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Luo Y, Li Y, Yin X, Deng W, Liao J, Pan Y, Jiang B, Yang H, Ding K, Jia Y. Transcriptomics analyses reveal the key genes involved in stamen petaloid formation in Alcea rosea L. BMC PLANT BIOLOGY 2024; 24:551. [PMID: 38877392 PMCID: PMC11177533 DOI: 10.1186/s12870-024-05263-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024]
Abstract
Alcea rosea L. is a traditional flower with a long cultivation history. It is extensively cultivated in China and is widely planted in green belt parks or used as cut flowers and potted ornamental because of its rich colors and flower shapes. Double-petal A. rosea flowers have a higher aesthetic value compared to single-petal flowers, a phenomenon determined by stamen petaloid. However, the underlying molecular mechanism of this phenomenon is still very unclear. In this study, an RNA-based comparative transcriptomic analysis was performed between the normal petal and stamen petaloid petal of A. rosea. A total of 3,212 differential expressed genes (DEGs), including 2,620 up-regulated DEGs and 592 down-regulated DEGs, were identified from 206,188 unigenes. Numerous DEGs associated with stamen petaloid were identified through GO and KEGG enrichment analysis. Notably, there were 63 DEGs involved in the plant hormone synthesis and signal transduction, including auxin, cytokinin, gibberellin, abscisic acid, ethylene, brassinosteroid, jasmonic acid, and salicylic acid signaling pathway and 56 key transcription factors (TFs), such as MADS-box, bHLH, GRAS, and HSF. The identification of these DEGs provides an important clue for studying the regulation pathway and mechanism of stamen petaloid formation in A. rosea and provides valuable information for molecular plant breeding.
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Affiliation(s)
- Yuanzhi Luo
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yifeng Li
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiancai Yin
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wanqing Deng
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jianwei Liao
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuanzhi Pan
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Beibei Jiang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hongchen Yang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Keying Ding
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yin Jia
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China.
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Zhao J, Xu Y, Zhang Z, Zhao M, Li K, Wang F, Sun K. Genome-wide analysis of the MADS-box gene family of sea buckthorn ( Hippophae rhamnoides ssp. sinensis) and their potential role in floral organ development. FRONTIERS IN PLANT SCIENCE 2024; 15:1387613. [PMID: 38938643 PMCID: PMC11208494 DOI: 10.3389/fpls.2024.1387613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 05/21/2024] [Indexed: 06/29/2024]
Abstract
Sea buckthorn (Hippophae rhamnoides ssp. sinensis) is a deciduous shrub or small tree in the Elaeagnaceae family. It is dioecious, featuring distinct structures in female and male flowers. The MADS-box gene family plays a crucial role in flower development and differentiation of floral organs in plants. However, systematic information on the MADS-box family in sea buckthorn is currently lacking. This study presents a genome-wide survey and expression profile of the MADS-box family of sea buckthorn. We identified 92 MADS-box genes in the H. rhamnoides ssp. Sinensis genome. These genes are distributed across 12 chromosomes and classified into Type I (42 genes) and Type II (50 genes). Based on the FPKM values in the transcriptome data, the expression profiles of HrMADS genes in male and female flowers of sea buckthorn showed that most Type II genes had higher expression levels than Type I genes. This suggesting that Type II HrMADS may play a more significant role in sea buckthorn flower development. Using the phylogenetic relationship between sea buckthorn and Arabidopsis thaliana, the ABCDE model genes of sea buckthorn were identified and some ABCDE model-related genes were selected for qRT-PCR analysis in sea buckthorn flowers and floral organs. Four B-type genes may be involved in the identity determination of floral organs in male flowers, and D-type genes may be involved in pistil development. It is hypothesized that ABCDE model genes may play an important role in the identity of sea buckthorn floral organs. This study analyzed the role of MADS-box gene family in the development of flower organs in sea buckthorn, which provides an important theoretical basis for understanding the regulatory mechanism of sex differentiation in sea buckthorn.
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Affiliation(s)
| | | | | | | | | | | | - Kun Sun
- College of Life Science, Northwest Normal University, Lanzhou, China
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3
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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.
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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.
