1
|
Jiang Z, Zhao Y, Gao B, Wei X, Jiao P, Zhang H, Liu S, Guan S, Ma Y. ZmARF16 Regulates ZCN12 to Promote the Accumulation of Florigen and Accelerate Flowering. Int J Mol Sci 2024; 25:9607. [PMID: 39273554 PMCID: PMC11395262 DOI: 10.3390/ijms25179607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/31/2024] [Accepted: 09/03/2024] [Indexed: 09/15/2024] Open
Abstract
Auxin response factors(ARFs) are a class of transcription factors that regulate the expression of auxin response genes and play a crucial role in plant growth and development. Florigen plays a crucial role in the process of flowering. However, the process by which auxin regulates the accumulation of florigen remains largely unclear. This study found that the expression of ZmARF16 in maize increases during flowering, and the genetic transformation of ZmARF16 accelerates the flowering process in Arabidopsis and maize. Furthermore, ZmARF16 was found to be positively correlated with the transcription of the ZCN12 gene. Similarly, the FT-like gene ZCN12 in maize rescues the late flowering phenotype of the FT mutation in Arabidopsis. Moreover, ZCN12 actively participates in the accumulation of florigen and the flowering process. Further research revealed that ZmARF16 positively responds to the auxin signal, and that the interaction between ZmARF16 and the ZCN12 promoter, as well as the subsequent promotion of ZCN12 gene expression, leads to early flowering. This was confirmed through a yeast one-hybrid and dual-luciferase assay. Therefore, the study provides evidence that the ZmARF16-ZCN12 module plays a crucial role in regulating the flowering process of maize.
Collapse
Affiliation(s)
- Zhenzhong Jiang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Changchun 130118, China
| | - Yang Zhao
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Changchun 130118, China
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Bai Gao
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Changchun 130118, China
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Xiaotong Wei
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Changchun 130118, China
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Peng Jiao
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Changchun 130118, China
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Honglin Zhang
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Changchun 130118, China
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Siyan Liu
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Changchun 130118, China
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Shuyan Guan
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Changchun 130118, China
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Yiyong Ma
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Changchun 130118, China
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| |
Collapse
|
2
|
Qian F, Zuo D, Zeng T, Gu L, Wang H, Du X, Zhu B, Ou J. Identification, Evolutionary Dynamics, and Gene Expression Patterns of the ACP Gene Family in Responding to Salt Stress in Brassica Genus. PLANTS (BASEL, SWITZERLAND) 2024; 13:950. [PMID: 38611479 PMCID: PMC11013218 DOI: 10.3390/plants13070950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024]
Abstract
Acyl carrier proteins (ACPs) have been reported to play a crucial role in responding to biotic and abiotic stresses, regulating growth and development. However, the biological function of the ACP gene family in the Brassica genus has been limited until now. In this study, we conducted a comprehensive analysis and identified a total of 120 ACP genes across six species in the Brassica genus. Among these, there were 27, 26, and 30 ACP genes in the allotetraploid B. napus, B. juncea, and B. carinata, respectively, and 14, 13, and 10 ACP genes in the diploid B. rapa, B. oleracea, and B. nigra, respectively. These ACP genes were further classified into six subclades, each containing conserved motifs and domains. Interestingly, the majority of ACP genes exhibited high conservation among the six species, suggesting that the genome evolution and polyploidization processes had relatively minor effects on the ACP gene family. The duplication modes of the six Brassica species were diverse, and the expansion of most ACPs in Brassica occurred primarily through dispersed duplication (DSD) events. Furthermore, most of the ACP genes were under purifying selection during the process of evolution. Subcellular localization experiments demonstrated that ACP genes in Brassica species are localized in chloroplasts and mitochondria. Cis-acting element analysis revealed that most of the ACP genes were associated with various abiotic stresses. Additionally, RNA-seq data revealed differential expression levels of BnaACP genes across various tissues in B. napus, with particularly high expression in seeds and buds. qRT-PCR analysis further indicated that BnaACP genes play a significant role in salt stress tolerance. These findings provide a comprehensive understanding of ACP genes in Brassica plants and will facilitate further functional analysis of these genes.
