells and influences CK-induced differentiation of columella stem cells. Thus, our results reveal a previously unrecognized mechanism by which the cleavage of WOX5 by DA1 connects CK signaling and root stem cell function in Arabidopsis.

Mutations in the WUSCHEL-related homeobox1 gene cause an increased leaflet number in soybean

WUSCHEL-related homeobox (WOX) transcription factors play a crucial role in lateral organ development in several plant species; however, their precise functions in soybean (Glycine max [L.] Merr.) were unclear. Here, we identified two independent multi-leaflet soybean mutants, mlw48-8 and mlw48-161, from a CRISPR/Cas9-engineered mutant library in the Williams 82 background. Both mutants exhibited irregular leaf margins, and the upper leaves were narrow and almost lanceolate at maturity. Molecular analysis revealed that these are allelic mutants with independent mutations in the WUSCHEL-related homeobox1 (GmWOX1A) gene. A transcriptome analysis demonstrated that GmWOX1A modulates the expression of auxin- and leaf development–related genes. Yeast two-hybrid and split-luciferase complementation imaging assays revealed that GmWOX1A interacts with the YABBY family protein GmYAB5, providing further evidence of its potential involvement in leaf development. Notably, the mlw48-161 mutant showed an increased seed number per plant. Consequently, our study not only provides valuable insights into the role of GmWOX1A in soybean leaf development but also offers a potential strategy for high-yield breeding.

Methionine Synthase 2 Represses Stem Cell Maintenance of Arabidopsis thaliana in Response to Salt Stress.

Salt stress represses the growth and development of plants that mainly depend on the continual propagation and differentiation of stem cells. WUSCHEL (WUS)/WUSCHEL-RELATED HOMEOBOX (WOX) family proteins determine stem cell fate in plants under ever-changing environments. It is not yet known how plant stem cell homeostasis is regulated under salt stress. Methionine synthase catalyzes the formation of methionine by methylating homocysteine in the one-carbon metabolism pathway. In this work, we investigated the role of Arabidopsis METHIONINE SYNTHASE 2 (AtMS2) in stem cell homeostasis under salt stress. The results showed that AtMS2 represses the stem cell maintenance of Arabidopsis in response to salt stress. Under normal growth conditions, AtMS2 is mainly localized in the cytoplasm. However, under salt stress, it exhibits significant accumulation in the nucleus. AtMS2 interacts with the WUS/WOX protein, and, together, they repress WUS/WOX expression by binding to its promoter. The mutation in AtMS2 resulted in enhanced salt tolerance. Therefore, AtMS2 might act as a key negative regulator to repress the stem cell maintenance and growth of Arabidopsis under salt stress.

Genome mining of WOX-ARF gene linkage in Machilus pauhoi underpinned cambial activity associated with IAA induction.

As an upright tree with multifunctional economic application, Machilus pauhoi is an excellent choice in modern forestry from Lauraceae. The growth characteristics is of great significance for its molecular breeding and improvement. However, there still lack the information of WUSCHEL-related homeobox (WOX) and Auxin response factor (ARF) gene family, which were reported as specific transcription factors in plant growth as well as auxin signaling. Here, a total of sixteen MpWOX and twenty-one MpARF genes were identified from the genome of M. pauhoi. Though member of WOX conserved in the Lauraceae, MpWOX and MpARF genes were unevenly distributed on 12 chromosomes as a result of region duplication. These genes presented 45 and 142 miRNA editing sites, respectively, reflecting a potential post-transcriptional restrain. Overall, MpWOX4, MpWOX13a, MpWOX13b, MpARF6b, MpARF6c, and MpARF19a were highly co-expressed in the vascular cambium, forming a working mode as WOX-ARF complex. MpWOXs contains typical AuxRR-core and TGA-element cis-acting regulatory elements in this auxin signaling linkage. In addition, under IAA and NPA treatments, MpARF2a and MpWOX1a was highly sensitive to IAA response, showing significant changes after 6 hours of treatment. And MpWOX1a was significantly inhibited by NPA treatment. Through all these solid analysis, our findings provide a genetic foundation to growth mechanism analysis and further molecular designing breeding in Machilus pauhoi.

