Integration of Quantitative Trait Loci Mapping and Expression Profiling Analysis to Identify Genes Potentially Involved in Ramie Fiber Lignin Biosynthesis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Experimental Population and Phenotypic Measurements
2.2. QTL Analyses
2.3. Identifying the Differentially Expressed Genes (DEGs) Located in the QTL Regions
2.4. DNA Extraction, Sequencing, and Sequence Comparison
3. Results
3.1. QTL Mapping for the Lignin Content Trait
3.2. Detecting DEGs Located in the QTL Regions
3.3. Identifying the Differentially Expressed Genes that Are Homologous with Arabidopsis Lignin Biosynthetic Genes from the QTL Regions
3.4. Sequence Comparison of the Three Identified Lignin Biosynthesis Gene Homologs
4. Discussion
4.1. Genetic Basis for the Trait of Lignin Content in Ramie Fibers
4.2. Potential Candidate Genes
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
- Gorshkova, T.; Brutch, N.; Chabbert, B.; Deyholos, M.; Hayashi, T.; Lev-Yadun, S.; Mellerowicz, E.; Morvan, C.; Neutelings, G.; Pilate, G. Plant Fiber Formation: State of the Art, Recent and Expected Progress, and Open Questions. Crit. Rev. Plant Sci. 2012, 31, 201–228. [Google Scholar] [CrossRef]
- Ye, Z.; Zhong, R. Molecular control of wood formation in trees. J. Exp. Bot. 2015, 66, 4119–4131. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zhong, R.; Ye, Z.H. Secondary cell walls: Biosynthesis, patterned deposition and transcriptional regulation. Plant Cell Physiol. 2015, 56, 195–214. [Google Scholar] [CrossRef] [PubMed]
- Li, H.L. The origin of cultivated plants in Southeast Asia. Econ. Bot. 1970, 24, 3–19. [Google Scholar]
- Sen, T.; Reddy, H.N. Various industrial applications of hemp, kenaf, flax and ramie natural fibres. Int. J. Innov. Manag. Technol. 2011, 2, 192–198. [Google Scholar]
- Aldaba, V.C. The structure and development of the cell wall in plants I. Bast fibers of Boehmeria and Linum. Am. J. Bot. 1927, 14, 16–22. [Google Scholar] [CrossRef]
- Liu, T.; Zhu, S.; Tang, Q.; Tang, S. QTL mapping for fiber yield-related traits by constructing the first genetic linkage map in ramie (Boehmeria nivea L. Gaud). Mol. Breed. 2014, 34, 883–892. [Google Scholar] [CrossRef]
- Liu, C.; Zhu, S.; Tang, S.; Wang, H.; Zheng, X.; Chen, X.; Dai, Q.; Liu, T. QTL analysis of four main stem bark traits using a GBS-SNP-based high-density genetic map in ramie. Sci. Rep. 2017, 7, 13458. [Google Scholar] [CrossRef] [Green Version]
- Tang, Y.H.; Liu, F.; Mao, K.Q.; Xing, H.C.; Chen, J.R.; Guo, Q.Q. Cloning and characterization of the key 4-coumarate CoA ligase genes in Boehmeria nivea. S. Afr. J. Bot. 2018, 116, 123–130. [Google Scholar] [CrossRef]
- Tang, Y.H.; Chen, J.R.; Liu, F.; Yuan, Y.M.; Guo, Q.Q.; Chang, H.T. cDNA cloning and analysis of cinnamoyl-CoA reductase gene from Boehmeria nivea. Acta Agron. Sin. 2015, 41, 1324. [Google Scholar] [CrossRef]
- Liu, F.; Chen, J.R.; Tang, Y.H.; Chang, H.T.; Yuan, Y.M.; Guo, Q.Q. Isolation and characterization of cinnamate 4-hydroxylase gene from cultivated ramie (Boehmeria nivea). Biotechnol. Biotechnol. Equip. 2018, 32, 324–331. [Google Scholar] [CrossRef]
- Huang, C.Q.; Guo, A.P.; Zhang, X.Y.; Liu, G.D. cDNA Cloning and Sequence Analysis of COMT Gene from Ramie. Chin. Agric. Sci. 2008, 5, 386–391. [Google Scholar]
- Zhu, W.Y.; Rong, C.J.; Yan, P.; Weng, Z.X.; Quan, G.Q.; Yan, Z. cDNA cloning and expression analysis of a lignin synthetase CAD gene in ramie (Boehmeria nivea (L.) Gaud.). J. Hunan Agric. Univ. (Nat. Sci.) 2014, 40, 483–488. [Google Scholar]
