Genome-wide identification and expression profiling reveal the regulatory role of U-box E3 ubiquitin ligase genes in strawberry fruit ripening and abiotic stresses resistance

Effects of cattle manure and sludge vermicompost on nutrient dynamics and yield in strawberry cultivation with distinct continuous cropping histories in a greenhouse

Continuous cropping has emerged as a significant challenge affecting yield and quality in greenhouse strawberries, particularly as the cultivation of strawberries as a protected crop continues to increase. To address this issue, substrates with 0 or 2 years of continuous cropping were fertilized with two types of organic materials: vermicompost derived from either sludge or cattle manure. A control group consisted of substrate without the addition of vermicompost. Both type of vermicompost improved substrate fertility, promoted plant growth and fruit quality. The cattle manure vermicompost had a better improvement effect at peak fruiting stage. Substrate nutrients were increased 14.58~38.52% (0-year substrate) and 12.04%~42.54% (2-year substrate), respectively. In both substrate types, there was a substantial increase in microbial population and enzyme activity, accompanied by a significant decrease in phenolic acid content. During the senescence stage, the use of cattle manure vermicompost led to enhancements in plant height, leaf area, and root length, with increases ranging from 15.01% to 32.77% and 23.75% to 32.78% across the two substrate types compared to the control group. Furthermore, the application of cattle manure vermicompost significantly improved both fruit yield and quality. Compared with the control (CK), the cattle manure vermicompost increased fruit yield by 18.29% and 19.64% in the 0- and 2-year substrates, respectively. The contents of soluble sugars, vitamin C, and free amino acids in the fruits increased by 21.42%~34.16% (0-year substrate) and 9.62%~42.62% (2-year substrate), at peak fruiting stage. Cattle manure vermicompost application to the 2-year substrate ranked higher in the membership function than the CK treatment at 0-year planting. In conclusion, the application of vermicompost can significantly improve strawberry fruit yield and quality, as well as substrate characteristics, thus effectively addressing challenges associated with continuous cropping. Furthermore, the use of cattle manure vermicompost produced more pronounced positive effects.

Genome-Wide Identification and Expression Analysis of the Alfalfa (Medicago sativa L.) U-Box Gene Family in Response to Abiotic Stresses

E3 ubiquitin ligases known as plant U-box (PUB) proteins regulate a variety of aspects of plant growth, development, and stress response. However, the functions and characteristics of the PUB gene family in alfalfa remain unclear. This work involved a genome-wide examination of the alfalfa U-box E3 ubiquitin ligase gene. In total, 210 members were identified and divided into five categories according to their homology with the members of the U-box gene family in Arabidopsis thaliana. The phylogenetic analysis, conserved motifs, chromosomal localization, promoters, and regulatory networks of this gene were investigated. Chromosomal localization and covariance analyses indicated that the MsPUB genes expanded MsPUB gene family members through gene duplication events during evolution. MsPUB genes may be involved in the light response, phytohormone response, growth, and development of several biological activities, according to cis-acting element analysis of promoters. In addition, transcriptome analysis and expression analysis by qRT-PCR indicated that most MsPUB genes were significantly upregulated under cold stress, drought stress, and salt stress treatments. Among them, MsPUBS106 and MsPUBS185 were significantly and positively correlated with cold resistance in alfalfa. MsPUBS110, MsPUBS067, MsPUBS111 and MsPUB155 were comprehensively involved in drought stress, low temperature, and salt stress resistance. All things considered, these discoveries offer fresh perspectives on the composition, development, and roles of the PUB gene family in alfalfa. They also provide theoretical guidance for further investigations into the mechanisms regulating the development, evolution, and stress tolerance of MsPUB.

Genome-Wide Identification and Expression Analysis of the PUB Gene Family in Zoysia japonica under Salt Stress

The U-box protein family of ubiquitin ligases is important in the biological processes of plant growth, development, and biotic and abiotic stress responses. Plants in the genus Zoysia are recognized as excellent warm-season turfgrass species with drought, wear and salt tolerance. In this study, we conducted the genome-wide identification of plant U-box (PUB) genes in Zoysia japonica based on U-box domain searching. In total, 71 ZjPUB genes were identified, and a protein tree was constructed of AtPUBs, OsPUBs, and ZjPUBs, clustered into five groups. The gene structures, characteristics, cis-elements and protein interaction prediction network were analyzed. There were mainly ABRE, ERE, MYB and MYC cis-elements distributed in the promoter regions of ZjPUBs. ZjPUBs were predicted to interact with PDR1 and EXO70B1, related to the abscisic acid signaling pathway. To better understand the roles of ZjPUBs under salt stress, the expression levels of 18 ZjPUBs under salt stress were detected using transcriptome data and qRT-PCR analysis, revealing that 16 ZjPUBs were upregulated in the roots under salt treatment. This indicates that ZjPUBs might participate in the Z. japonica salt stress response. This research provides insight into the Z. japonica PUB gene family and may support the genetic improvement in the molecular breeding of salt-tolerant zoysiagrass varieties.

Genome-wide identification and transcriptome profiling expression analysis of the U-box E3 ubiquitin ligase gene family related to abiotic stress in maize (Zea mays L.)

BACKGROUND

The U-box gene family encodes E3 ubiquitin ligases involved in plant hormone signaling pathways and abiotic stress responses. However, there has yet to be a comprehensive analysis of the U-box gene family in maize (Zea mays L.) and its responses to abiotic stress.

RESULTS

In this study, 85 U-box family proteins were identified in maize and were classified into four subfamilies based on phylogenetic analysis. In addition to the conserved U-box domain, we identified additional functional domains, including Pkinase, ARM, KAP and Tyr domains, by analyzing the conserved motifs and gene structures. Chromosomal localization and collinearity analysis revealed that gene duplications may have contributed to the expansion and evolution of the U-box gene family. GO annotation and KEGG pathway enrichment analysis identified a total of 105 GO terms and 21 KEGG pathways that were notably enriched, including ubiquitin-protein transferase activity, ubiquitin conjugating enzyme activity and ubiquitin-mediated proteolysis pathway. Tissue expression analysis showed that some ZmPUB genes were specifically expressed in certain tissues and that this could be due to their functions. In addition, RNA-seq data for maize seedlings under salt stress revealed 16 stress-inducible plant U-box genes, of which 10 genes were upregulated and 6 genes were downregulated. The qRT-PCR results for genes responding to abiotic stress were consistent with the transcriptome analysis. Among them, ZmPUB13, ZmPUB18, ZmPUB19 and ZmPUB68 were upregulated under all three abiotic stress conditions. Subcellular localization analysis showed that ZmPUB19 and ZmPUB59 were located in the nucleus.

CONCLUSIONS

Overall, our study provides a comprehensive analysis of the U-box gene family in maize and its responses to abiotic stress, suggesting that U-box genes play an important role in the stress response and providing insights into the regulatory mechanisms underlying the response to abiotic stress in maize.