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Chen M, Li L, Wang S, Wang P, Li Y. Transcriptome sequencing and screening of genes related to the MADS-box gene family in Clematis courtoisii. PLoS One 2024; 19:e0294426. [PMID: 38315679 PMCID: PMC10843124 DOI: 10.1371/journal.pone.0294426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/31/2023] [Indexed: 02/07/2024] Open
Abstract
The MADS-box gene family controls plant flowering and floral organ development; therefore, it is particularly important in ornamental plants. To investigate the genes associated with the MADS-box family in Clematis courtoisii, we performed full-length transcriptome sequencing on C. courtoisii using the PacBio Sequel third-generation sequencing platform, as no reference genome data was available. A total of 12.38 Gb of data, containing 9,476,585 subreads and 50,439 Unigenes were obtained. According to functional annotation, a total of 37,923 Unigenes (75.18% of the total) were assigned with functional annotations, and 50 Unigenes were identified as MADS-box related genes. Subsequently, we employed hmmerscan to perform protein sequence similarity search for the translated Unigene sequences and successfully identified 19 Unigenes associated with the MADS-box gene family, including MIKC*(1) and MIKCC (18) genes. Furthermore, within the MIKCC group, six subclasses can be further distinguished.
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Affiliation(s)
- Mingjian Chen
- Department of Ornamental Plant Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Linfang Li
- Department of Ornamental Plant Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Shu’an Wang
- Department of Ornamental Plant Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Peng Wang
- Department of Ornamental Plant Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Ya Li
- Department of Ornamental Plant Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
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Liang M, Du Z, Yang Z, Luo T, Ji C, Cui H, Li R. Genome-wide characterization and expression analysis of MADS-box transcription factor gene family in Perilla frutescens. FRONTIERS IN PLANT SCIENCE 2024; 14:1299902. [PMID: 38259943 PMCID: PMC10801092 DOI: 10.3389/fpls.2023.1299902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024]
Abstract
MADS-box transcription factors are widely involved in the regulation of plant growth, developmental processes, and response to abiotic stresses. Perilla frutescens, a versatile plant, is not only used for food and medicine but also serves as an economical oil crop. However, the MADS-box transcription factor family in P. frutescens is still largely unexplored. In this study, a total of 93 PfMADS genes were identified in P. frutescens genome. These genes, including 37 Type I and 56 Type II members, were randomly distributed across 20 chromosomes and 2 scaffold regions. Type II PfMADS proteins were found to contain a greater number of motifs, indicating more complex structures and diverse functions. Expression analysis revealed that most PfMADS genes (more than 76 members) exhibited widely expression model in almost all tissues. The further analysis indicated that there was strong correlation between some MIKCC-type PfMADS genes and key genes involved in lipid synthesis and flavonoid metabolism, which implied that these PfMADS genes might play important regulatory role in the above two pathways. It was further verified that PfMADS47 can effectively mediate the regulation of lipid synthesis in Chlamydomonas reinhardtii transformants. Using cis-acting element analysis and qRT-PCR technology, the potential functions of six MIKCC-type PfMADS genes in response to abiotic stresses, especially cold and drought, were studied. Altogether, this study is the first genome-wide analysis of PfMADS. This result further supports functional and evolutionary studies of PfMADS gene family and serves as a benchmark for related P. frutescens breeding studies.
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Affiliation(s)
- Mengjing Liang
- Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Zhongyang Du
- Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Ze Yang
- Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Tao Luo
- Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Chunli Ji
- Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Hongli Cui
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, China
| | - Runzhi Li
- Institute of Molecular Agriculture and Bioenergy, College of Agriculture, Shanxi Agricultural University, Jinzhong, Shanxi, China
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Wang J, Ye H, Li X, Lv X, Lou J, Chen Y, Yu S, Zhang L. Genome-Wide Analysis of the MADS-Box Gene Family in Hibiscus syriacus and Their Role in Floral Organ Development. Int J Mol Sci 2023; 25:406. [PMID: 38203576 PMCID: PMC10779063 DOI: 10.3390/ijms25010406] [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: 10/31/2023] [Revised: 12/16/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Hibiscus syriacus belongs to the Malvaceae family, and is a plant with medicinal, edible, and greening values. MADS-box transcription factor is a large family of regulatory factors involved in a variety of biological processes in plants. Here, we performed a genome-wide characterization of MADS-box proteins in H. syriacus and investigated gene structure, phylogenetics, cis-acting elements, three-dimensional structure, gene expression, and protein interaction to identify candidate MADS-box genes that mediate petal developmental regulation in H. syriacus. A total of 163 candidate MADS-box genes were found and classified into type I (Mα, Mβ, and Mγ) and type II (MIKC and Mδ). Analysis of cis-acting elements in the promoter region showed that most elements were correlated to plant hormones. The analysis of nine HsMADS expressions of two different H. syriacus cultivars showed that they were differentially expressed between two type flowers. The analysis of protein interaction networks also indicated that MADS proteins played a crucial role in floral organ identification, inflorescence and fruit development, and flowering time. This research is the first to analyze the MADS-box family of H. syriacus and provides an important reference for further study of the biological functions of the MADS-box, especially in flower organ development.