- Tang, Y.; Liu, F.; Xing, H.; Mao, K.; Chen, G.; Guo, Q.; Chen, J. Correlation analysis of lignin accumulation and expression of key genes involved in lignin biosynthesis of ramie (Boehmeria nivea). Genes 2019, 10, 389. [Google Scholar] [CrossRef]
- Chen, J.R.; Liu, F.; Tang, Y.H.; Yuan, Y.M.; Guo, Q.Q. Transcriptome sequencing and profiling of expressed genes in phloem and xylem of ramie (Boehmeria nivea L. Gaud). PLoS ONE 2014, 10, e0117896. [Google Scholar] [CrossRef]
- Wang, Y.; Zeng, Z.; Li, F.; Yang, X.; Gao, X.; Ma, Y.; Rao, J.; Wang, H.; Liu, T. A genomic resource derived from the integration of genome sequences, expressed transcripts and genetic markers in ramie. BMC Genom. 2019, 20, 476. [Google Scholar] [CrossRef]
- Van Ooijen, J.W.; Boer, M.P.; Jansen, R.C.; Maliepaard, C. MapQTL 4.0: Software for the Calculation of QTL Positions on Genetic Maps; Wageningen University & Research: Wageningen, The Netherlands, 2002. [Google Scholar]
- Chen, J.; Pei, Z.; Dai, L.; Wang, B.; Liu, L.; An, X.; Peng, D. Transcriptome profiling using pyrosequencing shows genes associated with bast fiber development in ramie (Boehmeria nivea L.). BMC Genom. 2014, 15, 919. [Google Scholar] [CrossRef]
- Langmead, B.; Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 2012, 9, 357. [Google Scholar] [CrossRef]
- Li, B.; Dewey, C.N. RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform. 2011, 12, 323. [Google Scholar] [CrossRef]
- Trapnell, C.; Williams, B.A.; Pertea, G.; Mortazavi, A.; Kwan, G.; Van Baren, M.J.; Salzberg, S.L.; Wold, B.J.; Pachter, L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 2010, 28, 511. [Google Scholar] [CrossRef]
- Love, M.I.; Huber, W.; Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014, 15, 550. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Ferreira, J.; Zwinderman, A. On the Benjamini–Hochberg method. Ann. Stat. 2006, 34, 1827–1849. [Google Scholar] [CrossRef]
- Luan, M.B.; Jian, J.B.; Chen, P.; Chen, J.H.; Chen, J.H.; Gao, Q.; Gao, G.; Zhou, J.H.; Chen, K.M.; Guang, X.M. Draft genome sequence of ramie, Boehmeria nivea (L.) Gaudich. Mol. Ecol. Resour. 2018, 18, 639–645. [Google Scholar] [CrossRef] [PubMed]
- Liu, T.; Zhu, S.; Tang, Q.; Tang, S. Genome-wide transcriptomic profiling of ramie (Boehmeria nivea L. Gaud) in response to cadmium stress. Gene 2015, 558, 131–137. [Google Scholar] [CrossRef] [PubMed]
- Sievers, F.; Wilm, A.; Dineen, D.; Gibson, T.J.; Karplus, K.; Li, W.; Lopez, R.; McWilliam, H.; Remmert, M.; Söding, J.; et al. Fast, scalable generation of high-quality protein multiple sequence alignments using clustal omega. Mol. Syst. Biol. 2011, 7, 539. [Google Scholar] [CrossRef] [PubMed]
- Edgar, R.C. Muscle: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32, 1792–1797. [Google Scholar] [CrossRef] [PubMed]
- Marchler, B.A.; Lu, S.; Anderson, J.B.; Chitsaz, F.; Derbyshire, M.K.; DeWeese-Scott, C.; Fong, J.H.; Geer, L.Y.; Geer, R.C.; Gonzales, N.R.; et al. CDD: A conserved domain database for the functional annotation of proteins. Nucleic Acids Res. 2011, 39, D225–D229. [Google Scholar] [CrossRef] [PubMed]
- Raes, J.; Rohde, A.; Christensen, J.H.; Peer, Y.V.; Boerjan, W. Genome-wide characterization of the lignification toolbox in Arabidopsis. Plant Physiol. 2003, 133, 1051–1071. [Google Scholar] [CrossRef]
- Zhao, Q.; Nakashima, J.; Chen, F.; Yin, Y.; Fu, C.; Yun, J.; Shao, H.; Wang, X.; Wang, Z.-Y.; Dixon, R.A. Laccase is necessary and nonredundant with peroxidase for lignin polymerization during vascular development in Arabidopsis. Plant Cell 2013, 25, 3976–3987. [Google Scholar] [CrossRef]
