Abstract
Background
Laccase (LAC) is the pivotal enzyme responsible for the polymerization of monolignols and stress responses in plants. However, the roles of LAC genes in plant development and tolerance to diverse stresses are still largely unknown, especially in tea plant (Camellia sinensis), one of the most economically important crops worldwide.
Results
In total, 51 CsLAC genes were identified, they were unevenly distributed on different chromosomes and classified into six groups based on phylogenetic analysis. The CsLAC gene family had diverse intron–exon patterns and a highly conserved motif distribution. Cis-acting elements in the promoter demonstrated that promoter regions of CsLACs encode various elements associated with light, phytohormones, development and stresses. Collinearity analysis identified some orthologous gene pairs in C. sinensis and many paralogous gene pairs among C. sinensis, Arabidopsis and Populus. Tissue-specific expression profiles revealed that the majority of CsLACs had high expression in roots and stems and some members had specific expression patterns in other tissues, and the expression patterns of six genes by qRT‒PCR were highly consistent with the transcriptome data. Most CsLACs showed significant variation in their expression level under abiotic (cold and drought) and biotic (insect and fungus) stresses via transcriptome data. Among them, CsLAC3 was localized in the plasma membrane and its expression level increased significantly at 13 d under gray blight treatment. We found that 12 CsLACs were predicted to be targets of cs-miR397a, and most CsLACs showed opposite expression patterns compared to cs-miR397a under gray blight infection. Additionally, 18 highly polymorphic SSR markers were developed, these markers can be widely used for diverse genetic studies of tea plants.
Conclusions
This study provides a comprehensive understanding of the classification, evolution, structure, tissue-specific profiles, and (a)biotic stress responses of CsLAC genes. It also provides valuable genetic resources for functional characterization towards enhancing tea plant tolerance to multiple (a)biotic stresses.
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Introduction
The tea plant (Camellia sinensis (L.) O. Kuntze) is one of the most important woody cash crops, which tender buds and leaves are the raw material for the most widely consumed non-alcoholic beverages worldwide [38]. The amplified fragments were separated on a 96-capillary automated DNA fragment analyzer (Fragment Analyzer™ 96, Advanced Analytical Technologies, Inc., Ames, IA). The separated DNA bands were visually scored using PROSize™ 2.0 software, which was included in the advanced Fragment Analyzer™ 96 system. Only one or two fragments were collected for each individual [37].
The number of alleles (Na), Shannon’s information index (I), observed heterozygosity (Ho), expected heterozygosity (He), genetic diversity (GD) and polymorphism information content (PIC) values were calculated with PowerMarker version 3.25 (http://statgen.ncsu.edu/powermarker/downloads.htm) (Liu and Muse 2005).
Results
Identification of the CsLAC gene family in tea plant
To identify the CsLAC genes, we used the tea plant reference genome [37, 38]. In tea plant, several previous studies of genomic SSR marker development showed that the average PIC values for 13, 30 and 36 markers were 0.860, 0.704 and 0.862, respectively [38, 59, 60], while two studies showed that the average PIC values of SSR markers were similar to the average PIC value in our study [61, 62]. Overall, the newly developed SSR markers can be used for various genetic studies in tea plant, such as genetic variation, evolutionary origin, fingerprinting, QTL map**, and marker-assisted selection breeding.
Conclusions
In this study, we performed a genome-wide analysis of the CsLAC gene family, generated a wide range of expression data, including tissue-specific expression patterns and expression profiles of CsLACs responding to abiotic and biotic stresses, and developed some highly polymorphic SSR markers. This study provides target genes for regulating lignin biosynthesis in tea plant and lays the foundation for understanding the function of CsLAC genes.
Availability of data and materials
The data generated and analyzed in this study are included in this article and its Supplementary materials. RNA-Seq data of Ectropis obliqua feeding treatment are available at the NCBI SRA database (https://www.ncbi.nlm.nih.gov/) under project accession number PRJNA901518.
Abbreviations
- PAL:
-
Phenylalanine ammonia-lyase
- 4CL:
-
4-(Hydroxy) cinnamoyl CoA ligase
- C3H:
-
P-coumarate 3-hydroxylase
- C4H:
-
Cinnamate 4-hydroxylase
- CAD:
-
Cinnamyl alcohol dehydrogenase
- CCoAOMT:
-
Caffeoyl CoA O-methyltransferase
- HCT:
-
Hydroxycinna-moyl-CoA:shikimate (SA)/quinate (QA) hydroxycinnamoyl transferase (HCT); CCR: Cinnamoyl CoA reductase
- COMT:
-
Caffeic acid/5-hydroxyferulic acid O-methyltransferase
- F5H:
-
Ferulate 5-hydroxylase
- LAC:
-
Laccase; TPM: Transcripts Per Million
- SSR:
-
Simple sequence repeat
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Acknowledgements
We appreciate the editor and anonymous reviewers for critically evaluating the manuscript and providing constructive comments for its improvement. We thank the Tea Plant Cultivar and Germplasm Resource Garden (Guohe town, Lu Jiang County, Anhui Province, China) for providing tea plant samples.
Funding
This work was supported by the National Natural Science Foundation of China (32272770 and 31800585), the Project of Science and Technology of Yunnan Province (202102AE090038), and the Natural Science Foundation of Anhui Province (1808085QC92).
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JXZ performed data analysis and real-time PCR. HXZ and KLH conducted real-time PCR, subcellular localization, data analysis, and SSR marker development. RG, HX, JYZ, JJZ, HLG, HRC, and GQL are involved in data analysis, sample collection, and DNA extraction. CLW revised the manuscript. SRL designed the research and wrote the manuscript. All authors have read and approved the manuscript.
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Supplementary Information
Additional file 1:
Table S1. CsLAC gene family CDs and protein sequences.
Additional file 2:
Table S2. Primers developed for six CsLAC genes for qRT‒PCR and CsLAC3 for subcellular localization.
Additional file 3:
Table S3. Proteins interacting with LAC proteins in Arabidopsis and C. sinensis.
Additional file 4:
Table S4. Primer pairs for 18 SSR markers and 45 tea plant samples used for SSR marker development.
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Zhu, J., Zhang, H., Huang, K. et al. Comprehensive analysis of the laccase gene family in tea plant highlights its roles in development and stress responses. BMC Plant Biol 23, 129 (2023). https://doi.org/10.1186/s12870-023-04134-w
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DOI: https://doi.org/10.1186/s12870-023-04134-w