-
Plants mine the surrounding soil for water and dissolved minerals to sustain growth and complete their life cycle. Cell wall lignification is essential for forming functional endodermis in the mature zone of plant roots. The lignified apoplastic structure in the endodermis is called the Casparian strip (CS), which is critical for the selective absorption of water and nutrients in plant roots[19]. Cucumber (Cucumis sativus L.) is an important vegetable crop with great economic value. Many important discoveries have been made regarding different developmental processes in cucumber[25−33]. However, there are few reports on the genes related to cucumber root development. In recent years, multiple key components of the molecular machinery promoting the formation of the CS have been identified, among which SHORT-ROOT and its downstream R2R3 type family gene MYB36 are the main regulatory factors[8−11]. A previous study showed that loss-of-function myb36 mutants have delayed and defective barrier formation in the Arabidopsis root endodermis[8−9]. In rice, knockout of all three OsMYB36 genes led to the complete absence of the CS in the endodermal cell layer and inhibited plant growth[7]. These results showed that the function of MYB36 in controlling the formation of the CS in plants is probably conservative. Interestingly, the transcription factor MYB36 is essential for yellow‒green peel formation in cucumber[15]. These results suggest that MYB36 not only plays a critical role in the formation of CS in the root but also functions in the development of fruit. Thus, we speculate that there are multiple CsMYB36s in cucumber, and their functions may be differentiated during long-term evolution. To mine MYB36s with functions in the root, we identified the CsMYB36 family genes in cucumber and analysed the expression patterns of CsMYB36s in different tissues and in response to different hormone treatments. Fifteen CsMYB36 family genes were identified in cucumber. Phylogenetic tree analysis of 15 CsMYB36s derived from dicotyledons, monocotyledons, a gymnosperm, a moss and a fern was divided into four subgroups: A, B, C, and D. Ten of the cucumber CsMYB36 homologues are closely related to AtMYB36, SlMYB36 and OsMYB36[8−10,12]. Genes with similar functions are clustered together in the phylogenetic tree. To date, MYB36 has been reported to be the key transcription factor regulating the formation of the CS in Arabidopsis, rice and tomato roots, which led us to hypothesize a similar function of the ten CsMYB36 genes in the maturation of the endodermis. Indeed, except for CsaV3_6G014240.1, the other nine CsMYB36 genes were highly expressed in roots. Among these nine CsMYB36 genes, CsaV3_2G025830.1 has been identified in cucumber. The peel of cucumber fruit is yellow–green in the CsaV3_2G025830.1 mutant plant. Consistent with the observed phenotypes, CsaV3_2G025830.1 is also highly expressed in the cucumber ovary[15]. This implies that subfunctionalisation of CsMYB36 homologues may have occurred during cucumber evolution. In addition, CsaV3_2G008030.1 and CsaV3_3G036040.1 were highly expressed in the root differentiation zone (Fig. 5b), which is consistent with the position of the CS in the root. Considering that CsaV3_2G008030.1 and CsaV3_3G036040.1 are only highly expressed in the root, we speculate that CsaV3_2G008030.1 and CsaV3_3G036040.1 may play a key role in the formation of the CS in cucumber root. Mosses have no roots, and we found that only one CsMYB36 (CsaV3_3G041870.1) paralogue was closely related to moss. However, this gene is not expressed in any cucumber tissue, indicating that the gene probably has no function in cucumber. A number of studies have reported that R2R3-type MYBs function in flower development[45−47]. We found that the transcript levels of CsaV3_5G038000.1 from subgroup D were higher in male flowers and female flowers than in other tissues, which indicates that CsaV3_5G038000.1 may play important roles in regulating flower development in cucumber. Interestingly, we found that CsaV3_5G038180.1 was not expressed in the root but was highly expressed in other tissues, implying that CsMYB36 may participate in a wide range of developmental processes in cucumber.
