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Zhao Y, Liu Z, She H, Xu Z, Zhang H, Zheng S, Qian W. Comparative Transcriptome Analysis of Gene Expression Between Female and Monoecious Spinacia oleracea L. Genes (Basel) 2024; 16:24. [PMID: 39858571 PMCID: PMC11764767 DOI: 10.3390/genes16010024] [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: 11/29/2024] [Revised: 12/23/2024] [Accepted: 12/24/2024] [Indexed: 01/27/2025] Open
Abstract
BACKGROUND Spinach (Spinacia oleracea L.) is an important leafy vegetable with dioecious and occasional monoecious plants. Monoecious lines are more suitable for hybrid production than dioecious lines due to their extended flowering period. However, genetic research on the sex determination of monoecism remains limited. METHODS In this study, RNA-seq analysis of monoecious and female spinach plants was performed at two distinct flowering stages. In total, we identified 4586 differentially expressed genes (DEGs), which were primarily involved in biological processes such as hormone signaling, cell wall biosynthesis, photosynthesis, and flower development, based on Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. RESULTS Among these DEGs, 354 transcription factors, including 27 genes associated with the ABCDE gene, were discovered. Furthermore, a co-expression gene regulatory network was built, identifying nine key genes that play important roles in regulating sex differentiation between female and monoecious plants. CONCLUSIONS Our findings provide crucial molecular insights into the mechanisms of monoecism in spinach and offer a scientific basis for future spinach breeding.
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Affiliation(s)
- Yingjie Zhao
- College of Horticulture, Shanxi Agricultural University, Taigu, Jinzhong 030801, China;
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Z.L.); (H.S.); (Z.X.); (H.Z.)
| | - Zhiyuan Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Z.L.); (H.S.); (Z.X.); (H.Z.)
| | - Hongbing She
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Z.L.); (H.S.); (Z.X.); (H.Z.)
| | - Zhaosheng Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Z.L.); (H.S.); (Z.X.); (H.Z.)
| | - Helong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Z.L.); (H.S.); (Z.X.); (H.Z.)
| | - Shaowen Zheng
- College of Horticulture, Shanxi Agricultural University, Taigu, Jinzhong 030801, China;
| | - Wei Qian
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Z.L.); (H.S.); (Z.X.); (H.Z.)
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Lephoto KS, Wang D, Liu S, Li L, Wang C, Liu R, Jiang Y, Wang A, Wang K, Zhao M, Chen P, Wang Y, Zhang M. Evolution, Structural and Functional Characteristics of the MADS-box Gene Family and Gene Expression Through Methyl Jasmonate Regulation in Panax ginseng C.A. Meyer. PLANTS (BASEL, SWITZERLAND) 2024; 13:3574. [PMID: 39771274 PMCID: PMC11677711 DOI: 10.3390/plants13243574] [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: 11/05/2024] [Revised: 12/11/2024] [Accepted: 12/19/2024] [Indexed: 01/11/2025]
Abstract
MADS-box genes are essential for plant development and secondary metabolism. The majority of genes within a genome exist in a gene family, each with specific functions. Ginseng is an herb used in medicine for its potential health benefits. The MADS-Box gene family in Jilin ginseng has not been studied. This study investigated the evolution and structural and functional diversification of the PgMADS gene family using bioinformatics and analyzed gene expression through methyl jasmonate (MeJA) regulation. The results revealed that the evolution of the PgMADS gene family is diverged into ten clusters of a constructed phylogenetic tree, of which the SOC1 cluster is the most prevalent with a higher number of PgMADS genes. Despite their distinct evolutionary clusters, a significant number of members contains common conserved motifs. The PgMADS gene family was functionally differentiated into three primary functional categories, biological process, molecular function, and cellular component. Their expression is variable within a tissue, at a developmental stage, and in cultivars. Regardless of the diversity of the functions of PgMADS genes and evolution, their expression correlated and formed a co-expression gene network. Weighted gene co-expression network analyses identified hub genes that could be regulating ginsenoside biosynthesis. Interestingly, the family also is involved in MeJA regulation. These findings provide a valuable reference for future investigations on PgMADS genes.
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Affiliation(s)
- Katleho Senoko Lephoto
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (K.S.L.); (D.W.); (S.L.); (L.L.); (C.W.); (R.L.); (Y.J.); (A.W.); (K.W.); (M.Z.); (P.C.)
- National University of Lesotho, P.O. Roma 180, Roma, Maseru 100, Lesotho
| | - Dinghui Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (K.S.L.); (D.W.); (S.L.); (L.L.); (C.W.); (R.L.); (Y.J.); (A.W.); (K.W.); (M.Z.); (P.C.)
| | - Sizhang Liu
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (K.S.L.); (D.W.); (S.L.); (L.L.); (C.W.); (R.L.); (Y.J.); (A.W.); (K.W.); (M.Z.); (P.C.)
| | - Li Li
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (K.S.L.); (D.W.); (S.L.); (L.L.); (C.W.); (R.L.); (Y.J.); (A.W.); (K.W.); (M.Z.); (P.C.)
| | - Chaofan Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (K.S.L.); (D.W.); (S.L.); (L.L.); (C.W.); (R.L.); (Y.J.); (A.W.); (K.W.); (M.Z.); (P.C.)
| | - Ruicen Liu
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (K.S.L.); (D.W.); (S.L.); (L.L.); (C.W.); (R.L.); (Y.J.); (A.W.); (K.W.); (M.Z.); (P.C.)
| | - Yue Jiang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (K.S.L.); (D.W.); (S.L.); (L.L.); (C.W.); (R.L.); (Y.J.); (A.W.); (K.W.); (M.Z.); (P.C.)
| | - Aimin Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (K.S.L.); (D.W.); (S.L.); (L.L.); (C.W.); (R.L.); (Y.J.); (A.W.); (K.W.); (M.Z.); (P.C.)
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (K.S.L.); (D.W.); (S.L.); (L.L.); (C.W.); (R.L.); (Y.J.); (A.W.); (K.W.); (M.Z.); (P.C.)
- Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (K.S.L.); (D.W.); (S.L.); (L.L.); (C.W.); (R.L.); (Y.J.); (A.W.); (K.W.); (M.Z.); (P.C.)
- Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Ping Chen
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (K.S.L.); (D.W.); (S.L.); (L.L.); (C.W.); (R.L.); (Y.J.); (A.W.); (K.W.); (M.Z.); (P.C.)
- Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (K.S.L.); (D.W.); (S.L.); (L.L.); (C.W.); (R.L.); (Y.J.); (A.W.); (K.W.); (M.Z.); (P.C.)
- Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China; (K.S.L.); (D.W.); (S.L.); (L.L.); (C.W.); (R.L.); (Y.J.); (A.W.); (K.W.); (M.Z.); (P.C.)
- Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
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Duan SF, Yu JC, Baldwin TC, Yuan Y, Xiang GS, Cui R, Zhao Y, Mo XC, Lu YC, Liang YL. Genome-wide identification of a MADS-box transcription factor family and their expression during floral development in Coptis teeta wall. BMC PLANT BIOLOGY 2024; 24:1023. [PMID: 39468440 PMCID: PMC11520390 DOI: 10.1186/s12870-024-05714-0] [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: 08/18/2023] [Accepted: 10/15/2024] [Indexed: 10/30/2024]
Abstract
BACKGROUND MADS-box transcription factors have been shown to be involved in multiple developmental processes, including the regulation of floral organ formation and pollen maturation. However, the role of the MADS-box gene family in floral development of the alpine plant species Coptis teeta Wall, which is widely used in Traditional Chinese Medicine (TCM), is unknown. RESULTS Sixty-six MADS-box genes were identified in the C. teeta genome. These genes were shown to be unevenly distributed throughout the genome of C. teeta. The majority of which (49) were classified as type I MADS-box genes and were further subdivided into four groups (Mα, Mβ, Mγ and Mδ). The remainder were identified as belonging to the type II MADS-box gene category. It was observed that four pairs of segmental and tandem duplication had occurred in the C. teeta MADS-box gene family, and that the ratios of Ka/Ks were less than 1, suggesting that these genes may have experienced purifying selection during evolution. Gene expression profiling analysis revealed that 38 MADS-box genes displayed differential expression patterns between the M and F floral phenotypes. Sixteen of these MADS-box genes were further verified by RT-qPCR. The 3D structure of each subfamily gene was predicted, further indicating that MADS-box genes of the same type possess structural similarities to the known template. CONCLUSIONS These data provide new insights into the molecular mechanism of dichogamy and herkogamy formation in C. teeta and establish a solid foundation for future studies of the MADS-box genes family in this medicinal plant species.
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Affiliation(s)
- Shao-Feng Duan
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Ji-Chen Yu
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Timothy Charles Baldwin
- Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton, WV1 1LY, UK
| | - Yuan Yuan
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Gui-Sheng Xiang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Rui Cui
- Yunnan Land and Resources Vocational College, Kunming, Yunnan, 650201, China
| | - Yan Zhao
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Xin-Chun Mo
- Department of Applied Technology, Lijiang Normal University, Lijiang, Yunnan, 674100, China.
- , Fengyuan Road, Panlong District, Kunming, 650201, China.
| | - Ying-Chun Lu
- Yunnan Agricultural University College of Education and Vocational Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
- , Fengyuan Road, Panlong District, Kunming, 650201, China.
| | - Yan-Li Liang
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
- , Fengyuan Road, Panlong District, Kunming, 650201, China.
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Liu F, Aziz RB, Wang Y, Xuan X, Yu M, Qi Z, Chen X, Wu Q, Qu Z, Dong T, Li S, Fang J, Wang C. Identification of VvAGL Genes Reveals Their Network's Involvement in the Modulation of Seed Abortion via Responding Multi-Hormone Signals in Grapevines. Int J Mol Sci 2024; 25:9849. [PMID: 39337335 PMCID: PMC11432271 DOI: 10.3390/ijms25189849] [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: 07/17/2024] [Revised: 09/08/2024] [Accepted: 09/10/2024] [Indexed: 09/30/2024] Open
Abstract
The formation of seedless traits is regulated by multiple factors. AGLs, which belong to the MADS-box family, were reported to be important regulators in this process; however, the underlying mechanism remains elusive. Here, we identified the VvAGL sub-family genes during the seed abortion process in seedless grapevine cv. 'JingkeJing' and found 40 differentially expressed VvAGL members and 1069 interacting proteins in this process. Interestingly, almost all members and their interacting proteins involved in the tryptophan metabolic pathway (K14486) and participated in the phytohormone signalling (KO04075) pathway, including the growth hormone (IAA), salicylic acid (SA), abscisic acid (ABA), cytokinin (CTK), and ethylene signalling pathways. The promoters of AGL sub-family genes contain cis-elements in response to hormones such as IAA, ABA, CTK, SA, and ETH, implying that they might respond to multi-hormone signals and involve in hormone signal transductions. Further expression analysis revealed VvAGL6-2, VvAGL11, VvAGL62-11, and VvAGL15 had the highest expression at the critical period of seed abortion, and there were positive correlations between ETH-VvAGL15-VvAGL6-2, ABA-VvAGL80, and SA-VvAGL62 in promoting seed abortion but negative feedback between IAA-VvAGL15-VvAGL6-2 and CTK-VvAGL11. Furthermore, many genes in the IAA, ABA, SA, CTK, and ETH pathways had a special expressional pattern in the seed, whereby we developed a regulatory network mediated by VvAGLs by responding to multihormonal crosstalk during grape seed abortion. Our findings provide new insights into the regulatory network of VvAGLs in multi-hormone signalling to regulate grape seed abortion, which could be helpful in the molecular breeding of high-quality seedless grapes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Chen Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (F.L.); (R.B.A.); (Y.W.); (X.X.); (M.Y.); (Z.Q.); (X.C.); (Q.W.); (Z.Q.); (T.D.); (S.L.); (J.F.)
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Tantisuwanichkul K, Komaki S, Watanabe M, Tohge T, Sirikantaramas S. Unveiling the regulatory role of DzAGL6-1 in carotenoid biosynthesis during durian (Durio zibethinus) fruit development. PLANT CELL REPORTS 2024; 43:217. [PMID: 39153055 DOI: 10.1007/s00299-024-03302-y] [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: 04/20/2024] [Accepted: 07/29/2024] [Indexed: 08/19/2024]
Abstract
KEY MESSAGE Approximately 119 MADS-box genes have been identified in durian. Moreover, DzAGL6-1 primarily expressed during fruit development, activates the DzPSY promoter. Transient expression of DzAGL6-1 in tomatoes influences carotenoid production. MADS-box transcription factors play a crucial role in regulating plant biological processes, including fruit ripening and associated events. This study aimed to comprehend the mechanisms involved in durian fruit development and ripening and carotenoid production by conducting a genome-wide analysis of MADS-box proteins in durian (Durio zibethinus L.), an economically important fruit in Southeast Asia. A total of 119 durian MADS-box proteins were identified from the genome of the 'Musang King' cultivar. Based on the phylogenetic analysis, the proteins were classified into types I and II, which exhibited similar conserved motif compositions. Notably, only 16 durian MADS-box genes exhibited fruit-specific expression patterns. Among these genes, DzAGL6-1 was predominantly expressed during fruit development, a stage at which carotenoid biosynthesis is activated. Transient expression of DzAGL6-1 in tomato fruit increased the transcript level of the carotenoid biosynthetic gene phytoene synthase (PSY) and the β-carotene content. Furthermore, DzAGL6-1 activated the promoter activity of DzPSY, as demonstrated by a dual-luciferase assay. These findings provide insights into the role of MADS-box transcription factors in regulating carotenoid biosynthesis during durian fruit development.