Collapse
Affiliation(s)
- Fang Qian
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Dan Zuo
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Tuo Zeng
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Lei Gu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Hongcheng Wang
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (F.Q.); (D.Z.); (T.Z.); (L.G.); (X.D.); (B.Z.)
| | - Jing Ou
- College of Forestry, Guizhou University, Guiyang 550025, China
| |
Collapse
|
3
|
Zhang SL, Wu Y, Zhang XH, Feng X, Wu HL, Zhou BJ, Zhang YQ, Cao M, Hou ZX. Characterization of the MIKC C-type MADS-box gene family in blueberry and its possible mechanism for regulating flowering in response to the chilling requirement. PLANTA 2024; 259:77. [PMID: 38421445 DOI: 10.1007/s00425-024-04349-7] [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: 09/07/2023] [Accepted: 01/23/2024] [Indexed: 03/02/2024]
Abstract
MAIN CONCLUSION The expression peak of VcAP1.4, VcAP1.6, VcAP3.1, VcAP3.2, VcAG3, VcFLC2, and VcSVP9 coincided with the endo-dormancy release of flower buds. Additionally, GA4+7 not only increased the expression of these genes but also promoted flower bud endo-dormancy release. The MIKCC-type MADS-box gene family is involved in the regulation of flower development. A total of 109 members of the MIKCC-type MADS-box gene family were identified in blueberry. According to the phylogenetic tree, these 109 MIKCC-type MADS-box proteins were divided into 13 subfamilies, which were distributed across 40 Scaffolds. The results of the conserved motif analysis showed that among 20 motifs, motifs 1, 3, and 9 formed the MADS-box structural domain, while motifs 2, 4, and 6 formed the K-box structural domain. The presence of 66 pairs of fragment duplication events in blueberry suggested that gene duplication events contributed to gene expansion and functional differentiation. Additionally, the presence of cis-acting elements revealed that VcFLC2, VcAG3, and VcSVP9 might have significant roles in the endo-dormancy release of flower buds. Meanwhile, under chilling conditions, VcAP3.1 and VcAG7 might facilitate flower bud dormancy release. VcSEP11 might promote flowering following the release of endo-dormancy, while the elevated expression of VcAP1.7 (DAM) could impede the endo-dormancy release of flower buds. The effect of gibberellin (GA4+7) treatment on the expression pattern of MIKCC-type MADS-box genes revealed that VcAP1.4, VcAP1.6, VcAP3.1, VcAG3, and VcFLC2 might promote flower bud endo-dormancy release, while VcAP3.2, VcSEP11, and VcSVP9 might inhibit its endo-dormancy release. These results indicated that VcAP1.4, VcAP1.6, VcAP1.7 (DAM), VcAP3.1, VcAG3, VcAG7, VcFLC2, and VcSVP9 could be selected as key regulatory promoting genes for controlling the endo-dormancy of blueberry flower buds.
Collapse
Affiliation(s)
- Sui-Lin Zhang
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Blueberry Research & Development Center, Beijing, 100083, China
| | - Yan Wu
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Blueberry Research & Development Center, Beijing, 100083, China
| | - Xiao-Han Zhang
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Blueberry Research & Development Center, Beijing, 100083, China
| | - Xin Feng
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Blueberry Research & Development Center, Beijing, 100083, China
| | - Hui-Ling Wu
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Blueberry Research & Development Center, Beijing, 100083, China
| | - Bing-Jie Zhou
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Blueberry Research & Development Center, Beijing, 100083, China
| | - Ya-Qian Zhang
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Blueberry Research & Development Center, Beijing, 100083, China
| | - Man Cao
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Blueberry Research & Development Center, Beijing, 100083, China
| | - Zhi-Xia Hou
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Blueberry Research & Development Center, Beijing, 100083, China.