Through expression pattern analyses of cucumber CsMYB36 family genes in response to temperature and photoperiod stresses, only one CsMYB36, CsaV3_1G013560.1, was identified to respond to high temperature stress. This result was not found in the other plant MYB36 genes. This suggests that CsMYB36 also plays an important role in the response to high-temperature stress, which provides a new clue for the genetic improvement of high-temperature tolerance in cucumber. In addition, four cucumber CsMYB36s were upregulated after GA treatment. Among the four CsMYB36s, we found that the promoter sequences of three CsMYB36s presented GA response elements. Thus, it is believed that CsMYB36 genes are related to the response to GA stress. ABA does not affect the expression levels of AtMYB36 at either the transcriptional or translational levels[12]. However, we found that CsMYB36s respond to ABA treatment. In Arabidopsis thaliana, AtMYB74 and AtMYB68 homologues of AtMYB36 all respond to ABA, and their overexpression increases lignification and suberization of the root endodermis[16,48]. It is suggested that the three CsMYB36s expressed in roots may mediate ABA signalling-induced root lignification. Moreover, we found that nearly all the promoter sequences of CsMYB36 contain anaerobic induction elements. The high number of anaerobic induction element-specific inducibility would lead to the high expression of CsMYB36 family genes in anaerobic environments, such as waterlogging. An oxygen-deficient state will occur when plants are in a flooded state for a long time[49]. Research has shown that roots establish a lateral diffusion barrier to minimize radial oxygen loss from flooded roots to the soil. For example, Zea nicaraguensis (teosinte) is a wild relative of Zea mays (maize), but unlike maize, it is tolerant to waterlogging. Compared with maize roots, the deposition of lignin and suberin in the outer cell layers of teosinte roots is enhanced under flooded conditions, which increases the gas impermeability of the root surface, thus greatly reducing the radial loss of oxygen in teosinte[50]. Similarly, lignification and suberin deposition in the root exodermal cell layer of rice provide a barrier for radial oxygen loss[51]. Consistent with these observations, expression of CsMYB36s is highly significantly upregulated after waterlogging[52]. Therefore, we speculate that plants adapt to hypoxia by regulating the expression levels of CsMYB36s, thereby affecting formation under flooded conditions.
In conclusion, we identified 15 CsMYB36s in the cucumber genome. The comprehensive expression pattern of CsMYB36s in different tissues and in the root differentiation zone indicated significant differential expression of CsMYB36s and putative root development-associated gene members. Our study lays a foundation for further screening the MYB36 genes necessary for the development of the CS by reverse genetics and discovering possible new functions of CsMYB36s in other development or stress processes.
-
About this article
Cite this article
Wang C, Shen X, Yang T, Yao H, Peng X, et al. 2023. Genome-wide characterization and identification of root development and stress-related CsMYB36 genes. Vegetable Research 3:19 doi: 10.48130/VR-2023-0019
Genome-wide characterization and identification of root development and stress-related CsMYB36 genes
- Received: 28 December 2022
- Accepted: 03 April 2023
- Published online: 14 June 2023
Abstract: Cucumber (Cucumis sativus L.) is an important vegetable crop worldwide. Over the last two decades, there have been many breakthroughs in the understanding of various developmental processes in cucumber, such as shoot branching, sex differentiation, and leaf and fruit size and shape. Roots play an important role in plant growth and development and nutrient absorption, affect crop yield, and participate in the interaction between plants and abiotic stress signals. However, the discovery of essential genes in cucumber roots is very limited. MYB36 is a critical transcription factor for whole development that negatively regulates cell proliferation and thus orchestrates Casparian strip (CS) formation in the root endodermis. To identify CsMYB36 genes with functions in the CS of cucumber and their responses to stress, we described in detail the characteristics of the CsMYB36 gene family in cucumber in this study. A total of 15 CsMYB36 genes were found in the cucumber genome. Through phylogenetic and tissue-specific expression analysis, CsaV3_2G008030.1 and CsaV3_3G036040.1 were selected as candidates regulating CS formation. In addition, all CsMYB36s were found to have anaerobic induction elements, indicating that MYB36 is likely to be highly responsive to anaerobic environments, such as waterlogging. We also identified one potential candidate CsMYB36 (CsaV3_1G013560.1) that participates in high-temperature stress responses. This work provides valuable information for understanding the characteristics of the CsMYB36 gene family in cucumber and provides new clues for researchers to study high temperature, waterlogging stress and the formation of CS.
-
Key words:
- Cucumber /
- CsMYB36 /
- Expression profles /
- Gene family