Genome-Wide Analysis of the WOX Family and Its Expression Pattern in Root Development of Paeonia ostii.

Tree peony (Paeonia suffruticosa Andr.) is a woody plant with high ornamental, medicinal, and oil values. However, its low rooting rate and poor rooting quality are bottleneck issues in the micropropagation of P. ostii. The WUSCHEL-related homeobox (WOX) family plays a crucial role in root development. In this study, based on the screening of the genome and root transcriptome database, we identified ten WOX members in P. ostii. Phylogenetic analysis revealed that the ten PoWOX proteins clustered into three major clades, the WUS, intermediate, and ancient clade, respectively. The conserved motifs and tertiary structures of PoWOX proteins located in the same clade exhibited higher similarity. The analysis of cis-regulatory elements in the promoter indicated that PoWOX genes are involved in plant growth and development, phytohormones, and stress responses. The expression analysis revealed that PoWOX genes are expressed in distinct tissues. PoWOX4, PoWOX5, PoWOX11, and PoWOX13b are preferentially expressed in roots at the early stage of root primordium formation, suggesting their role in the initiation and development of roots. These results will provide a comprehensive reference for the evolution and potential function of the WOX family and offer guidance for further study on the root development of tree peony.

Evolutionary analysis of genes from WOX family and their expression profile in grape (Vitis vinifera) under different stresses.

The WUSCHEL-related homeobox (WOX) transcription factor family plays critical roles in plant growth, development, and stress adaptation, but the biological functions in response to various stress of the WOX gene family have not been extensively researched in grapevine (Vitis vinifera ). In this study, 12 grapevine WOXs were identified from the grapevine genome. Quantitative PCR and microarray expression profiling found that the expression of WOXs had an obvious tissue-specific pattern. Conjoint analysis between various tissues and treated materials indicated VvWUS1 expression is associated with expression of genes from grapevine rupestris stem pitting-associated virus; and VvWOX3 with grapevine fanleaf virus. The gene expression patterns of the WOXs in grape were different under salt stress, with VvWOX8/9 , VvWUS1 , and VvWOX3 responding more strongly to salt stress than control by 18.20-, 9.50-, and 9.19-fold. This study further improves understanding of the evolution and function of the WOX gene family, and offers a theoretical framework and reference for breeding grapevine to better tolerate adversity and permit cultivation of seedlings free of viruses.

PaWOX3 and PaWOX3B Regulate Flower Number and the Lip Symmetry of Phalaenopsis.

The standout characteristic of the orchid perianth is the transformation of the upper median petal into a distinctively formed lip, which gives orchid flowers their typically zygomorphic symmetry and makes them the most popular ornamental plants worldwide. To study orchid flower development, two WUSCHEL-related homeobox (WOX) genes, PaWOX3 and PaWOX3B, were identified in Phalaenopsis. PaWOX3 and PaWOX3B mRNAs accumulate abundantly during early reproductive development and perianths of young buds, significantly decreasing in mature flowers and absent in vegetative leaves and roots. PaWOX3 and PaWOX3B virus-induced gene silencing (VIGS) knockdown in Phalaenopsis significantly reduces floral bud numbers, suggesting that PaWOX3/PaWOX3B may be involved in flower initiation. Transgenic Arabidopsis ectopically expressing repressor forms of PaWOX3/PaWOX3B and their Oncidium ortholog, OnPRS, exhibit lateral organ development defects, implicating these genes likely have function in regulating growth and differentiation for lateral organs. Neither PaWOX3, PaWOX3B single nor PaWOX3/PaWOX3B double VIGS Phalaenopsis altered the flower morphology. Interestingly, double silencing of PaWOX3 or PaWOX3B with OAGL6-2, which controlled the identity/formation of lips, altered the symmetry of 'BigLip' produced in OAGL6-2 VIGS. This result indicated that the levels of PaWOX3/PaWOX3B are still sufficient to maintain the symmetry for the OAGL6-2 VIGS 'BigLip'. However, the symmetry of the OAGL6-2 VIGS 'BigLip' cannot be maintained once the expression of PaWOX3 or PaWOX3B is further reduced. Thus, in addition to controlling lip identity, this study further found that OAGL6-2 could cooperate with functionally redundant PaWOX3/PaWOX3B in maintaining the symmetric axis of lip.