| |
Collapse
|
4
|
Peng Y, Zhao K, Zheng R, Chen J, Zhu X, Xie K, Huang R, Zhan S, Su Q, Shen M, Niu M, Chen X, Peng D, Ahmad S, Liu ZJ, Zhou Y. A Comprehensive Analysis of Auxin Response Factor Gene Family in Melastoma dodecandrum Genome. Int J Mol Sci 2024; 25:806. [PMID: 38255880 PMCID: PMC10815038 DOI: 10.3390/ijms25020806] [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: 12/05/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Auxin Response Factors (ARFs) mediate auxin signaling and govern diverse biological processes. However, a comprehensive analysis of the ARF gene family and identification of their key regulatory functions have not been conducted in Melastoma dodecandrum, leading to a weak understanding of further use and development for this functional shrub. In this study, we successfully identified a total of 27 members of the ARF gene family in M. dodecandrum and classified them into Class I-III. Class II-III showed more significant gene duplication than Class I, especially for MedARF16s. According to the prediction of cis-regulatory elements, the AP2/ERF, BHLH, and bZIP transcription factor families may serve as regulatory factors controlling the transcriptional pre-initiation expression of MedARF. Analysis of miRNA editing sites reveals that miR160 may play a regulatory role in the post-transcriptional expression of MeARF. Expression profiles revealed that more than half of the MedARFs exhibited high expression levels in the stem compared to other organs. While there are some specific genes expressed only in flowers, it is noteworthy that MedARF16s, MedARF7A, and MedARF9B, which are highly expressed in stems, also demonstrate high expressions in other organs of M. dodecandrum. Further hormone treatment experiments revealed that these MedARFs were sensitive to auxin changes, with MedARF6C and MedARF7A showing significant and rapid changes in expression upon increasing exogenous auxin. In brief, our findings suggest a crucial role in regulating plant growth and development in M. dodecandrum by responding to changes in auxin. These results can provide a theoretical basis for future molecular breeding in Myrtaceae.
Collapse
Affiliation(s)
- Yukun Peng
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Kai Zhao
- College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; (K.Z.); (M.S.)
| | - Ruiyue Zheng
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Jiemin Chen
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Xuanyi Zhu
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Kai Xie
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Ruiliu Huang
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Suying Zhan
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Qiuli Su
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Mingli Shen
- College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; (K.Z.); (M.S.)
| | - Muqi Niu
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Xiuming Chen
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Donghui Peng
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Sagheer Ahmad
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Zhong-Jian Liu
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Yuzhen Zhou
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| |
Collapse
|
5
|
Jiang J, Wang Z, Chen Z, Wu Y, Mu M, Nie W, Zhao S, Cui G, Yin X. Identification and Evolutionary Analysis of the Auxin Response Factor (ARF) Family Based on Transcriptome Data from Caucasian Clover and Analysis of Expression Responses to Hormones. Int J Mol Sci 2023; 24:15357. [PMID: 37895037 PMCID: PMC10607010 DOI: 10.3390/ijms242015357] [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: 09/05/2023] [Revised: 10/07/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Caucasian clover (Trifolium ambiguum M. Bieb.) is an excellent perennial plant in the legume family Fabaceae, with a well-developed rhizome and strong clonal growth. Auxin is one of the most important phytohormones in plants and plays an important role in plant growth and development. Auxin response factor (ARF) can regulate the expression of auxin-responsive genes, thus participating in multiple pathways of auxin transduction signaling in a synergistic manner. No genomic database has been established for Caucasian clover. In this study, 71 TaARF genes were identified through a transcriptomic database of Caucasian clover rhizome development. Phylogenetic analysis grouped the TaARFs into six (1-6) clades. Thirty TaARFs contained a complete ARF structure, including three relatively conserved regions. Physical and chemical property analysis revealed that TaARFs are unstable and hydrophilic proteins. We also analyzed the expression pattern of TaARFs in different tissues (taproot, horizontal rhizome, swelling of taproot, rhizome bud and rhizome bud tip). Quantitative real-time RT-PCR revealed that all TaARFs were responsive to phytohormones (indole-3-acetic acid, gibberellic acid, abscisic acid and methyl jasmonate) in roots, stems and leaves. These results helped elucidate the role of ARFs in responses to different hormone treatments in Caucasian clover.