- Nakano, Y.; Yamaguchi, M.; Endo, H.; Rejab, N.A.; Ohtani, M. NAC-MYB-based transcriptional regulation of secondary cell wall biosynthesis in land plants. Front. Plant Sci. 2015, 6, 288. [Google Scholar] [CrossRef]
- Liu, T.; Tang, S.; Zhu, S.; Tang, Q.; Zheng, X. Transcriptome comparison reveals the patterns of selection in domesticated and wild ramie (Boehmeria nivea L. Gaud). Plant Mol. Biol. 2014, 86, 85–92. [Google Scholar] [CrossRef] [PubMed]
- Zhu, S.; Zheng, X.; Dai, Q.; Tang, S.; Liu, T. Identification of quantitative trait loci for flowering time traits in ramie (Boehmeria nivea L. Gaud). Euphytica 2016, 210, 367–374. [Google Scholar] [CrossRef]
- Liu, T.; Zhu, S.; Tang, Q.; Chen, P.; Yu, Y.; Tang, S. De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L. Gaud). BMC Genom. 2013, 14, 125. [Google Scholar] [CrossRef]
- Zheng, X.; Zhu, S.; Tang, S.; Liu, T. Identification of drought, cadmium and root-lesion nematode infection stress-responsive transcription factors in ramie. Open Life Sci. 2016, 11, 191–199. [Google Scholar] [CrossRef]
- Liu, T.; Zhu, S.; Tang, Q.; Tang, S. Identification of 32 full-length NAC transcription factors in ramie (Boehmeria nivea L. Gaud) and characterization of the expression pattern of these genes. Mol. Genet. Genom. 2014, 289, 675–684. [Google Scholar] [CrossRef] [PubMed]
Environment | Population | Parents | ||
---|---|---|---|---|
Range (%) | Mean ± SD (%) | ZSZ1 (%) | BNT (%) | |
Environment 1 | 1.95–12.09 | 5.55 ± 2.07 | 10.91 | 2.97 |
Environment 2 | 1.96–10.20 | 4.54 ± 1.63 | 10.27 | 2.73 |
Environment | QTL | Linkage Group | Interval | LOD a | Add b (%) | Dom c (%) | D/A d | Var% e |
---|---|---|---|---|---|---|---|---|
Environment 1 | qLC3 | 3 | Marker_4740–Marker_967 | 3.36 | 1.31 | −1.55 | −1.18 | 19.1 |
qLC5 | 5 | Marker_4067–Marker_213 | 4.02 | 1.22 | −2.11 | −1.73 | 22.4 | |
qLC10 | 10 | Marker_317–Marker_1605 | 4.04 | 1.08 | 1.32 | 1.22 | 22.5 | |
qLC13 | 13 | Marker_5976–Marker_1274 | 4.23 | 1.13 | −0.18 | −0.16 | 23.4 | |
Environment 2 | qLC7 | 7 | Marker_5787–Marker_4916 | 3.84 | 0.86 | −0.72 | −0.84 | 16.1 |
qLC10 | 10 | Marker_317–Marker_1605 | 3.02 | 0.90 | 1.16 | 1.29 | 12.9 | |
qLC13 | 13 | Marker_5976–Marker_1274 | 5.01 | 0.94 | −0.13 | −0.14 | 20.4 |
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Chen, J.; Rao, J.; Wang, Y.; Zeng, Z.; Liu, F.; Tang, Y.; Chen, X.; Liu, C.; Liu, T. Integration of Quantitative Trait Loci Mapping and Expression Profiling Analysis to Identify Genes Potentially Involved in Ramie Fiber Lignin Biosynthesis. Genes 2019, 10, 842. https://doi.org/10.3390/genes10110842
Chen J, Rao J, Wang Y, Zeng Z, Liu F, Tang Y, Chen X, Liu C, Liu T. Integration of Quantitative Trait Loci Mapping and Expression Profiling Analysis to Identify Genes Potentially Involved in Ramie Fiber Lignin Biosynthesis. Genes. 2019; 10(11):842. https://doi.org/10.3390/genes10110842
Chicago/Turabian StyleChen, Jianrong, Jing Rao, Yanzhou Wang, Zheng Zeng, Fang Liu, Yinghong Tang, Xiaorong Chen, Chan Liu, and Touming Liu. 2019. "Integration of Quantitative Trait Loci Mapping and Expression Profiling Analysis to Identify Genes Potentially Involved in Ramie Fiber Lignin Biosynthesis" Genes 10, no. 11: 842. https://doi.org/10.3390/genes10110842
APA StyleChen, J., Rao, J., Wang, Y., Zeng, Z., Liu, F., Tang, Y., Chen, X., Liu, C., & Liu, T. (2019). Integration of Quantitative Trait Loci Mapping and Expression Profiling Analysis to Identify Genes Potentially Involved in Ramie Fiber Lignin Biosynthesis. Genes, 10(11), 842. https://doi.org/10.3390/genes10110842