1
|
Li L, Xu JB, Zhu ZW, Ma R, Wu XZ, Geng YK. Genome-wide identification and expression analysis of the SPL transcription factor family and its response to abiotic stress in Pisum sativum L. BMC Genomics 2024; 25:539. [PMID: 38822248 PMCID: PMC11140923 DOI: 10.1186/s12864-024-10262-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/27/2024] [Indexed: 06/02/2024] Open
Abstract
Squamous promoter binding protein-like (SPL) genes encode plant-specific transcription factors (TFs) that play essential roles in modulating plant growth, development, and stress response. Pea (Pisum sativum L.) is a coarse grain crop of great importance in food production, biodiversity conservation and molecular genetic research, providing genetic information and nutritional resources for improving agricultural production and promoting human health. However, only limited researches on the structure and functions of SPL genes exist in pea (PsSPLs). In this study, we identified 22 PsSPLs and conducted a genome-wide analysis of their physical characteristics, chromosome distribution, gene structure, phylogenetic evolution and gene expression patterns. As a result, the PsSPLs were unevenly distributed on the seven chromosomes of pea and harbored the SBP domain, which is composed of approximately 76 amino acid residues. The phylogenetic analysis revealed that the PsSPLs clustered into eight subfamilies and showed high homology with SPL genes in soybean. Further analysis showed the presence of segmental duplications in the PsSPLs. The expression patterns of 22 PsSPLs at different tissues, developmental stages and under various stimulus conditions were evaluated by qRT-PCR method. It was found that the expression patterns of PsSPLs from the same subfamily were similar in different tissues, the transcripts of most PsSPLs reached the maximum peak value at 14 days after anthesis in the pod. Abiotic stresses can cause significantly up-regulated PsSPL19 expression with spatiotemporal specificity, in addition, four plant hormones can cause the up-regulated expression of most PsSPLs including PsSPL19 in a time-dependent manner. Therefore, PsSPL19 could be a key candidate gene for signal transduction during pea growth and development, pod formation, abiotic stress and plant hormone response. Our findings should provide insights for the elucidating of development regulation mechanism and breeding for resistance to abiotic stress pea.
Collapse
Affiliation(s)
- Long Li
- Minzu University of China, 100010, Beijing, P.R. China
- College of Agronomy, Hebei Agricultural University, 071001, Baoding, P.R. China
| | - Jian Bo Xu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China
| | - Zhi Wen Zhu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China
| | - Rui Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 712100, Yangling, Shaanxi, P.R. China
| | - Xiao Zong Wu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China.
- Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China.
| | - Yu Ke Geng
- Minzu University of China, 100010, Beijing, P.R. China.
| |
Collapse
|
2
|
Wu JW, Zhao ZY, Hu RC, Huang YF. Genome-wide identification, stress- and hormone-responsive expression characteristics, and regulatory pattern analysis of Scutellaria baicalensis SbSPLs. PLANT MOLECULAR BIOLOGY 2024; 114:20. [PMID: 38363403 PMCID: PMC10873456 DOI: 10.1007/s11103-023-01410-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/11/2023] [Indexed: 02/17/2024]
Abstract
SQUAMOSA PROMOTER BINDING PROTEIN-LIKEs (SPLs) encode plant-specific transcription factors that regulate plant growth and development, stress response, and metabolite accumulation. However, there is limited information on Scutellaria baicalensis SPLs. In this study, 14 SbSPLs were identified and divided into 8 groups based on phylogenetic relationships. SbSPLs in the same group had similar structures. Abscisic acid-responsive (ABRE) and MYB binding site (MBS) cis-acting elements were found in the promoters of 8 and 6 SbSPLs. Segmental duplications and transposable duplications were the main causes of SbSPL expansion. Expression analysis based on transcriptional profiling showed that SbSPL1, SbSPL10, and SbSPL13 were highly expressed in roots, stems, and flowers, respectively. Expression analysis based on quantitative real-time polymerase chain reaction (RT‒qPCR) showed that most SbSPLs responded to low temperature, drought, abscisic acid (ABA) and salicylic acid (SA), among which the expression levels of SbSPL7/9/10/12 were significantly upregulated in response to abiotic stress. These results indicate that SbSPLs are involved in the growth, development and stress response of S. baicalensis. In addition, 8 Sba-miR156/157 s were identified, and SbSPL1-5 was a potential target of Sba-miR156/157 s. The results of target gene prediction and coexpression analysis together indicated that SbSPLs may be involved in the regulation of L-phenylalanine (L-Phe), lignin and jasmonic acid (JA) biosynthesis. In summary, the identification and characterization of the SbSPL gene family lays the foundation for functional research and provides a reference for improved breeding of S. baicalensis stress resistance and quality traits.
Collapse
Affiliation(s)
- Jia-Wen Wu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150000, China
| | - Zi-Yi Zhao
- Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Guangxi Institute of Chinese Medicine and Pharmaceutical Science, Nanning, 530022, China
| | - Ren-Chuan Hu
- Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Guangxi Institute of Chinese Medicine and Pharmaceutical Science, Nanning, 530022, China
| | - Yun-Feng Huang
- Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Guangxi Institute of Chinese Medicine and Pharmaceutical Science, Nanning, 530022, China.
| |
Collapse
|
3
|
Hu XG, Zhuang H, Lin E, Borah P, Du M, Gao S, Wang T, Tong Z, Huang H. Full-Length Transcriptome Sequencing and Comparative Transcriptomic Analyses Provide Comprehensive Insight Into Molecular Mechanisms of Cellulose and Lignin Biosynthesis in Cunninghamia lanceolata. FRONTIERS IN PLANT SCIENCE 2022; 13:883720. [PMID: 35712576 PMCID: PMC9194830 DOI: 10.3389/fpls.2022.883720] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/06/2022] [Indexed: 05/31/2023]
Abstract
Cunninghamia lanceolata is an essential timber species that provide 20%-30% raw materials for China's timber industry. Although a few transcriptomes have been published in C. lanceolata, full-length mRNA transcripts and regulatory mechanisms behind the cellulose and lignin biosynthesis have not been thoroughly investigated. Here, PacBio Iso-seq and RNA-seq analyses were adapted to identify the full-length and differentially expressed transcripts along a developmental gradient from apex to base of C. lanceolata shoots. A total of 48,846 high-quality full-length transcripts were obtained, of which 88.0% are completed transcriptome based on benchmarking universal single-copy orthologs (BUSCO) assessment. Along stem developmental gradient, 18,714 differentially expressed genes (DEGs) were detected. Further, 28 and 125 DEGs were identified as enzyme-coding genes of cellulose and lignin biosynthesis, respectively. Moreover, 57 transcription factors (TFs), including MYB and NAC, were identified to be involved in the regulatory network of cellulose and lignin biosynthesis through weighted gene co-expression network analysis (WGCNA). These TFs are composed of a comparable regulatory network of secondary cell wall formation in angiosperms, revealing a similar mechanism may exist in gymnosperms. Further, through qRT-PCR, we also investigated eight specific TFs involved in compression wood formation. Our findings provide a comprehensive and valuable source for molecular genetics breeding of C. lanceolata and will be beneficial for molecular-assisted selection.
Collapse
Affiliation(s)
- Xian-Ge Hu
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Hebi Zhuang
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Erpei Lin
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Priyanka Borah
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Mingqiu Du
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Shiya Gao
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Tongli Wang
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC, Canada
| | - Zaikang Tong
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Huahong Huang
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| |
Collapse
|