Ectopic expression of OsWOX9A alters leaf anatomy and plant architecture in rice.

Ectopic expression of OsWOX9A induces narrow adaxially rolled rice leaves with larger bulliform cells and fewer large veins, probably through regulating the expression of auxin-related and expansin genes. The WUSCHEL-related homeobox (WOX) family plays a pivotal role in plant development by regulating genes involved in various aspects of growth and differentiation. OsWOX9A (DWT1) has been linked to tiller growth, uniform plant growth, and flower meristem activity. However, its impact on leaf growth and development in rice has not been studied. In this study, we investigated the biological role of OsWOX9A in rice growth and development using transgenic plants. Overexpression of OsWOX9A conferred narrow adaxially rolled rice leaves and altered plant architecture. These plants exhibited larger bulliform cells and fewer larger veins compared to wild-type plants. OsWOX9A overexpression also reduced plant height, tiller number, and seed-setting rate. Comparative transcriptome analysis revealed several differentially expressed auxin-related and expansin genes in OsWOX9A overexpressing plants, consistent with their roles in leaf and plant development. These results indicate that the ectopic expression of OsWOX9A may have multiple effects on the development and growth of rice, providing a more comprehensive picture of how the WOX9 subfamily contributes to leaf development and plant architecture.

Genome-Wide Identification of the WUSCHEL-Related Homeobox (WOX) Gene Family in Three Cymbidium Species and Expression Patterns in C. goeringii

Numerous members of the WOX gene family play pivotal roles during the processes of growth and development in many plants, as has been demonstrated. Cymbidium goeringii, Cymbidium ensifolium, and Cymbidium sinense are ornamental plants with a fascinating floral morphology that are economically important in China. However, there is limited knowledge about the members of the WOX gene family and their functions in these three Cymbidium species. Hence, the WOX genes in three Cymbidium species were identified on the ground of the genomes data of C. goeringii, C. ensifolium, and C. sinense in this study. These identified WOX genes were further studied for their physicochemical properties, evolutionary relationship, gene structure, protein structure, and cis-acting elements of promoters, as well as the expression pattern of the WOX genes in different tissues of C. goeringii. The findings revealed that eight WOX genes in C. goeringii, twelve WOX genes in C. ensifolium, and nine WOX genes were identified. These WOX genes were further subdivided into WUS, ancient, and intermediate clades. The length of the coding region ranged from 149 to 335 aa, and it was predicted that all WOX genes would be located on the cell nucleus. The promoter cis-acting elements primarily comprised stress response, phytohormone response, plant growth and development, and transcription factor elements. Furthermore, both the transcriptomic data and RT-qPCR analysis showed that most WOX genes may be involved in multiple developmental stages of C. goeringii. To sum up, these results may serve as a theoretical foundation for further study of the function analysis of WOX genes in orchids.

The WUSCHEL-related homeobox transcription factor CsWOX3 negatively regulates fruit spine morphogenesis in cucumber (Cucumis sativus L.).

Cucumber (Cucumis sativus L.) is a widely cultivated crop with rich germplasm resources, holding significant nutritional value. It also serves as an important model for studying epidermal cell fate and sex determination. Cucumbers are covered with multicellular and unbranched trichomes, including a specific type called spines found on the surface of the fruit. The presence and density of these fruit spines determine the visual quality of cucumber fruits. However, the key regulatory genes and mechanisms underlying cucumber fruit spine development remain poorly understood. In this study, we identified a WUSCHEL-related homeobox (WOX) family gene CsWOX3, which functioned as a typical transcriptional repressor and played a negative role in fruit spine development. Spatial-temporal expression analysis revealed that CsWOX3 exhibited a relatively high expression level in the cucumber female floral organs, particularly in the fruit exocarp. Knockout of CsWOX3 using CRISPR/Cas9 resulted in a significant 2-to-3-fold increase in the diameter of fruit spines base, while overexpression led to a 17% decrease in the diameter compared to the wild-type. A SQUAMOSA PROMOTER BINDING PROTEIN-LIKE transcription factor CsSPL15 could directly bind and activate the expression of CsWOX3, thereby suppressing the expression of downstream auxin-related genes, such as CsARF18. Additionally, the RING-finger type E3 ubiquitin ligase CsMIEL1-like interacted with the HD domain of CsWOX3, which might result in the ubiquitination and subsequent alteration in protein stability of CsWOX3. Collectively, our study uncovered a WOX transcription factor CsWOX3 and elucidated its expression pattern and biological function. This discovery enhances our comprehension of the molecular mechanism governing cucumber fruit spine morphogenesis.

