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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.
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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.
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Feng X, Zhou B, Wu X, Wu H, Zhang S, Jiang Y, Wang Y, Zhang Y, Cao M, Guo B, Su S, Hou Z. Molecular characterization of SPL gene family during flower morphogenesis and regulation in blueberry. BMC PLANT BIOLOGY 2023; 23:40. [PMID: 36650432 PMCID: PMC9847132 DOI: 10.1186/s12870-023-04044-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
The SPL gene is a plant-specific transcription factor involved in the regulation of plant growth and development, which have been identified in woody plants. The process of floral bud differentiation affects the timing of flowering and fruit set and regulates plant growth, however, the mechanism of regulation of flower development by SPL genes is less studied. In this study, 56 VcSPL genes were identified in the tetraploid blueberry. The VcSPL gene family was classified into six subfamilies, and analysis of cis-elements showed that VcSPL genes were regulated by light, phytohormones (abscisic acid, MeJA), and low temperature. In the evolutionary analysis, segmental replication may play an important role in VcSPL gene amplification. Interestingly, we also studied diploid blueberry (Bilberry), in which 24 SPL genes were identified, and 36 homologous pairs were found, suggesting a high degree of convergence in the syntenic relationship between blueberry (Vaccinium corymbosum L) and bilberry (Vaccinium darrowii). Based on the expression profile, VcSPL genes were expressed at high levels in flowers, shoots, and roots, indicating a diversity of gene functions. Then we selected 20 differentially-expressed SPL genes to further investigate the role of VcSPL in floral induction and initiation. It showed that the genes VcSPL40, VcSPL35, VcSPL45, and VcSPL53 may play a crucial role in the blueberry floral transition phase (from vegetative growth to flower initiation). These results provided important information for understanding and exploring the role of VcSPLs in flower morphogenesis and plant growth.
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Affiliation(s)
- Xin Feng
- Key Laboratory for Silviculture and Conservation of Ministry of Education, Research and Development Center of Blueberry, Beijing Forestry University, Beijing, 100083, China
| | - Bingjie Zhou
- Key Laboratory for Silviculture and Conservation of Ministry of Education, Research and Development Center of Blueberry, Beijing Forestry University, Beijing, 100083, China
| | - Xinliang Wu
- Key Laboratory for Silviculture and Conservation of Ministry of Education, Research and Development Center of Blueberry, Beijing Forestry University, Beijing, 100083, China
| | - Huiling Wu
- Key Laboratory for Silviculture and Conservation of Ministry of Education, Research and Development Center of Blueberry, Beijing Forestry University, Beijing, 100083, China
| | - Suilin Zhang
- Key Laboratory for Silviculture and Conservation of Ministry of Education, Research and Development Center of Blueberry, Beijing Forestry University, Beijing, 100083, China
| | - Ying Jiang
- Key Laboratory for Silviculture and Conservation of Ministry of Education, Research and Development Center of Blueberry, Beijing Forestry University, Beijing, 100083, China
| | - Yaping Wang
- Key Laboratory for Silviculture and Conservation of Ministry of Education, Research and Development Center of Blueberry, Beijing Forestry University, Beijing, 100083, China
| | - Yaqian Zhang
- Key Laboratory for Silviculture and Conservation of Ministry of Education, Research and Development Center of Blueberry, Beijing Forestry University, Beijing, 100083, China
| | - Man Cao
- Key Laboratory for Silviculture and Conservation of Ministry of Education, Research and Development Center of Blueberry, Beijing Forestry University, Beijing, 100083, China
| | - Baoshi Guo
- Key Laboratory for Silviculture and Conservation of Ministry of Education, Research and Development Center of Blueberry, Beijing Forestry University, Beijing, 100083, China
| | - Shuchai Su
- Key Laboratory for Silviculture and Conservation of Ministry of Education, Research and Development Center of Blueberry, Beijing Forestry University, Beijing, 100083, China
| | - Zhixia Hou
- Key Laboratory for Silviculture and Conservation of Ministry of Education, Research and Development Center of Blueberry, Beijing Forestry University, Beijing, 100083, China.