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Affiliation(s)
- Jie Wang
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China; (J.W.); (H.Y.); (X.L.); (J.L.); (Y.C.)
| | - Heng Ye
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China; (J.W.); (H.Y.); (X.L.); (J.L.); (Y.C.)
| | - Xiaolong Li
- College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China;
| | - Xue Lv
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China; (J.W.); (H.Y.); (X.L.); (J.L.); (Y.C.)
| | - Jiaqi Lou
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China; (J.W.); (H.Y.); (X.L.); (J.L.); (Y.C.)
| | - Yulu Chen
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China; (J.W.); (H.Y.); (X.L.); (J.L.); (Y.C.)
| | - Shuhan Yu
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China; (J.W.); (H.Y.); (X.L.); (J.L.); (Y.C.)
| | - Lu Zhang
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China; (J.W.); (H.Y.); (X.L.); (J.L.); (Y.C.)
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Paull RE, Ksouri N, Kantar M, Zerpa‐Catanho D, Chen NJ, Uruu G, Yue J, Guo S, Zheng Y, Wai CMJ, Ming R. Differential gene expression during floral transition in pineapple. PLANT DIRECT 2023; 7:e541. [PMID: 38028646 PMCID: PMC10644199 DOI: 10.1002/pld3.541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 12/01/2023]
Abstract
Pineapple (Ananas comosus var. comosus) and ornamental bromeliads are commercially induced to flower by treatment with ethylene or its analogs. The apex is transformed from a vegetative to a floral meristem and shows morphological changes in 8 to 10 days, with flowers developing 8 to 10 weeks later. During eight sampling stages ranging from 6 h to 8 days after treatment, 7961 genes were found to exhibit differential expression (DE) after the application of ethylene. In the first 3 days after treatment, there was little change in ethylene synthesis or in the early stages of the ethylene response. Subsequently, three ethylene response transcription factors (ERTF) were up-regulated and the potential gene targets were predicted to be the positive flowering regulator CONSTANS-like 3 (CO), a WUSCHEL gene, two APETALA1/FRUITFULL (AP1/FUL) genes, an epidermal patterning gene, and a jasmonic acid synthesis gene. We confirm that pineapple has lost the flowering repressor FLOWERING LOCUS C. At the initial stages, the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) was not significantly involved in this transition. Another WUSCHEL gene and a PHD homeobox transcription factor, though not apparent direct targets of ERTF, were up-regulated within a day of treatment, their predicted targets being the up-regulated CO, auxin response factors, SQUAMOSA, and histone H3 genes with suppression of abscisic acid response genes. The FLOWERING LOCUS T (FT), TERMINAL FLOWER (TFL), AGAMOUS-like APETELAR (AP2), and SEPETALA (SEP) increased rapidly within 2 to 3 days after ethylene treatment. Two FT genes were up-regulated at the apex and not at the leaf bases after treatment, suggesting that transport did not occur. These results indicated that the ethylene response in pineapple and possibly most bromeliads act directly to promote the vegetative to flower transition via APETALA1/FRUITFULL (AP1/FUL) and its interaction with SPL, FT, TFL, SEP, and AP2. A model based on AP2/ERTF DE and predicted DE target genes was developed to give focus to future research. The identified candidate genes are potential targets for genetic manipulation to determine their molecular role in flower transition.