Analysis of the potential involvement of lncRNAs in embryogenic competence of Solanum betaceum Cav. (tamarillo) calli

Somatic embryogenesis (SE) is a process by which somatic cells reprogram, acquire totipotency and embark on embryo formation. Although SE is a valuable tool for micropropagation in many crops, it presents specific challenges in woody species due to some bottlenecks, such as loss of embryogenic competence during subcultures and the often-low somatic embryo conversion into plantlets. Hence, great interest exists in exploring the regulatory networks involved on SE. As transcription modulators, long non-coding RNAs (lncRNAs) have been found essential in a wide range of biological processes. This work aimed to identify lncRNAs related to the embryogenic competence in Solanum betaceum Cav. (tamarillo). Nanopore® long-read sequencing was conducted in cell lines with distinct cell fates and, based on their coding potential, 60 transcripts were selected as lncRNA candidates. Similar expression patterns were found among embryogenic cell lines (EC) and cells that lost their embryogenic potential (herein long-term callus, LTC), whereas non-EC (NEC) showed differentially expressed lncRNAs. Whereas lncRNAs upregulated in EC and LTC were predicted to target embryogenesis-related genes, such as AGAMOUS-like 15 and WUSCHEL-related HOMEOBOX 2, lncRNAs upregulated in NEC were predicted to target mainly genes involved in carbohydrate metabolism, cell wall formation, auxin and ethylene signalling pathways. Altogether, these results show the involvement of lncRNA in the process of somatic embryogenesis in S. betaceum, indicating that EC present a pattern of lncRNA expression that suggests its action on genes that directly modulate the morphogenic response in vitro, while in NEC the modulation through this type of RNAs seems to be predominantly reflected in genes more related to cellular physiology.Graphical

WUSCHEL-RELATED HOMEOBOX genes are crucial for normal vascular organization and wood formation in poplar

Vascular cambium in tree species is a cylindrical domain of meristematic cells that are responsible for producing secondary xylem (also called wood) inward and secondary phloem outward. The poplar (Populus trichocarpa) WUSCHEL (WUS)-RELATED HOMEOBOX (WOX) family members, PtrWUSa and PtrWOX13b, were previously shown to be expressed in vascular cambium and differentiating xylem cells in poplar stems, but their functions remain unknown. Here, we investigated roles of PtrWUSa, PtrWOX13b and their close homologs in vascular organization and wood formation. Expression analysis showed that like PtrWUSa and PtrWOX13b, their close homologs, PtrWUSb, PtrWUS4a/b and PtrWOX13a/c, were also expressed in vascular cambium and differentiating xylem cells in poplar stems. PtrWUSa also exhibited a high level of expression in developing phloem fibers. Expression of PtrWUSa fused with the dominant EAR repression domain (PtrWUSa-DR) in transgenic poplar caused retarded growth of plants with twisted stems and curled leaves and a severe disruption of vascular organization. In PtrWUSa-DR stems, a drastic proliferation of cells occurred in the phloem region between vascular cambium and phloem fibers and they formed islands of ectopic vascular tissues or phloem fiber-like sclerenchyma cells. A similar proliferation of cells was also observed in PtrWUSa-DR leaf petioles and midveins. On the other hand, overexpression of PtrWOX4a-DR caused ectopic formation of vascular bundles in the cortical region, and overexpression of PtrWOX13a-DR and PtrWOX13b-DR led to a reduction in wood formation without affecting vascular organization in transgenic poplar plants. Together, these findings indicate crucial roles of PtrWUSa and PtrWOX13a/b in regulating vascular organization and wood formation, which furthers our understanding of the functions of WOX genes in regulating vascular cambium activity in tree species.