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Affiliation(s)
- Kittiya Tantisuwanichkul
- Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Shinichiro Komaki
- Plant Secondary Metabolism, Division of Biological Science, NARA Institute of Science and Technology, Nara, Japan
| | - Mutsumi Watanabe
- Plant Secondary Metabolism, Division of Biological Science, NARA Institute of Science and Technology, Nara, Japan
| | - Takayuki Tohge
- Plant Secondary Metabolism, Division of Biological Science, NARA Institute of Science and Technology, Nara, Japan
| | - Supaart Sirikantaramas
- Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
- Omics Sciences and Bioinformatics Center, Chulalongkorn University, Bangkok, Thailand.
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Zhu Y, Liu C, Zhao M, Duan Y, Xie J, Wang C. Transcriptome profiling reveals key regulatory factors and metabolic pathways associated with curd formation and development in broccoli. FRONTIERS IN PLANT SCIENCE 2024; 15:1418319. [PMID: 39070909 PMCID: PMC11273133 DOI: 10.3389/fpls.2024.1418319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 06/25/2024] [Indexed: 07/30/2024]
Abstract
Broccoli, a cruciferous vegetable, has a unique indeterminate inflorescence structure known as curds. It is the main edible organ of broccoli and has a rich nutritional value and health benefits. However, the formation and development mechanism of the curd is still not well understood. In the present study, the shoot apical meristem (SAM) stage and three different development stages of curd (formation stage (FS), expansion stage (ES), and maturation stage (MS)) were identified and subjected to transcriptome sequencing to uncover the potential genes and regulatory networks involved in curd formation and development. The results indicated that the genes associated with the development of SAM such as BolAP1A, BolAP1C, BolCAL, and BolAGL6 play an important role in the abnormal differentiation of the curd apical buds. The genes, BolFRI, BolbHLH89, BolKAN4, BolAGL12, and BolAGL24, displayed significantly differential expression patterns in curd development may function in the regulation of the transition from inflorescence meristem (IM) to floral meristem (FM). Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the differentially expressed genes (DEGs) indicate that phytohormones, such as auxin (AUX), gibberellins (GA), and abscisic acid (ABA) also play an important role in SAM proliferation and the transition from SAM to IM. In addition, the genes regulating photosynthetic reaction (BolLHCA1, BolLHCB1, BolPsbO, etc.) have a key involvement in the differentiation of secondary IMs during curd expansion. The genes associated with the metabolism of starch and sucrose (e.g., BolSPS4, BolBAM4) were significantly upregulated at the MS should contribute to the maturation of the curd. These findings provide new insights into the potential key regulatory factors and metabolic pathways involved in the formation and development of broccoli curds.
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Affiliation(s)
- Yinxia Zhu
- College of Life Sciences, Nankai University, Tianjin, China
| | - Ce Liu
- Cucumber Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
- State Key Laboratory of Vegetable Biobreeding, Tianjin, China
| | - Mengyao Zhao
- College of Life Sciences, Nankai University, Tianjin, China
| | - Yuxuan Duan
- College of Life Sciences, Nankai University, Tianjin, China
| | - Jingjing Xie
- College of Life Sciences, Nankai University, Tianjin, China
| | - Chunguo Wang
- College of Life Sciences, Nankai University, Tianjin, China
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Mou L, Zhang L, Qiu Y, Liu M, Wu L, Mo X, Chen J, Liu F, Li R, Liu C, Tian M. Endogenous Hormone Levels and Transcriptomic Analysis Reveal the Mechanisms of Bulbil Initiation in Pinellia ternata. Int J Mol Sci 2024; 25:6149. [PMID: 38892337 PMCID: PMC11173086 DOI: 10.3390/ijms25116149] [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: 03/10/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Pinellia ternata is a medicinal plant that has important pharmacological value, and the bulbils serve as the primary reproductive organ; however, the mechanisms underlying bulbil initiation remain unclear. Here, we characterized bulbil development via histological, transcriptomic, and targeted metabolomic analyses to unearth the intricate relationship between hormones, genes, and bulbil development. The results show that the bulbils initiate growth from the leaf axillary meristem (AM). In this stage, jasmonic acid (JA), abscisic acid (ABA), isopentenyl adenosine (IPA), and salicylic acid (SA) were highly enriched, while indole-3-acetic acid (IAA), zeatin, methyl jasmonate (MeJA), and 5-dexoxystrigol (5-DS) were notably decreased. Through OPLS-DA analysis, SA has emerged as the most crucial factor in initiating and positively regulating bulbil formation. Furthermore, a strong association between IPA and SA was observed during bulbil initiation. The transcriptional changes in IPT (Isopentenyltransferase), CRE1 (Cytokinin Response 1), A-ARR (Type-A Arabidopsis Response Regulator), B-ARR (Type-B Arabidopsis Response Regulator), AUX1 (Auxin Resistant 1), ARF (Auxin Response Factor), AUX/IAA (Auxin/Indole-3-acetic acid), GH3 (Gretchen Hagen 3), SAUR (Small Auxin Up RNA), GA2ox (Gibberellin 2-oxidase), GA20ox (Gibberellin 20-oxidase), AOS (Allene oxide synthase), AOC (Allene oxide cyclase), OPR (Oxophytodienoate Reductase), JMT (JA carboxy l Methyltransferase), COI1 (Coronatine Insensitive 1), JAZ (Jasmonate ZIM-domain), MYC2 (Myelocytomatosis 2), D27 (DWARF27), SMAX (Suppressor of MAX2), PAL (Phenylalanine Ammonia-Lyase), ICS (Isochorismate Synthase), NPR1 (Non-expressor of Pathogenesis-related Genes1), TGA (TGACG Sequence-specific Binding), PR-1 (Pathogenesis-related), MCSU (Molybdenium Cofactor Sulfurase), PP2C (Protein Phosphatase 2C), and SnRK (Sucrose Non-fermenting-related Protein Kinase 2) were highly correlated with hormone concentrations, indicating that bulbil initiation is coordinately controlled by multiple phytohormones. Notably, eight TFs (transcription factors) that regulate AM initiation have been identified as pivotal regulators of bulbil formation. Among these, WUS (WUSCHEL), CLV (CLAVATA), ATH1 (Arabidopsis Thaliana Homeobox Gene 1), and RAX (Regulator of Axillary meristems) have been observed to exhibit elevated expression levels. Conversely, LEAFY demonstrated contrasting expression patterns. The intricate expression profiles of these TFs are closely associated with the upregulated expression of KNOX(KNOTTED-like homeobox), suggesting a intricate regulatory network underlying the complex process of bulbil initiation. This study offers a profound understanding of the bulbil initiation process and could potentially aid in refining molecular breeding techniques specific to P. ternata.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Mengliang Tian
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (L.M.); (L.Z.); (Y.Q.); (M.L.); (L.W.); (X.M.); (J.C.); (F.L.); (R.L.); (C.L.)