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Affiliation(s)
- Robert E. Paull
- Tropical Plant & Soil SciencesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Najla Ksouri
- Laboratory of Genomics, Genetics and Breeding of Fruits and Grapevine, Experimental Aula Dei‐CSICZaragozaSpain
| | - Michael Kantar
- Tropical Plant & Soil SciencesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | | | - Nancy Jung Chen
- Tropical Plant & Soil SciencesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Gail Uruu
- Tropical Plant & Soil SciencesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Jingjing Yue
- Center for Genomics and BiotechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Shiyong Guo
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational MedicineKunming University of Science and TechnologyKunmingYunnanChina
| | - Yun Zheng
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational MedicineKunming University of Science and TechnologyKunmingYunnanChina
| | | | - Ray Ming
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Center for Genomics and BiotechnologyFujian Agriculture and Forestry UniversityFuzhouChina
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Lin Z, He Z, Ye D, Deng H, Lin L, Wang J, Lv X, Deng Q, Luo X, Liang D, Xia H. Genome-wide identification of the AcMADS-box family and functional validation of AcMADS32 involved in carotenoid biosynthesis in Actinidia. FRONTIERS IN PLANT SCIENCE 2023; 14:1159942. [PMID: 37404538 PMCID: PMC10315656 DOI: 10.3389/fpls.2023.1159942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/02/2023] [Indexed: 07/06/2023]
Abstract
MADS-box is a large transcription factor family in plants and plays a crucial role in various plant developmental processes; however, it has not been systematically analyzed in kiwifruit. In the present study, 74 AcMADS genes were identified in the Red5 kiwifruit genome, including 17 type-I and 57 type-II members according to the conserved domains. The AcMADS genes were randomly distributed across 25 chromosomes and were predicted to be mostly located in the nucleus. A total of 33 fragmental duplications were detected in the AcMADS genes, which might be the main force driving the family expansion. Many hormone-associated cis-acting elements were detected in the promoter region. Expression profile analysis showed that AcMADS members had tissue specificity and different responses to dark, low temperature, drought, and salt stress. Two genes in the AG group, AcMADS32 and AcMADS48, had high expression levels during fruit development, and the role of AcMADS32 was further verified by stable overexpression in kiwifruit seedlings. The content of α-carotene and the ratio of zeaxanthin/β-carotene was increased in transgenic kiwifruit seedlings, and the expression level of AcBCH1/2 was significantly increased, suggesting that AcMADS32 plays an important role in regulating carotenoid accumulation. These results have enriched our understanding of the MADS-box gene family and laid a foundation for further research of the functions of its members during kiwifruit development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Hui Xia
- *Correspondence: Dong Liang, ; Hui Xia,
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Zhang A, He H, Li Y, Wang L, Liu Y, Luan X, Wang J, Liu H, Liu S, Zhang J, Yao D. MADS-Box Subfamily Gene GmAP3 from Glycine max Regulates Early Flowering and Flower Development. Int J Mol Sci 2023; 24:ijms24032751. [PMID: 36769078 PMCID: PMC9917172 DOI: 10.3390/ijms24032751] [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: 12/17/2022] [Revised: 12/30/2022] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
AP3 has been studied and is reported to affect structural changes in floral organs in various plants. However, the function of the soybean AP3 genes in flower development is unknown. Here, the full-length cDNA sequence of GmAP3 was obtained by RACE and it was verified that it belongs to the MADS-box subfamily by a bioinformatics analysis. The expression of GmAP3 is closely related to the expression of essential enzyme genes related to flower development. Yeast two-hybrid assays demonstrated that GmAP3 interacts with AP1 to determine the identity of flower organ development. A follow-up analysis showed that overexpression of the GmAP3 gene advanced flowering time and resulted in changes in floral organ morphology. The average flowering time of overexpressed soybean and tobacco plants was 6-8 days earlier than that of wild-type plants, and the average flowering time of gene-edited soybean and tobacco plants was 6-11 days later than that of wild-type plants. In conclusion, GmAP3 may directly or indirectly affect the flower development of soybean. The results of this study lay the foundation for further research on the biological functions of MADS transcriptional factors in soybeans.
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Affiliation(s)
- Aijing Zhang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Haobo He
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Yue Li
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Lixue Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Yixuan Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Xinchao Luan
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Jiaxin Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Huijing Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Shuying Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Jun Zhang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (J.Z.); (D.Y.)
| | - Dan Yao
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (J.Z.); (D.Y.)
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10
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Ye LX, Luo MM, Wang Z, Bai FX, Luo X, Gao L, Peng J, Chen QH, Zhang L. Genome-wide analysis of MADS-box gene family in kiwifruit (Actinidia chinensis var. chinensis) and their potential role in floral sex differentiation. Front Genet 2022; 13:1043178. [PMID: 36468015 PMCID: PMC9714460 DOI: 10.3389/fgene.2022.1043178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022] Open
Abstract
Kiwifruit (Actinidia chinensis Planch.) is a functionally dioecious plant, which displays diverse morphology in male and female flowers. MADS-box is an ancient and huge gene family that plays a key role in plant floral organ differentiation. In this study, we have identified 89 MADS-box genes from A. chinensis Red 5 genome. These genes are distributed on 26 chromosomes and are classified into type I (21 genes) and type II (68 genes). Overall, type II AcMADS-box genes have more complex structures than type I with more exons, protein domains, and motifs, indicating that type II genes may have more diverse functions. Gene duplication analysis showed that most collinearity occurred in type II AcMADS-box genes, which was consistent with a large number of type II genes. Analysis of cis-acting elements in promoters showed that AcMADS-box genes are mainly associated with light and phytohormone responsiveness. The expression profile of AcMADS-box genes in different tissues showed that most genes were highly expressed in flowers. Further, the qRT-PCR analysis of the floral organ ABCDE model-related genes in male and female flowers revealed that AcMADS4, AcMADS56, and AcMADS70 were significantly expressed in female flowers. It indicated that those genes may play an important role in the sex differentiation of kiwifruit. This work provided a comprehensive analysis of the AcMADS-box genes and may help facilitate our understanding of the sex differentiation regulatory mechanism in kiwifruit.
