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Yang K, Li L, Lou Y, Zhu C, Li X, Gao Z. A regulatory network driving shoot lignification in rapidly growing bamboo. PLANT PHYSIOLOGY 2021; 187:900-916. [PMID: 34608957 PMCID: PMC8491019 DOI: 10.1093/plphys/kiab289] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 05/31/2021] [Indexed: 05/24/2023]
Abstract
Woody bamboo is environmentally friendly, abundant, and an alternative to conventional timber. Degree of lignification and lignin content and deposition affect timber properties. However, the lignification regulatory network in monocots is poorly understood. To elucidate the regulatory mechanism of lignification in moso bamboo (Phyllostachys edulis), we conducted integrated analyses using transcriptome, small RNA, and degradome sequencing followed by experimental verification. The lignification degree and lignin content increased with increased bamboo shoot height, whereas phenylalanine ammonia-lyase and Laccase activities first increased and then decreased with shoot growth. Moreover, we identified 11,504 differentially expressed genes (DEGs) in different portions of the 13th internodes of different height shoots; most DEGs associated with cell wall and lignin biosynthesis were upregulated, whereas some DEGs related to cell growth were downregulated. We identified a total of 1,502 miRNAs, of which 687 were differentially expressed. Additionally, in silico and degradome analyses indicated that 5,756 genes were targeted by 691 miRNAs. We constructed a regulatory network of lignification, including 11 miRNAs, 22 transcription factors, and 36 enzyme genes, in moso bamboo. Furthermore, PeLAC20 overexpression increased lignin content in transgenic Arabidopsis (Arabidopsis thaliana) plants. Finally, we proposed a reliable miRNA-mediated "MYB-PeLAC20" module for lignin monomer polymerization. Our findings provide definite insights into the genetic regulation of bamboo lignification. In addition to providing a platform for understanding related mechanisms in other monocots, these insights could be used to develop strategies to improve bamboo timber properties.
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Affiliation(s)
- Kebin Yang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Lichao Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Yongfeng Lou
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
- Jiangxi Academy of Forestry, Jiangxi Provincial Key Laboratory of Plant Biotechnology, Nanchang 330013, China
| | - Chenglei Zhu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Xueping Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Zhimin Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
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Haplotype- and SNP-Based GWAS for Growth and Wood Quality Traits in Eucalyptus cladocalyx Trees under Arid Conditions. PLANTS 2021; 10:plants10010148. [PMID: 33450896 PMCID: PMC7828368 DOI: 10.3390/plants10010148] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 12/14/2022]
Abstract
The agricultural and forestry productivity of Mediterranean ecosystems is strongly threatened by the adverse effects of climate change, including an increase in severe droughts and changes in rainfall distribution. In the present study, we performed a genome-wide association study (GWAS) to identify single-nucleotide polymorphisms (SNPs) and haplotype blocks associated with the growth and wood quality of Eucalyptus cladocalyx, a tree species suitable for low-rainfall sites. The study was conducted in a progeny-provenance trial established in an arid site with Mediterranean patterns located in the southern Atacama Desert, Chile. A total of 87 SNPs and 3 haplotype blocks were significantly associated with the 6 traits under study (tree height, diameter at breast height, slenderness coefficient, first bifurcation height, stem straightness, and pilodyn penetration). In addition, 11 loci were identified as pleiotropic through Bayesian multivariate regression and were mainly associated with wood hardness, height, and diameter. In general, the GWAS revealed associations with genes related to primary metabolism and biosynthesis of cell wall components. Additionally, associations coinciding with stress response genes, such as GEM-related 5 and prohibitin-3, were detected. The findings of this study provide valuable information regarding genetic control of morphological traits related to adaptation to arid environments.
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Pu Y, Liu L, Wu J, Zhao Y, Bai J, Ma L, Yue J, Jin J, Niu Z, Fang Y, Sun W. Transcriptome Profile Analysis of Winter Rapeseed ( Brassica napus L.) in Response to Freezing Stress, Reveal Potentially Connected Events to Freezing Stress. Int J Mol Sci 2019; 20:ijms20112771. [PMID: 31195741 PMCID: PMC6600501 DOI: 10.3390/ijms20112771] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/30/2019] [Accepted: 06/03/2019] [Indexed: 11/16/2022] Open
Abstract
Winter rapeseed is not only an important oilseed crop, but also a winter cover crop in Northern China, where its production was severely limited by freezing stress. As an overwinter crop, the production is severely limited by freezing stress. Therefore, understanding the physiological and molecular mechanism of winter rapeseed (Brassica napus L.) in freezing stress responses becomes essential for the improvement and development of freezing-tolerant varieties of Brassica napus. In this study, morphological, physiological, ultrastructure and transcriptome changes in the Brassica napus line "2016TS(G)10" (freezing-tolerance line) that was exposed to -2 °C for 0 h, 1 h, 3 h and 24 h were characterized. The results showed that freezing stress caused seedling dehydration, and chloroplast dilation and degradation. The content of malondialdehyde (MDA), proline, soluble protein and soluble sugars were increased, as well as the relative electrolyte leakage (REL) which was significantly increased at frozen 24 h. Subsequently, RNA-seq analysis revealed a total of 98,672 UniGenes that were annotated in Brassica napus and 3905 UniGenes were identified as differentially expressed genes after being exposed to freezing stress. Among these genes, 2312 (59.21%) were up-regulated and 1593 (40.79%) were down-regulated. Most of these DEGs were significantly annotated in the carbohydrates and energy metabolism, signal transduction, amino acid metabolism and translation. Most of the up-regulated DEGs were especially enriched in plant hormone signal transduction, starch and sucrose metabolism pathways. Transcription factor enrichment analysis showed that the AP2/ERF, WRKY and MYB families were also significantly changed. Furthermore, 20 DEGs were selected to validate the transcriptome profiles via quantitative real-time PCR (qRT-PCR). In conclusion, the results provide an overall view of the dynamic changes in physiology and insights into the molecular regulation mechanisms of winter Brassica napus in response to freezing treatment, expanding our understanding on the complex molecular mechanism in plant response to freezing stress.
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Affiliation(s)
- Yuanyuan Pu
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
| | - Lijun Liu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
| | - Junyan Wu
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
| | - Yuhong Zhao
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
| | - Jing Bai
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
| | - Li Ma
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
| | - Jinli Yue
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
| | - Jiaojiao Jin
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
| | - Zaoxia Niu
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
| | - Yan Fang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
| | - Wancang Sun
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China.
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