WUSCHEL RELATED HOMEOBOX5 and 7 maintain callus development by promoting cell division in Arabidopsis

In tissue culture, a high concentration of auxin in the callus induction medium (CIM) stimulates cell division and subsequent callus formation, which acquires root primordium-like characteristics necessary for cell pluripotency. In Arabidopsis, WUSCHEL-RELATED HOMEOBOX5 (WOX5) and its closest homolog WOX7, which are abundant in the middle cell layer of mature callus, play a crucial role in maintaining pluripotency by promoting auxin accumulation and enhancing cytokinin sensitivity. However, the mechanism by which WOX5/7 regulate callus formation remains unclear. In this study, we found that mutations in WOX5/7 resulted in a significant down-regulation of genes involved in the G2M and S phases during callus induction. Loss-of-function mutants of WOX5/7 exhibited reduced callus formation, which was correlated with decreased expression of CYCB1;1 compared to the wild-type. Furthermore, we provided evidence that WOX5 physically interacts with PHYTOCHROME A SIGNAL TRANSDUCTION1 (PAT1), which spatio-temporally co-expresses with WOX5 in early-induced callus, and up-regulates a subset of cycle-regulating genes targeted by PAT1. Collectively, our findings suggest a critical role for the WOX5-PAT1 protein complex in regulating cell cycle progression, thereby promoting the continuous growth capacity of pluripotent callus.

The Evolution of the WUSCHEL-Related Homeobox Gene Family in Dendrobium Species and Its Role in Sex Organ Development in D. chrysotoxum.

The WUSCHEL-related homeobox (WOX) transcription factor plays a vital role in stem cell maintenance and organ morphogenesis, which are essential processes for plant growth and development. Dendrobium chrysotoxum, D. huoshanense, and D. nobile are valued for their ornamental and medicinal properties. However, the specific functions of the WOX gene family in Dendrobium species are not well understood. In our study, a total of 30 WOX genes were present in the genomes of the three Dendrobium species (nine DchWOXs, 11 DhuWOXs, and ten DnoWOXs). These 30 WOXs were clustered into ancient clades, intermediate clades, and WUS/modern clades. All 30 WOXs contained a conserved homeodomain, and the conserved motifs and gene structures were similar among WOXs belonging to the same branch. D. chrysotoxum and D. huoshanense had one pair of fragment duplication genes and one pair of tandem duplication genes, respectively; D. nobile had two pairs of fragment duplication genes. The cis-acting regulatory elements (CREs) in the WOX promoter region were mainly enriched in the light response, stress response, and plant growth and development regulation. The expression pattern and RT-qPCR analysis revealed that the WOXs were involved in regulating the floral organ development of D. chrysotoxum. Among them, the high expression of DchWOX3 suggests that it might be involved in controlling lip development, whereas DchWOX5 might be involved in controlling ovary development. In conclusion, this work lays the groundwork for an in-depth investigation into the functions of WOX genes and their regulatory role in Dendrobium species' floral organ development.

Genome-wide prediction and functional analysis of WOX genes in blueberry.

WOX genes are a class of plant-specific transcription factors. The WUSCHEL-related homeobox (WOX) family is a member of the homeobox transcription factor superfamily. Previous studies have shown that WOX members play important roles in plant growth and development. However, studies of the WOX gene family in blueberry plants have not been reported. In order to understand the biological function of the WOX gene family in blueberries, bioinformatics were used methods to identify WOX gene family members in the blueberry genome, and analyzed the basic physical and chemical properties, gene structure, gene motifs, promoter cis-acting elements, chromosome location, evolutionary relationships, expression pattern of these family members and predicted their functions. Finally, 12 genes containing the WOX domain were identified and found to be distributed on eight chromosomes. Phylogenetic tree analysis showed that the blueberry WOX gene family had three major branches: ancient branch, middle branch, and WUS branch. Blueberry WOX gene family protein sequences differ in amino acid number, molecular weight, isoelectric point and hydrophobicity. Predictive analysis of promoter cis-acting elements showed that the promoters of the VdWOX genes contained abundant light response, hormone, and stress response elements. The VdWOX genes were induced to express in both stems and leaves in response to salt and drought stress. Our results provided comprehensive characteristics of the WOX gene family and important clues for further exploration of its role in the growth, development and resistance to various stress in blueberry plants.