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Affiliation(s)
- Li-Xia Ye
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Min-Min Luo
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
- College of Horticulture and Gardening, Yangtze University, Jingzhou, China
| | - Zhi Wang
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Fu-Xi Bai
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Xuan Luo
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Lei Gao
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Jue Peng
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Qing-Hong Chen
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
- *Correspondence: Qing-Hong Chen, ; Lei Zhang,
| | - Lei Zhang
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
- *Correspondence: Qing-Hong Chen, ; Lei Zhang,
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Li H, Li Y, Zhang X, Cai K, Li Y, Wang Q, Qu G, Han R, Zhao X. Genome-wide identification and expression analysis of the MADS-box gene family during female and male flower development in Juglans mandshurica. FRONTIERS IN PLANT SCIENCE 2022; 13:1020706. [PMID: 36388573 PMCID: PMC9664150 DOI: 10.3389/fpls.2022.1020706] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
The MADS-box gene family plays a crucial role in multiple developmental processes of plants, especially in floral organ specification and the regulation of fruit development and ripening. Juglans mandshurica is a precious fruit material whose quality and yield are determined by floral organ development. The molecular mechanism of J. mandshurica female and male flower development depending on MADS-box genes remains unclear. In our study, 67 JmMADS genes were identified and unevenly distributed on 15 of 16 J. mandshurica chromosomes. These genes were divided into two types [type I (Mα, Mγ, Mδ) and type II (MIKC)]. The gene structure and motif analyses showed that most genes belonging to the same type had similar gene structures and conserved motifs. The analysis of syntenic relationships showed that MADS-box genes in J. mandshurica, J. sigillata, and J. regia exhibited the highest homology and great collinearity. Analysis of cis-acting elements showed that JmMADS gene promoter regions contained light, stress and hormone response cis-acting elements. The gene expression patterns demonstrated that 30 and 26 JmMADS genes were specifically expressed in the female and male flowers, respectively. In addition, 12 selected genes common to J. mandshurica female and male flowers were significantly upregulated at the mature stage and were used to validate the reliability of the transcriptome data using quantitative real-time PCR. This comprehensive and systematic analysis of J. mandshurica MADS-box genes lays a foundation for future studies on MADS-box gene family functions.
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Affiliation(s)
- Hanxi Li
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
| | - Yuxi Li
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xinxin Zhang
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Kewei Cai
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yan Li
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
| | - Qingcheng Wang
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Guanzheng Qu
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Rui Han
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
| | - Xiyang Zhao
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
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12
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Pan X, Ouyang Y, Wei Y, Zhang B, Wang J, Zhang H. Genome-wide analysis of MADS-box families and their expressions in flower organs development of pineapple ( Ananas comosus (L.) Merr.). FRONTIERS IN PLANT SCIENCE 2022; 13:948587. [PMID: 36311063 PMCID: PMC9597317 DOI: 10.3389/fpls.2022.948587] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
MADS-box genes play crucial roles in plant vegetative and reproductive growth, better development of inflorescences, flower, and fruit. Pineapple is a typical collective fruit, and a comprehensive analysis of the MADS-box gene family in the development of floral organs of pineapple is still lacking. In this study, the whole-genome survey and expression profiling of the MADS-box family in pineapple were introduced. Forty-four AcMADS genes were identified in pineapple, 39 of them were located on 18 chromosomes and five genes were distributed in five scaffolds. Twenty-two AcMADS genes were defined as 15 pairs of segmental duplication events. Most members of the type II subfamily of AcMADS genes had higher expression levels in floral organs compared with type I subfamily, thereby suggesting that AcMADS of type II may play more crucial roles in the development of floral organs of pineapple. Six AcMADS genes have significant tissue-specificity expression, thereby suggesting that they may participate in the formation of one or more floral organs. This study provides valuable insights into the role of MADS-box gene family in the floral organ development of pineapple.