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Liu Y, Guan C, Chen Y, Shi Y, Long O, Lin H, Zhang K, Zhou M. Evolutionary analysis of MADS-box genes in buckwheat species and functional study of FdMADS28 in flavonoid metabolism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108637. [PMID: 38670031 DOI: 10.1016/j.plaphy.2024.108637] [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: 12/22/2023] [Revised: 04/01/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024]
Abstract
The MADS-box gene family is a transcription factor family that is widely expressed in plants. It controls secondary metabolic processes in plants and encourages the development of tissues like roots and flowers. However, the phylogenetic analysis and evolutionary model of MADS-box genes in Fagopyrum species has not been reported yet. This study identified the MADS-box genes of three buckwheat species at the whole genome level, and conducted systematic evolution and physicochemical analysis. The results showed that these genes can be divided into four subfamilies, with fragment duplication being the main way for the gene family expansion. During the domestication process from golden buckwheat to tartary buckwheat and the common buckwheat, the Ka/Ks ratio indicated that most members of the family experienced strong purification selection pressure, and with individual gene pairs experiencing positive selection. In addition, we combined the expression profile data of the MADS genes, mGWAS data, and WGCNA data to mine genes FdMADS28/48/50 that may be related to flavonoid metabolism. The results also showed that overexpression of FdMADS28 could increase rutin content by decreasing Kaempferol pathway content in hairy roots, and increase the resistance and growth of hairy roots to PEG and NaCl. This study systematically analyzed the evolutionary relationship of MADS-box genes in the buckwheat species, and elaborated on the expression patterns of MADS genes in different tissues under biotic and abiotic stresses, laying an important theoretical foundation for further elucidating their role in flavonoid metabolism.
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Affiliation(s)
- Yang Liu
- Sanya Nan Fan Research Institute of Chinese Academy of Agricultural Sciences, Sanya, 572024, Hainan, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chaonan Guan
- Sanya Nan Fan Research Institute of Chinese Academy of Agricultural Sciences, Sanya, 572024, Hainan, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuanyuan Chen
- College of Agriculture, Yangtze University, Jingzhou, 434023, Hubei, China
| | - Yaliang Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ou Long
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hao Lin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Meiliang Zhou
- Sanya Nan Fan Research Institute of Chinese Academy of Agricultural Sciences, Sanya, 572024, Hainan, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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9
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Mostafa K, Yerlikaya BA, Abdulla MF, Aydin A, Yerlikaya S, Kavas M. Genome-wide analysis of PvMADS in common bean and functional characterization of PvMADS31 in Arabidopsis thaliana as a player in abiotic stress responses. THE PLANT GENOME 2024; 17:e20432. [PMID: 38327143 DOI: 10.1002/tpg2.20432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 02/09/2024]
Abstract
Changing climatic conditions with rising temperatures and altered precipitation patterns pose significant challenges to agricultural productivity, particularly for common bean crops. Transcription factors (TFs) are crucial regulators that can mitigate the impact of biotic and abiotic stresses on crop production. The MADS-box TFs family has been implicated in various plant physiological processes, including stress-responsive mechanisms. However, their role in common bean and their response to stressful conditions remain poorly understood. Here, we identified 35 MADS-box gene family members in common bean, with conserved MADS-box domains and other functional domains. Gene duplication events were observed, suggesting the significance of duplication in the evolutionary development of gene families. The analysis of promoter regions revealed diverse elements, including stress-responsive elements, indicating their potential involvement in stress responses. Notably, PvMADS31, a member of the PvMADS-box gene family, demonstrated rapid upregulation under various abiotic stress conditions, including NaCl, polyethylene glycol, drought, and abscisic acid (ABA) treatments. Transgenic plants overexpressing PvMADS31 displayed enhanced lateral root development, root elongation, and seed germination under stress conditions. Furthermore, PvMADS31 overexpression in Arabidopsis resulted in improved drought tolerance, likely attributed to the enhanced scavenging of ROS and increased proline accumulation. These findings suggest that PvMADS31 might play a crucial role in modulating seed germination, root development, and stress responses, potentially through its involvement in auxin and ABA signaling pathways. Overall, this study provides valuable insights into the potential roles of PvMADS-box genes in abiotic stress responses in common bean, offering prospects for crop improvement strategies to enhance resilience under changing environmental conditions.
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Affiliation(s)
- Karam Mostafa
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
- The Central Laboratory for Date Palm Research and Development, Agricultural Research Center (ARC), Giza, Egypt
| | - Bayram Ali Yerlikaya
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
| | - Mohamed Farah Abdulla
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
| | - Abdullah Aydin
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
| | - Seher Yerlikaya
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
| | - Musa Kavas
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
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10
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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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11
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Gambhir P, Raghuvanshi U, Kumar R, Sharma AK. Transcriptional regulation of tomato fruit ripening. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:289-303. [PMID: 38623160 PMCID: PMC11016043 DOI: 10.1007/s12298-024-01424-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/15/2024] [Accepted: 02/27/2024] [Indexed: 04/17/2024]
Abstract
An intrinsic and genetically determined ripening program of tomato fruits often depends upon the appropriate activation of tissue- and stage-specific transcription factors in space and time. The past two decades have yielded considerable progress in detailing these complex transcriptional as well as hormonal regulatory circuits paramount to fleshy fruit ripening. This non-linear ripening process is strongly controlled by the MADS-box and NOR family of proteins, triggering a transcriptional response associated with the progression of fruit ripening. Deepening insights into the connection between MADS-RIN and plant hormones related transcription factors, such as ERFs and ARFs, further conjugates the idea that several signaling units work in parallel to define an output fruit ripening transcriptome. Besides these TFs, the role of other families of transcription factors such as MYB, GLK, WRKY, GRAS and bHLH have also emerged as important ripening regulators. Other regulators such as EIN and EIL proteins also determine the transcriptional landscape of ripening fruits. Despite the abundant knowledge of the complex spectrum of ripening networks in the scientific domain, identifying more ripening effectors would pave the way for a better understanding of fleshy fruit ripening at the molecular level. This review provides an update on the transcriptional regulators of tomato fruit ripening.