Collapse
Affiliation(s)
- Jingwen Jiang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Zicheng Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Zirui Chen
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Yuchen Wu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Meiqi Mu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Wanting Nie
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Siwen Zhao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Guowen Cui
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Xiujie Yin
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| |
Collapse
|
6
|
Wang Y, Xu Y, Liao F, Li T, Li X, Wu B, Hong SB, Xu K, Zang Y, Zheng W. Genome-wide identification of GH9 gene family and the assessment of its role during fruit abscission zone formation in Vaccinium ashei. PLANT CELL REPORTS 2023; 42:1589-1609. [PMID: 37474780 DOI: 10.1007/s00299-023-03049-y] [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: 04/06/2023] [Accepted: 07/07/2023] [Indexed: 07/22/2023]
Abstract
KEY MESSAGE The genomic location and stage-specific expression pattern of GH9 genes reveal their critical roles during fruit abscission zone formation in Vaccinium ashei. Glycosyl hydrolase family 9 (GH9) cellulases play a crucial role in both cellulose synthesis and hydrolysis during plant growth and development. Despite this importance, there is currently no study on the involvement of GH9-encoding genes, specifically VaGH9s, in abscission zone formation of rabbiteye blueberries (Vaccinium ashei). In this study, we identified a total of 61 VaGH9s in the genome, which can be classified into 3 subclasses based on conserved motifs and domains, gene structures, and phylogenetic analyses. Our synteny analysis revealed that VaGH9s are more closely related to the GH9s of Populus L. than to those of Arabidopsis, Vitis vinifera, and Citrus sinensis. In silico structural analysis predicted that most of VaGH9s are hydrophilic, and localized in cell membrane and/or cell wall, and the variable sets of cis-acting regulatory elements and functional diversity with four categories of stress response, hormone regulation, growth and development, and transcription factor-related elements are present in the promoter sequence of VaGH9s genes. Transcriptomic analysis showed that there were 22 differentially expressed VaGH9s in fruit abscission zone tissue at the veraison stage, and the expression of VaGH9B2 and VaGH9C10 was continuously increased during fruit maturation, which were in parallel with the increasing levels of cellulase activity and oxidative stress indicators, suggesting that they are involved in the separation stage of fruit abscission in Vaccinium ashei. Our work identified 22 VaGH9s potentially involved in different stages of fruit abscission and would aid further investigation into the molecular regulation of abscission in rabbiteye blueberries fruit.
Collapse
Affiliation(s)
- Yingying Wang
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Wusu Road 666, Hangzhou, 311300, Zhejiang, China
| | - Yue Xu
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Wusu Road 666, Hangzhou, 311300, Zhejiang, China
| | - Fangfang Liao
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Wusu Road 666, Hangzhou, 311300, Zhejiang, China
| | - Ting Li
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Wusu Road 666, Hangzhou, 311300, Zhejiang, China
| | - Xiaolong Li
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Wusu Road 666, Hangzhou, 311300, Zhejiang, China
| | - Boping Wu
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Wusu Road 666, Hangzhou, 311300, Zhejiang, China
| | - Seung-Beom Hong
- Department of Biotechnology, University of Houston Clear Lake, Houston, TX, 77058-1098, USA
| | - Kai Xu
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Wusu Road 666, Hangzhou, 311300, Zhejiang, China
| | - Yunxiang Zang
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Wusu Road 666, Hangzhou, 311300, Zhejiang, China
| | - Weiwei Zheng
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Wusu Road 666, Hangzhou, 311300, Zhejiang, China.