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Genome-wide identification, phylogenetic and expression pattern analysis of MADS-box family genes in foxtail millet (Setaria italica). Sci Rep 2022; 12:4979. [PMID: 35322041 PMCID: PMC8943164 DOI: 10.1038/s41598-022-07103-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/10/2022] [Indexed: 11/28/2022] Open
Abstract
Foxtail millet (Setaria italica) is rich in nutrients and extremely beneficial to human health. We identified and comprehensively analyzed 89 MADS-box genes in the foxtail millet genome. According to the classification of MADS-box genes in Arabidopsis thaliana and rice, the SiMADS-box genes were divided into M-type (37) and MIKC-type (52). During evolution, the differentiation of MIKC-type MADS-box genes occurred before that of monocotyledons and dicotyledons. The SiMADS-box gene structure has undergone much differentiation, and the number of introns in the MIKC-type subfamily is much greater than that in the M-type subfamily. Analysis of gene duplication events revealed that MIKC-type MADS-box gene segmental duplication accounted for the vast majority of gene duplication events, and MIKC-type MADS-box genes played a major role in the amplification of SiMADS-box genes. Collinearity analysis showed highest collinearity between foxtail millet and maize MADS-box genes. Analysis of tissue-specific expression showed that SiMADS-box genes are highly expressed throughout the grain-filling process. Expression analysis of SiMADS-box genes under eight different abiotic stresses revealed many stress-tolerant genes, with induced expression of SiMADS33 and SiMADS78 under various stresses warranting further attention. Further, some SiMADS-box proteins may interact under external stress. This study provides insights for MADS-box gene mining and molecular breeding of foxtail millet in the future.
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Zhang Q, Hou S, Sun Z, Chen J, Meng J, Liang D, Wu R, Guo Y. Genome-Wide Identification and Analysis of the MADS-Box Gene Family in Theobroma cacao. Genes (Basel) 2021; 12:genes12111799. [PMID: 34828404 PMCID: PMC8622960 DOI: 10.3390/genes12111799] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 01/03/2023] Open
Abstract
The MADS-box family gene is a class of transcription factors that have been extensively studied and involved in several plant growth and development processes, especially in floral organ specificity, flowering time and initiation and fruit development. In this study, we identified 69 candidate MADS-box genes and clustered these genes into five subgroups (Mα: 11; Mβ: 2; Mγ: 14; Mδ: 9; MIKC: 32) based on their phylogenetical relationships with Arabidopsis. Most TcMADS genes within the same subgroup showed a similar gene structure and highly conserved motifs. Chromosomal distribution analysis revealed that all the TcMADS genes were evenly distributed in 10 chromosomes. Additionally, the cis-acting elements of promoter, physicochemical properties and subcellular localization were also analyzed. This study provides a comprehensive analysis of MADS-box genes in Theobroma cacao and lays the foundation for further functional research.
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Affiliation(s)
- Qianqian Zhang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
| | - Sijia Hou
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
| | - Zhenmei Sun
- Institute of Marine Materials Science and Engineering, College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China;
| | - Jing Chen
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
| | - Jianqiao Meng
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
| | - Dan Liang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
| | - Yunqian Guo
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
- Correspondence:
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15
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Guan H, Wang H, Huang J, Liu M, Chen T, Shan X, Chen H, Shen J. Genome-Wide Identification and Expression Analysis of MADS-Box Family Genes in Litchi ( Litchi chinensis Sonn.) and Their Involvement in Floral Sex Determination. PLANTS 2021; 10:plants10102142. [PMID: 34685951 PMCID: PMC8540616 DOI: 10.3390/plants10102142] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/08/2021] [Accepted: 09/18/2021] [Indexed: 11/16/2022]
Abstract
Litchi possesses unique flower morphology and adaptive reproduction strategies. Although previous attention has been intensively devoted to the mechanisms underlying its floral induction, the molecular basis of flower sex determination remains largely unknown. MADS-box genes are promising candidates for this due to their significant roles in various aspects of inflorescence and flower organogenesis. Here, we present a detailed overview of phylogeny and expression profiles of 101 MADS-box genes that were identified in litchi. These LcMADSs are unevenly located across the 15 chromosomes and can be divided into type I and type II genes. Fifty type I MADS-box genes are subdivided into Mα, Mβ and Mγ subgroups, while fifty-one type II LcMADSs consist of 37 MIKCC -type and 14 MIKC *-type genes. Promoters of both types of LcMADS genes contain mainly ABA and MeJA response elements. Tissue-specific and development-related expression analysis reveal that LcMADS51 could be positively involved in litchi carpel formation, while six MADS-box genes, including LcMADS42/46/47/75/93/100, play a possible role in stamen development. GA is positively involved in the sex determination of litchi flowers by regulating the expression of LcMADS51 (LcSTK). However, JA down-regulates the expression of floral organ identity genes, suggesting a negative role in litchi flower development.