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Affiliation(s)
- Priya Gambhir
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021 India
| | - Utkarsh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021 India
| | - Rahul Kumar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046 India
| | - Arun Kumar Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021 India
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12
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Li R, Zhang B, Li T, Yao X, Feng T, Ai H, Huang X. Identification and Characterization of the BZR Transcription Factor Genes Family in Potato ( Solanum tuberosum L.) and Their Expression Profiles in Response to Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2024; 13:407. [PMID: 38337940 PMCID: PMC10856970 DOI: 10.3390/plants13030407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/20/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024]
Abstract
Brassinazole resistant (BZR) genes act downstream of the brassinosteroid signaling pathway regulating plant growth and development and participating in plant stress responses. However, the BZR gene family has not systematically been characterized in potato. We identified eight BZR genes in Solanum tuberosum, which were distributed among seven chromosomes unequally and were classified into three subgroups. Potato and tomato BZR proteins were shown to be closely related with high levels of similarity. The BZR gene family members in each subgroup contained similar conserved motifs. StBZR genes exhibited tissue-specific expression patterns, suggesting their functional differentiation during evolution. StBZR4, StBZR7, and StBZR8 were highly expressed under white light in microtubers. StBZR1 showed a progressive up-regulation from 0 to 6 h and a progressive down-regulation from 6 to 24 h after drought and salt stress. StBZR1, StBZR2, StBZR4, StBZR5, StBZR6, StBZR7 and StBZR8 were significantly induced from 0 to 3 h under BR treatment. This implied StBZR genes are involved in phytohormone and stress response signaling pathways. Our results provide a theoretical basis for understanding the functional mechanisms of BZR genes in potato.
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Affiliation(s)
- Ruining Li
- Center for Crop Biotechnology, Anhui Science and Technology University, Chuzhou 239000, China
| | - Bolin Zhang
- Center for Crop Biotechnology, Anhui Science and Technology University, Chuzhou 239000, China
| | - Ting Li
- Center for Crop Biotechnology, Anhui Science and Technology University, Chuzhou 239000, China
| | - Xuyang Yao
- Center for Crop Biotechnology, Anhui Science and Technology University, Chuzhou 239000, China
| | - Tingting Feng
- Center for Crop Biotechnology, Anhui Science and Technology University, Chuzhou 239000, China
| | - Hao Ai
- Center for Crop Biotechnology, Anhui Science and Technology University, Chuzhou 239000, China
| | - Xianzhong Huang
- Center for Crop Biotechnology, Anhui Science and Technology University, Chuzhou 239000, China
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13
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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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14
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Zounková A, Konečný J, Lipavská H, Mašková P. BEL transcription factors in prominent Solanaceae crops: the missing pieces of the jigsaw in plant development. PLANTA 2023; 259:14. [PMID: 38070043 DOI: 10.1007/s00425-023-04289-8] [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: 04/17/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023]
Abstract
MAIN CONCLUSION Understanding BEL transcription factors roles in potato and tomato varies considerably with little overlap. The review suggests reciprocal use of gained results to proceed with the knowledge in both crops The proper development of organs that plants use for reproduction, like fruits or tubers, is crucial for the survival and competitiveness of the species and thus subject to strict regulations. Interestingly, the controls of potato (Solanum tuberosum) tuber and tomato (S. lycopersicum) fruit development use common mechanisms, including the action of the BEL transcription factors (TFs). Although more than ten BEL genes have been identified in either genome, only a few of them have been characterized. The review summarizes knowledge of BEL TFs' roles in these closely related Solanaceae species, focusing on those that are essential for tuberization in potato, namely StBEL5, StBEL11 and StBEL29, and for fruit development in tomato - SlBEL11, SlBL2 and SIBL4. Comprehension of the roles of individual BEL TFs, however, is not yet sufficient. Different levels of understanding of important characteristics are described, such as BEL transcript accumulation patterns, their mobility, BEL protein interaction with KNOX partners, subcellular localisation, and their target genes during initiation and development of the organs in question. A comparison of the knowledge on BEL TFs and their mechanisms of action in potato and tomato may provide inspiration for faster progress in the study of both models through the exchange of information and ideas. Both crops are extremely important for human nutrition. In addition, their production is likely to be threatened by the upcoming climate change, so there is a particular need for breeding using a deep knowledge of control mechanisms.
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Affiliation(s)
- Andrea Zounková
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 12800, Prague 2, Czech Republic
| | - Jan Konečný
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 12800, Prague 2, Czech Republic
| | - Helena Lipavská
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 12800, Prague 2, Czech Republic
| | - Petra Mašková
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 12800, Prague 2, Czech Republic.
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15
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Liang MH, Li XY. Involvement of Transcription Factors and Regulatory Proteins in the Regulation of Carotenoid Accumulation in Plants and Algae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18660-18673. [PMID: 38053506 DOI: 10.1021/acs.jafc.3c05662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Carotenoids are essential for photosynthesis and photoprotection in photosynthetic organisms, which are widely used in food coloring, feed additives, nutraceuticals, cosmetics, and pharmaceuticals. Carotenoid biofortification in crop plants or algae has been considered as a sustainable strategy to improve human nutrition and health. However, the regulatory mechanisms of carotenoid accumulation are still not systematic and particularly scarce in algae. This article focuses on the regulatory mechanisms of carotenoid accumulation in plants and algae through regulatory factors (transcription factors and regulatory proteins), demonstrating the complexity of homeostasis regulation of carotenoids, mainly including transcriptional regulation as the primary mechanism, subsequent post-translational regulation, and cross-linking with other metabolic processes. Different organs of plants and different plant/algal species usually have specific regulatory mechanisms for the biosynthesis, storage, and degradation of carotenoids in response to the environmental and developmental signals. In plants and algae, regulators such as MYB, bHLH, MADS, bZIP, AP2/ERF, WRKY, and orange proteins can be involved in the regulation of carotenoid metabolism. And many more regulators, regulatory networks, and mechanisms need to be explored. Our paper will provide a basis for multitarget or multipathway engineering for carotenoid biofortification in plants and algae.