Hydrogen Peroxide Signaling in the Maintenance of Plant Root Apical Meristem Activity.

Hydrogen peroxide (H2O2) is a prevalent reactive oxygen species (ROS) found in cells and takes a central role in plant development and stress adaptation. The root apical meristem (RAM) has evolved strong plasticity to adapt to complex and changing environmental conditions. Recent advances have made great progress in explaining the mechanism of key factors, such as auxin, WUSCHEL-RELATED HOMEOBOX 5 (WOX5), PLETHORA (PLT), SHORTROOT (SHR), and SCARECROW (SCR), in the regulation of RAM activity maintenance. H2O2 functions as an emerging signaling molecule to control the quiescent center (QC) specification and stem cell niche (SCN) activity. Auxin is a key signal for the regulation of RAM maintenance, which largely depends on the formation of auxin regional gradients. H2O2 regulates the auxin gradients by the modulation of intercellular transport. H2O2 also modulates the expression of WOX5, PLTs, SHR, and SCR to maintain RAM activity. The present review is dedicated to summarizing the key factors in the regulation of RAM activity and discussing the signaling transduction of H2O2 in the maintenance of RAM activity. H2O2 is a significant signal for plant development and environmental adaptation.

Identification and Expression Analysis of the WOX Transcription Factor Family in Foxtail Millet (Setaria italica L.).

WUSCHEL-related homeobox (WOX) transcription factors are unique to plants and play pivotal roles in plant development and stress responses. In this investigation, we acquired protein sequences of foxtail millet WOX gene family members through homologous sequence alignment and a hidden Markov model (HMM) search. Utilizing conserved domain prediction, we identified 13 foxtail millet WOX genes, which were classified into ancient, intermediate, and modern clades. Multiple sequence alignment results revealed that all WOX proteins possess a homeodomain (HD). The SiWOX genes, clustered together in the phylogenetic tree, exhibited analogous protein spatial structures, gene structures, and conserved motifs. The foxtail millet WOX genes are distributed across 7 chromosomes, featuring 3 pairs of tandem repeats: SiWOX1 and SiWOX13, SiWOX4 and SiWOX5, and SiWOX11 and SiWOX12. Collinearity analysis demonstrated that WOX genes in foxtail millet exhibit the highest collinearity with green foxtail, followed by maize. The SiWOX genes primarily harbor two categories of cis-acting regulatory elements: Stress response and plant hormone response. Notably, prominent hormones triggering responses include methyl jasmonate, abscisic acid, gibberellin, auxin, and salicylic acid. Analysis of SiWOX expression patterns and hormone responses unveiled potential functional diversity among different SiWOX genes in foxtail millet. These findings lay a solid foundation for further elucidating the functions and evolution of SiWOX genes.

A WOX homolog disrupted by a transposon led to the loss of spines and contributed to the domestication of lettuce.

The loss of spines is one of the most important domestication traits for lettuce (Lactuca sativa). However, the genetics and regulation of spine development in lettuce remain unclear. We examined the genetics of spines in lettuce using a segregating population derived from a cross between cultivated and wild lettuce (Lactuca serriola). A gene encoding WUSCHEL-related homeobox transcription factor, named as WOX-SPINE1 (WS1), was identified as the candidate gene controlling the spine development in lettuce, and its function on spines was verified. A CACTA transposon was found to be inserted into the first exon of the ws1 allele, knocking out its function and leading to the lack of spines in cultivated lettuce. All lettuce cultivars investigated have the nonfunctional ws1 gene, and a selection sweep was found at the WS1 locus, suggesting its important role in lettuce domestication. The expression levels of WS1 were associated with the density of spines among different accessions of wild lettuce. At least two independent loss-of-function mutations in the ws1 gene caused the loss of spines in wild lettuce. These findings provide new insights into the development of spines and facilitate the exploitation of wild genetic resources in future lettuce breeding programs.