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Affiliation(s)
- Hongling Guan
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; (H.G.); (H.W.); (J.H.); (M.L.); (T.C.); (X.S.)
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Han Wang
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; (H.G.); (H.W.); (J.H.); (M.L.); (T.C.); (X.S.)
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jianjun Huang
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; (H.G.); (H.W.); (J.H.); (M.L.); (T.C.); (X.S.)
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Mingxin Liu
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; (H.G.); (H.W.); (J.H.); (M.L.); (T.C.); (X.S.)
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Ting Chen
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; (H.G.); (H.W.); (J.H.); (M.L.); (T.C.); (X.S.)
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Xiaozhen Shan
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; (H.G.); (H.W.); (J.H.); (M.L.); (T.C.); (X.S.)
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Houbin Chen
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; (H.G.); (H.W.); (J.H.); (M.L.); (T.C.); (X.S.)
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
- Correspondence: (H.C.); (J.S.); Tel.: +86-20-85280231 (H.C. & J.S.)
| | - Jiyuan Shen
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; (H.G.); (H.W.); (J.H.); (M.L.); (T.C.); (X.S.)
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
- Correspondence: (H.C.); (J.S.); Tel.: +86-20-85280231 (H.C. & J.S.)
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Dong X, Deng H, Ma W, Zhou Q, Liu Z. Genome-wide identification of the MADS-box transcription factor family in autotetraploid cultivated alfalfa (Medicago sativa L.) and expression analysis under abiotic stress. BMC Genomics 2021; 22:603. [PMID: 34362293 PMCID: PMC8348820 DOI: 10.1186/s12864-021-07911-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/23/2021] [Indexed: 02/06/2023] Open
Abstract
Background Alfalfa, the “queen of forage”, is the most extensively cultivated forage legume in the world. The development and yield of alfalfa are seriously limited by abiotic stress. MADS-box transcription factors are one of the largest gene families and play a pivotal role in plant development and abiotic stress. However, little is known regarding the MADS-box transcription factors in autotetraploid cultivated alfalfa. Results In the present study, we identified 120 MsMADS-box genes in the alfalfa genome. Phylogenetic analysis indicated that 75 type-I MsMADS-box genes were classified into the Mα, Mβ, and Mγ subgroups, and 45 type-II MsMADS-box genes were classified into 11 subgroups. The promoter region of MsMADS-box genes containing several hormone and stress related elements. Chromosomal location analysis revealed that 117 MsMADS-box genes were unevenly distributed on 32 chromosomes, and the remaining three genes were located on unmapped scaffolds. A total of nine pairs of segmental duplications and four groups of tandem duplications were found. Expression analysis showed that MsMADS-box genes were differentially expressed in various tissues and under abiotic stresses. qRT-PCR analysis revealed that the expression profiles of eight selected MsMADS-box genes were distinct under various stresses. Conclusions In this study, MsMADS-box genes were identified in the cultivated alfalfa genome based on autotetraploid level, and further confirmed by Gene Ontology (GO) analysis, phylogenetic analysis, sequence features and expression analysis. Taken together, these findings will provide clues for further study of MsMADS-box functions and alfalfa molecular breeding. Our study is the first to systematically identify and characterize the MADS-box transcription factors in autotetraploid cultivated alfalfa (Medicago sativa L.), and eight MsMADS-box genes were significantly involved in response to various stresses. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07911-9.
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Affiliation(s)
- Xueming Dong
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, 730000, Lanzhou, People's Republic of China
| | - Hao Deng
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, 730000, Lanzhou, People's Republic of China
| | - Wenxue Ma
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, 730000, Lanzhou, People's Republic of China
| | - Qiang Zhou
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, 730000, Lanzhou, People's Republic of China
| | - Zhipeng Liu
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, 730000, Lanzhou, People's Republic of China.