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Affiliation(s)
- Ming-Hua Liang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Xian-Yi Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
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16
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Li G, Dang J, Pan J, Liu J, Peng T, Chen G, Wang R, Hu S, Li X, Hu X. Genome-Wide Analysis of the DC1 Domain Protein Gene Family in Tomatoes under Abiotic Stress. Int J Mol Sci 2023; 24:16994. [PMID: 38069320 PMCID: PMC10707348 DOI: 10.3390/ijms242316994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
DC1 (Divergent C1) domain proteins are a new class of proteins that have been discovered in recent years, which play an important role in plant growth, development, and stress response. In order to better study the distribution and function of DC1 domain proteins in tomatoes, a genome-wide identification was conducted. It was found that there are twenty-one DC1 domain protein genes distributed on nine chromosomes of tomatoes, named SlCHP1-21. Phylogenetic analysis shows that twenty-one SlCHP genes are divided into six subfamilies. Most of the SlCHP genes in tomatoes have no or very short introns. All SlCHP proteins, with the exception of SlCHP8 and SlCHP17, contain variable amounts of C1 domain. Analysis of the SlCHP gene promoter sequence revealed multiple cis-elements responsive to plant stress. qRT-CR analysis showed that most members of SlCHP gene expressed in the roots. The SlCHP11, 13, 16, 17, and SlCHP20 genes showed specific responses to high temperature, low temperature, salt, and drought stress. In addition, the subcellular localization and interaction proteins of SlCHP were analyzed and predicted. Together, these results provides a theoretical basis for further exploration of the function and mechanism of the SlCHP gene in tomatoes.
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Affiliation(s)
- Guobin Li
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (G.L.); (J.D.); (J.P.); (J.L.); (T.P.); (G.C.); (R.W.); (S.H.); (X.L.)
- Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling 712100, China
- Shaanxi Protected Agriculture Research Centre, Yangling 712100, China
| | - Jiao Dang
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (G.L.); (J.D.); (J.P.); (J.L.); (T.P.); (G.C.); (R.W.); (S.H.); (X.L.)
- Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling 712100, China
- Shaanxi Protected Agriculture Research Centre, Yangling 712100, China
| | - Jiaqi Pan
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (G.L.); (J.D.); (J.P.); (J.L.); (T.P.); (G.C.); (R.W.); (S.H.); (X.L.)
- Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling 712100, China
- Shaanxi Protected Agriculture Research Centre, Yangling 712100, China
| | - Jingyi Liu
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (G.L.); (J.D.); (J.P.); (J.L.); (T.P.); (G.C.); (R.W.); (S.H.); (X.L.)
| | - Tieli Peng
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (G.L.); (J.D.); (J.P.); (J.L.); (T.P.); (G.C.); (R.W.); (S.H.); (X.L.)
- Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling 712100, China
- Shaanxi Protected Agriculture Research Centre, Yangling 712100, China
| | - Guo Chen
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (G.L.); (J.D.); (J.P.); (J.L.); (T.P.); (G.C.); (R.W.); (S.H.); (X.L.)
| | - Rongqun Wang
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (G.L.); (J.D.); (J.P.); (J.L.); (T.P.); (G.C.); (R.W.); (S.H.); (X.L.)
| | - Songshen Hu
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (G.L.); (J.D.); (J.P.); (J.L.); (T.P.); (G.C.); (R.W.); (S.H.); (X.L.)
- Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling 712100, China
- Shaanxi Protected Agriculture Research Centre, Yangling 712100, China
| | - Xiaojing Li
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (G.L.); (J.D.); (J.P.); (J.L.); (T.P.); (G.C.); (R.W.); (S.H.); (X.L.)
- Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling 712100, China
- Shaanxi Protected Agriculture Research Centre, Yangling 712100, China
| | - Xiaohui Hu
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (G.L.); (J.D.); (J.P.); (J.L.); (T.P.); (G.C.); (R.W.); (S.H.); (X.L.)
- Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling 712100, China
- Shaanxi Protected Agriculture Research Centre, Yangling 712100, China
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Cheng JL, Wei XP, Chen Y, Qi YD, Zhang BG, Liu HT. Comparative transcriptome analysis reveals candidate genes related to the sex differentiation of Schisandra chinensis. Funct Integr Genomics 2023; 23:344. [PMID: 37991590 DOI: 10.1007/s10142-023-01264-0] [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: 09/19/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 11/23/2023]
Abstract
Schisandra chinensis is a monoecious plant with unisex flowers. The fruit of S. chinensis is of high medical with economic value. The yield of S. chinensis fruit is related to the ratio of its female and male flowers. However, there is little research on its floral development and sex differentiation. To elucidate the possible mechanism for the sex differentiation of S. chinensis, we collected 18 samples of female and male flowers from three developmental stages and performed a comparative RNA-seq analysis aimed at identifying differentially expressed genes (DEGs) that may be related to sex differentiation. The results showed 936, 7179, and 6890 differentially expressed genes between female and male flowers at three developmental stages, respectively, and 466 candidate genes may play roles in sex differentiation. KEGG analysis showed genes involved in the flavonoid biosynthesis pathway and DNA replication pathway were essential for the development of female flowers. 51 MADS-box genes and 10 YABBY genes were identified in S. chinensis. The DEGs analysis indicated that MADS-box and YABBY genes were strongly related to the sex determination of S. chinensis. RT-qPCR confirmed the RNA-seq results of 20 differentially expressed genes, including three male-biased genes and 17 female-biased genes. A possible regulatory model of sex differentiation in S. chinensis was proposed according to our results. This study helps reveal the sex-differentiation mechanism of S. chinensis and lays the foundation for regulating the male-female ratio of S. chinensis in the future.
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Affiliation(s)
- Ji-Long Cheng
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xue-Ping Wei
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Yu Chen
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yao-Dong Qi
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ben-Gang Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hai-Tao Liu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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18
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Shamshad A, Rashid M, Zaman QU. In-silico analysis of heat shock transcription factor (OsHSF) gene family in rice (Oryza sativa L.). BMC PLANT BIOLOGY 2023; 23:395. [PMID: 37592226 PMCID: PMC10433574 DOI: 10.1186/s12870-023-04399-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND One of the most important cash crops worldwide is rice (Oryza sativa L.). Under varying climatic conditions, however, its yield is negatively affected. In order to create rice varieties that are resilient to abiotic stress, it is essential to explore the factors that control rice growth, development, and are source of resistance. HSFs (heat shock transcription factors) control a variety of plant biological processes and responses to environmental stress. The in-silico analysis offers a platform for thorough genome-wide identification of OsHSF genes in the rice genome. RESULTS In this study, 25 randomly dispersed HSF genes with significant DNA binding domains (DBD) were found in the rice genome. According to a gene structural analysis, all members of the OsHSF family share Gly-66, Phe-67, Lys-69, Trp-75, Glu-76, Phe-77, Ala-78, Phe-82, Ile-93, and Arg-96. Rice HSF family genes are widely distributed in the vegetative organs, first in the roots and then in the leaf and stem; in contrast, in reproductive tissues, the embryo and lemma exhibit the highest levels of gene expression. According to chromosomal localization, tandem duplication and repetition may have aided in the development of novel genes in the rice genome. OsHSFs have a significant role in the regulation of gene expression, regulation in primary metabolism and tolerance to environmental stress, according to gene networking analyses. CONCLUSION Six genes viz; Os01g39020, Os01g53220, Os03g25080, Os01g54550, Os02g13800 and Os10g28340 were annotated as promising genes. This study provides novel insights for functional studies on the OsHSFs in rice breeding programs. With the ultimate goal of enhancing crops, the data collected in this survey will be valuable for performing genomic research to pinpoint the specific function of the HSF gene during stress responses.