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Wang M, Mo Z, Lin R, Zhu C. Characterization and expression analysis of the SPL gene family during floral development and abiotic stress in pecan ( Carya illinoinensis). PeerJ 2021; 9:e12490. [PMID: 34966577 PMCID: PMC8667720 DOI: 10.7717/peerj.12490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 10/25/2021] [Indexed: 12/14/2022] Open
Abstract
SQUAMOSA promoter binding protein-like (SPL) genes are a type of plant-specific transcription factors that play crucial roles in the regulation of phase transition, floral transformation, fruit development, and various stresses. Although SPLs have been characterized in several model species, no systematic analysis has been studied in pecans, an important woody oil tree species. In this study, a total of 32 SPL genes (CiSPLs) were identified in the pecan genome. After conducting phylogenetic analysis of the conserved SBP proteins from Arabidopsis, rice, and poplar, the CiSPLs were separated into eight subgroups. The CiSPL genes within the same subgroup contained very similar exon-intron structures and conserved motifs. Nine segmentally duplicated gene pairs in the pecan genome and 16 collinear gene pairs between the CiSPL and AtSPL genes were identified. Cis-element analysis showed that CiSPL genes may regulate plant meristem differentiation and seed development, participate in various biological processes, and respond to plant hormones and environmental stresses. Therefore, we focused our study on the expression profiles of CiSPL genes during flower and fruit development. Most of the CiSPL genes were predominantly expressed in buds and/or female flowers. Additionally, quantitative real time PCR (qRT-PCR) analyses confirmed that CiSPL genes showed distinct spatiotemporal expression patterns in response to drought and salt treatments. The study provides foundation for the further exploration of the function and evolution of SPL genes in pecan.
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Affiliation(s)
- Min Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China.,Horticulture Research Institute, Shanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Zhenghai Mo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Ruozhu Lin
- Key laboratory of Forest Protection of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Cancan Zhu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
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Jiang M, He Y, Chen X, Zhang X, Guo Y, Yang S, Huang J, Traw MB. CRISPR-based assessment of genomic structure in the conserved SQUAMOSA promoter-binding-like gene clusters in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1301-1314. [PMID: 32996244 DOI: 10.1111/tpj.15001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/14/2020] [Accepted: 09/03/2020] [Indexed: 05/07/2023]
Abstract
Although SQUAMOSA promoter-binding-like (SPL) transcription factors are important regulators of development in rice (Oryza sativa), prior assessments of the SPL family have been limited to single genes. A functional comparison across the full gene family in standardized genetic backgrounds has not been reported previously. Here, we demonstrate that the SPL gene family in rice is enriched due to the most recent whole genome duplication (WGD). Notably, 10 of 19 rice SPL genes (52%) cluster in four units that have persisted for at least 50 million years. We show that SPL gene grouping and retention following WGD is widespread in angiosperms, suggesting the conservatism and importance of this gene arrangement. We used Cas9 editing to generate transformation lines for all 19 SPL genes in a common set of backgrounds, and found that knockouts of 14 SPL genes exhibited defects in plant height, 10 exhibited defects in panicle size, and nine had altered grain lengths. We observed subfunctionalization of genes in the paleoduplicated pairs, but little evidence of neofunctionalization. Expression of OsSPL3 was negatively correlated with that of its closest neighbor in its synteny group, OsSPL4, and its sister paired gene, OsSPL12, in the opposing group. Nucleotide diversity was lower in eight of the nine singleton genes in domesticated rice, relative to wild rice, whereas the reverse was true for the paired genes. Together, these results provide functional information on eight previously unexamined OsSPL family members and suggest that paleoduplicate pair redundancy benefits plant survival and innovation.
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Affiliation(s)
- Mengmeng Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ying He
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaonan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yanru Guo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ju Huang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - M Brian Traw
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
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