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Genome-wide identification and expression analysis of the MADS-box transcription factor family in Camellia sinensis. J Appl Genet 2021; 62:249-264. [PMID: 33598859 DOI: 10.1007/s13353-021-00621-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 02/06/2021] [Accepted: 02/11/2021] [Indexed: 10/22/2022]
Abstract
The MADS-box genes are an important class of transcription factors and play critical roles in flower development. However, the functions of these genes in the economically important drinking plant, Camellia sinensis, are still not reported. Here, an evolutionary analysis of tea MADS-box genes was performed at whole genome level. A total of 83 MADS-box genes were identified in tea, and their gene structures and expression patterns were further analyzed. The tea MADS-box genes were classified into Mα (26), Mβ (12), Mγ (9), MIKC* (7), and MIKCC (29) clade according to their phylogenetic relationship with Arabidopsis thaliana. Several cis-elements were identified in the promoter regions of the CsMADS genes that are important in regulating growth, development, light responses, and the response to several stresses. Most CsMADS genes display clear different expression patterns in different organs and different species of tea plant. The expression of CsMADS genes can be regulated by abiotic stresses and phytohormone treatment. Our results lay the foundation for future research on the function of CsMADS genes and beneficial for improving tea agricultural traits in the future.
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18
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Shi Y, Zhang X, Chang X, Yan M, Zhao H, Qin Y, Wang H. Integrated analysis of DNA methylome and transcriptome reveals epigenetic regulation of CAM photosynthesis in pineapple. BMC PLANT BIOLOGY 2021; 21:19. [PMID: 33407144 PMCID: PMC7789485 DOI: 10.1186/s12870-020-02814-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/22/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND Crassulacean acid metabolism (CAM) photosynthesis is an important carbon fixation pathway especially in arid environments because it leads to higher water-use efficiency compared to C3 and C4 plants. However, the role of DNA methylation in regulation CAM photosynthesis is not fully understood. RESULTS Here, we performed temporal DNA methylome and transcriptome analysis of non-photosynthetic (white base) and photosynthetic (green tip) tissues of pineapple leaf. The DNA methylation patterns and levels in these two tissues were generally similar for the CG and CHG cytosine sequence contexts. However, CHH methylation was reduced in white base leaf tissue compared with green tip tissue across diel time course in both gene and transposon regions. We identified thousands of local differentially methylated regions (DMRs) between green tip and white base at different diel periods. We also showed that thousands of genes that overlapped with DMRs were differentially expressed between white base and green tip leaf tissue across diel time course, including several important CAM pathway-related genes, such as beta-CA, PEPC, PPCK, and MDH. CONCLUSIONS Together, these detailed DNA methylome and transcriptome maps provide insight into DNA methylation changes and enhance our understanding of the relationships between DNA methylation and CAM photosynthesis.
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Affiliation(s)
- Yan Shi
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xingtan Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xiaojun Chang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Maokai Yan
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Heming Zhao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yuan Qin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - Haifeng Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China.
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Genome-wide study of flowering-related MADS-box genes family in Cardamine hirsuta. 3 Biotech 2020; 10:518. [PMID: 33194522 DOI: 10.1007/s13205-020-02521-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/28/2020] [Indexed: 10/23/2022] Open
Abstract
MADS-box genes take part in diverse biological functions especially in development of reproductive structures and control of flowering time. Recently, Cardamine hirsuta has emerged as an exclusively powerful genetic system in comparative studies of development. Although the C. hirsuta genome sequence is available but a comprehensive analysis of its MADS-box family genes is still lacking. Here, we determined 50 Cardamine MADS-box genes through bioinformatics tools and classified them into 2 Mβ, 6 Mα and 2 Mγ and 40 MIKC-type (35 MIKCc and 5MIKC*) genes based on a phylogenetic analysis. The C. hirsuta MIKC subfamily could be further classified into 14 subgroups as Arabidopsis. However the number of MADS-box proteins was not equal among these subgroups. Based on the structural diversity among 50 MADS-box genes, 2 lineages were obtained, type I and type II. The lowest number of introns (0 or 1) was found in the Mα, Mβ, and Mγ groups of the type I genes. The most Cardamine MADS-box genes were randomly distributed on only three chromosomes. C. hirsuta had a relatively lower number of flowering MADS-box genes than A. thaliana and probably tandem duplication event resulted in the expansion of FLC, SQUA and TM3 family members in Arabidopsis. Moreover among the conserved motifs, ChMADS5 of SQUA, ChMADS34 of TM3 and ChMADS51 of AGL15 families had no K-domain. This study provides a basis for further functional investigation of MADS-box genes in C. hirsuta.
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