| |
Collapse
|
7
|
Huang J, Zhang G, Li Y, Lyu M, Zhang H, Zhang N, Chen R. Integrative genomic and transcriptomic analyses of a bud sport mutant 'Jinzao Wuhe' with the phenotype of large berries in grapevines. PeerJ 2023; 11:e14617. [PMID: 36620751 PMCID: PMC9817954 DOI: 10.7717/peerj.14617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/01/2022] [Indexed: 01/05/2023] Open
Abstract
Background Bud sport mutation occurs frequently in fruit plants and acts as an important approach for grapevine improvement and breeding. 'Jinzao Wuhe' is a bud sport of the elite cultivar 'Himord Seedless' with obviously enlarged organs and berries. To date, the molecular mechanisms underlying berry enlargement caused by bud sport in grapevines remain unclear. Methods Whole genome resequencing (WGRS) was performed for two pairs of bud sports and their maternal plants with similar phenotype to identify SNPs, InDels and structural variations (SVs) as well as related genes. Furthermore, transcriptomic sequencing at different developmental stages and weighted gene co-expression network analysis (WGCNA) for 'Jinzao Wuhe' and its maternal plant 'Himord Seedless' were carried out to identify the differentially expressed genes (DEGs), which were subsequently analyzed for Gene Ontology (GO) and function annotation. Results In two pairs of enlarged berry bud sports, a total of 1,334 SNPs, 272 InDels and 74 SVs, corresponding to 1,022 target genes related to symbiotic microorganisms, cell death and other processes were identified. Meanwhile, 1,149 DEGs associated with cell wall modification, stress-response and cell killing might be responsible for the phenotypic variation were also determined. As a result, 42 DEGs between 'Himord Seedless' and 'Jinzao Wuhe' harboring genetic variations were further investigated, including pectin esterase, cellulase A, cytochromes P450 (CYP), UDP-glycosyltransferase (UGT), zinc finger protein, auxin response factor (ARF), NAC transcription factor (TF), protein kinase, etc. These candidate genes offer important clues for a better understanding of developmental regulations of berry enlargement in grapevine. Conclusion Our results provide candidate genes and valuable information for dissecting the underlying mechanisms of berry development and contribute to future improvement of grapevine cultivars.
Collapse
Affiliation(s)
- Jianquan Huang
- The Research Institute of Forestry and Pomology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Guan Zhang
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
- College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Yanhao Li
- The Research Institute of Forestry and Pomology, Tianjin Academy of Agricultural Sciences, Tianjin, China
- College of Horticulture and Gardening, Tianjin Agricultural University, Tianjin, China
| | - Mingjie Lyu
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - He Zhang
- The Research Institute of Forestry and Pomology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Na Zhang
- The Research Institute of Forestry and Pomology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Rui Chen
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| |
Collapse
|
8
|
Ge H, Xu J, Hua M, An W, Wu J, Wang B, Li P, Fang H. Genome-wide identification and analysis of ACP gene family in Sorghum bicolor (L.) Moench. BMC Genomics 2022; 23:538. [PMID: 35879672 PMCID: PMC9310384 DOI: 10.1186/s12864-022-08776-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 07/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acyl carrier proteins (ACP) constitute a very conserved carrier protein family. Previous studies have found that ACP not only takes part in the fatty acid synthesis process of almost all organisms, but also participates in the regulation of plant growth, development, and metabolism, and makes plants adaptable to stresses. However, this gene family has not been systematically studied in sorghum. RESULTS Nine ACP family members were identified in the sorghum genome, which were located on chromosomes 1, 2, 5, 7, 8 and 9, respectively. Evolutionary analysis among different species divided the ACP family into four subfamilies, showing that the SbACPs were more closely related to maize. The prediction results of subcellular localization showed that SbACPs were mainly distributed in chloroplasts and mitochondria, while fluorescence localization showed that SbACPs were mainly localized in chloroplasts in tobacco leaf. The analysis of gene structure revealed a relatively simple genetic structure, that there were 1-3 introns in the sorghum ACP family, and the gene structure within the same subfamily had high similarity. The amplification method of SbACPs was mainly large fragment replication, and SbACPs were more closely related to ACPs in maize and rice. In addition, three-dimensional structure analysis showed that all ACP genes in sorghum contained four α helices, and the second helix structure was more conserved, implying a key role in function. Cis-acting element analysis indicated that the SbACPs might be involved in light response, plant growth and development regulation, biotic and abiotic stress response, plant hormone regulation, and other physiological processes. What's more, qRT-PCR analysis uncovered that some of SbACPs might be involved in the adaptive regulation of drought and salt stresses, indicating the close relationship between fatty acids and the resistance to abiotic stresses in sorghum. CONCLUSIONS In summary, these results showed a comprehensive overview of the SbACPs and provided a theoretical basis for further studies on the biological functions of SbACPs in sorghum growth, development and abiotic stress responses.
Collapse
Affiliation(s)
- Hanqiu Ge
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Jingjing Xu
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Mingzhu Hua
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Wenwen An
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Junping Wu
- Nantong Changjiang Seed Co., Ltd, Nantong, 226368, Jiangsu, People's Republic of China
| | - Baohua Wang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China.
| | - Ping Li
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China.
| | - Hui Fang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China.
| |
Collapse
|