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Affiliation(s)
- Areeqa Shamshad
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Muhammad Rashid
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Qamar Uz Zaman
- Department of Environmental Sciences, The University of Lahore, Lahore, 54590, Pakistan.
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19
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Lin Y, Qi X, Wan Y, Chen Z, Fang H, Liang C. Genome-wide analysis of the MADS-box gene family in Lonicera japonica and a proposed floral organ identity model. BMC Genomics 2023; 24:447. [PMID: 37553575 PMCID: PMC10408238 DOI: 10.1186/s12864-023-09509-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 07/08/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Lonicera japonica Thunb. is widely used in traditional Chinese medicine. Medicinal L. japonica mainly consists of dried flower buds and partially opened flowers, thus flowers are an important quality indicator. MADS-box genes encode transcription factors that regulate flower development. However, little is known about these genes in L. japonica. RESULTS In this study, 48 MADS-box genes were identified in L. japonica, including 20 Type-I genes (8 Mα, 2 Mβ, and 10 Mγ) and 28 Type-II genes (26 MIKCc and 2 MIKC*). The Type-I and Type-II genes differed significantly in gene structure, conserved domains, protein structure, chromosomal distribution, phylogenesis, and expression pattern. Type-I genes had a simpler gene structure, lacked the K domain, had low protein structure conservation, were tandemly distributed on the chromosomes, had more frequent lineage-specific duplications, and were expressed at low levels. In contrast, Type-II genes had a more complex gene structure; contained conserved M, I, K, and C domains; had highly conserved protein structure; and were expressed at high levels throughout the flowering period. Eleven floral homeotic MADS-box genes that are orthologous to the proposed Arabidopsis ABCDE model of floral organ identity determination, were identified in L. japonica. By integrating expression pattern and protein interaction data for these genes, we developed a possible model for floral organ identity determination. CONCLUSION This study genome-widely identified and characterized the MADS-box gene family in L. japonica. Eleven floral homeotic MADS-box genes were identified and a possible model for floral organ identity determination was also developed. This study contributes to our understanding of the MADS-box gene family and its possible involvement in floral organ development in L. japonica.
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Affiliation(s)
- Yi Lin
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
- Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xiwu Qi
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Yan Wan
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
- Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zequn Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Hailing Fang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China
| | - Chengyuan Liang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, 210014, Jiangsu Province, China.
- Nanjing University of Chinese Medicine, Nanjing, 210023, China.
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20
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Zahn IE, Roelofsen C, Angenent GC, Bemer M. TM3 and STM3 Promote Flowering Together with FUL2 and MBP20, but Act Antagonistically in Inflorescence Branching in Tomato. PLANTS (BASEL, SWITZERLAND) 2023; 12:2754. [PMID: 37570908 PMCID: PMC10420972 DOI: 10.3390/plants12152754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023]
Abstract
The moment at which a plant transitions to reproductive development is paramount to its life cycle and is strictly controlled by many genes. The transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) plays a central role in this process in Arabidopsis. However, the role of SOC1 in tomato (Solanum lycopersicum) has been sparsely studied. Here, we investigated the function of four tomato SOC1 homologs in the floral transition and inflorescence development. We thoroughly characterized the SOC1-like clade throughout the Solanaceae and selected four tomato homologs that are dynamically expressed upon the floral transition. We show that of these homologs, TOMATO MADS 3 (TM3) and SISTER OF TM3 (STM3) promote the primary and sympodial transition to flowering, while MADS-BOX PROTEIN 23 (MBP23) and MBP18 hardly contribute to flowering initiation in the indeterminate cultivar Moneyberg. Protein-protein interaction assays and whole-transcriptome analysis during reproductive meristem development revealed that TM3 and STM3 interact and share many targets with FRUITFULL (FUL) homologs, including cytokinin regulators. Furthermore, we observed that mutating TM3/STM3 affects inflorescence development, but counteracts the inflorescence-branching phenotype of ful2 mbp20. Collectively, this indicates that TM3/STM3 promote the floral transition together with FUL2/MBP20, while these transcription factors have opposite functions in inflorescence development.
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Affiliation(s)
- Iris E. Zahn
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (I.E.Z.); (G.C.A.)
| | - Chris Roelofsen
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (I.E.Z.); (G.C.A.)
| | - Gerco C. Angenent
- Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (I.E.Z.); (G.C.A.)
- Business Unit Bioscience, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Marian Bemer
- Business Unit Bioscience, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
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21
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Chen J, Yang Y, Li C, Chen Q, Liu S, Qin B. Genome-Wide Identification of MADS-Box Genes in Taraxacum kok-saghyz and Taraxacum mongolicum: Evolutionary Mechanisms, Conserved Functions and New Functions Related to Natural Rubber Yield Formation. Int J Mol Sci 2023; 24:10997. [PMID: 37446175 DOI: 10.3390/ijms241310997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
MADS-box transcription regulators play important roles in plant growth and development. However, very few MADS-box genes have been isolated in the genus Taraxacum, which consists of more than 3000 species. To explore their functions in the promising natural rubber (NR)-producing plant Taraxacum kok-saghyz (TKS), MADS-box genes were identified in the genome of TKS and the related species Taraxacum mongolicum (TM; non-NR-producing) via genome-wide screening. In total, 66 TkMADSs and 59 TmMADSs were identified in the TKS and TM genomes, respectively. From diploid TKS to triploid TM, the total number of MADS-box genes did not increase, but expansion occurred in specific subfamilies. Between the two genomes, a total of 11 duplications, which promoted the expansion of MADS-box genes, were identified in the two species. TkMADS and TmMADS were highly conserved, and showed good collinearity. Furthermore, most TkMADS genes exhibiting tissue-specific expression patterns, especially genes associated with the ABCDE model, were preferentially expressed in the flowers, suggesting their conserved and dominant functions in flower development in TKS. Moreover, by comparing the transcriptomes of different TKS lines, we identified 25 TkMADSs related to biomass formation and 4 TkMADSs related to NR content, which represented new targets for improving the NR yield of TKS.
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Affiliation(s)
- Jiaqi Chen
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Institute of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yushuang Yang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Chuang Li
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Institute of Tropical Crops, Hainan University, Haikou 570228, China
| | - Qiuhui Chen
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Shizhong Liu
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Bi Qin
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
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22
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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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23
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He Y, Wu Q, Cui C, Tian Q, Zhang D, Zhang Y. ChIP-Seq Analysis of SlAREB1 Downstream Regulatory Network during Tomato Ripening. Foods 2023; 12:2357. [PMID: 37372568 DOI: 10.3390/foods12122357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
SlAREB1, a member of the abscisic acid (ABA) response element-binding factors (AREB/ABFs) family, was reported to play a crucial role in the expression of ABA-regulated downstream genes and affect the ripening of tomato fruit. However, the downstream genes of SlAREB1 are still unclear. Chromatin immunoprecipitation (ChIP) is a powerful tool and a standard method for studying the interactions between DNA and proteins at the genome-wide level. In the present study, SlAREB1 was proved to continually increase until the mature green stage and then decrease during the ripening period, and a total of 972 gene peaks were identified downstream of SlAREB1 by ChIP-seq analysis, mainly located in the intergenic and promoter regions. Further gene ontology (GO) annotation analysis revealed that the target sequence of SlAREB1 was the most involved in biological function. Kyoto Encylopaedia of Genes and Genomes (KEGG) pathway analysis showed that the identified genes were mainly involved in the oxidative phosphorylation and photosynthesis pathways, and some of them were associated with tomato phytohormone synthesis, the cell wall, pigment, and the antioxidant characteristic of the fruit as well. Based on these results, an initial model of SlAREB1 regulation on tomato fruit ripening was constructed, which provided a theoretical basis for further exploring the effects of the regulation mechanism of SlAREB1 and ABA on tomato fruit ripening.
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Affiliation(s)
- Yanan He
- Engineering Center of Ministry of Education, School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou 450001, China
| | - Qiong Wu
- Engineering Center of Ministry of Education, School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou 450001, China
| | - Chunxiao Cui
- Engineering Center of Ministry of Education, School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou 450001, China
| | - Qisheng Tian
- Engineering Center of Ministry of Education, School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou 450001, China
| | - Dongdong Zhang
- Engineering Center of Ministry of Education, School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou 450001, China
| | - Yurong Zhang
- Engineering Center of Ministry of Education, School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou 450001, China
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24
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Yunrui X, Rui S, Xing Y, Zhe Z, Keqin Z, Nanyi Z. Comparative transcriptomic analysis reveals differences in MADS-box genes of different hypericum in Changbai Mountains. Ecol Evol 2023; 13:e10196. [PMID: 37325719 PMCID: PMC10261973 DOI: 10.1002/ece3.10196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 04/13/2023] [Accepted: 05/30/2023] [Indexed: 06/17/2023] Open
Abstract
To explore the differences between the hypericum in the Changbai Mountains, we carried out a transcriptome analysis of two common hypericums in the area, which was Hypericum attenuatum Choisy and Hypericum longistylum Oliv. We screened the MADS-box genes to analyze divergence time and evolutionary selection expression, and determine their expression levels. The results showed that we detected 9287 differentially expressed genes in the two species, of which shared 6044 genes by the two species. Analysis of the selected MADS genes revealed that the species was in an environment adapted to its natural evolution. The divergence time estimation showed that the segregation of these genes in the two species was related to the changes of external environment and genome replication events. The results of relative expression showed that the later flowering period of Hypericum attenuatum Choisy was related to the higher expression of the SVP (SHORT VEGETATIVE PHASE) and the AGL12 (AGAMOUS LIKE 12), while the lower expression of the FUL (FRUITFULL).
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Affiliation(s)
- Xia Yunrui
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland ScienceJilin Agricultural UniversityChangchunJilin ProvinceChina
| | - Song Rui
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland ScienceJilin Agricultural UniversityChangchunJilin ProvinceChina
| | - Yang Xing
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland ScienceJilin Agricultural UniversityChangchunJilin ProvinceChina
| | - Zhao Zhe
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland ScienceJilin Agricultural UniversityChangchunJilin ProvinceChina
| | - Zhang Keqin
- Jilin Agricultural Science and Technology UniversityJilinJilin ProvinceChina
| | - Zhang Nanyi
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland ScienceJilin Agricultural UniversityChangchunJilin ProvinceChina
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25
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Gao H, Suo X, Zhao L, Ma X, Cheng R, Wang G, Zhang H. Molecular evolution, diversification, and expression assessment of MADS gene family in Setaria italica, Setaria viridis, and Panicum virgatum. PLANT CELL REPORTS 2023; 42:1003-1024. [PMID: 37012438 DOI: 10.1007/s00299-023-03009-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/20/2023] [Indexed: 05/12/2023]
Abstract
KEY MESSAGE This paper sheds light on the evolution and expression patterns of MADS genes in Setaria and Panicum virgatum. SiMADS51 and SiMADS64 maybe involved in the ABA-dependent pathway of drought response. The MADS gene family is a key regulatory factor family that controls growth, reproduction, and response to abiotic stress in plants. However, the molecular evolution of this family is rarely reported. Here, a total of 265 MADS genes were identified in Setaria italica (foxtail millet), Setaria viridis (green millet), and Panicum virgatum (switchgrass) and analyzed by bioinformatics, including physicochemical characteristics, subcellular localization, chromosomal position and duplicate, motif distribution, genetic structure, genetic evolvement, and expression patterns. Phylogenetic analysis was used to categorize these genes into M and MIKC types. The distribution of motifs and gene structure were similar for the corresponding types. According to a collinearity study, the MADS genes have been mostly conserved during evolution. The principal cause of their expansion is segmental duplication. However, the MADS gene family tends to shrink in foxtail millet, green millet, and switchgrass. The MADS genes were subjected to purifying selection, but several positive selection sites were also identified in three species. And most of the promoters of MADS genes contain cis-elements related to stress and hormonal response. RNA-seq and quantitative Real-time PCR (qRT-PCR) analysis also were examined. SiMADS genes expression levels are considerably changed in reaction to various treatments, following qRT-PCR analysis. This sheds fresh light on the evolution and expansion of the MADS family in foxtail millet, green millet, and switchgrass, and lays the foundation for further research on their functions.
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Affiliation(s)
- Hui Gao
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Department of Life Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, Hebei, China
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Xiaoman Suo
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Department of Life Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, Hebei, China
| | - Ling Zhao
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Xinlei Ma
- Hebei Key Laboratory of Crop Stress Biology (in Preparation), Department of Life Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, Hebei, China
| | - Ruhong Cheng
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.
| | - Genping Wang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.
| | - Haoshan Zhang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.
- Chinese Academy of Agricultural Sciences Institute of Crop Sciences, Beijing, 100081, China.
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Huang J, Xu W, Zhai J, Hu Y, Guo J, Zhang C, Zhao Y, Zhang L, Martine C, Ma H, Huang CH. Nuclear phylogeny and insights into whole-genome duplications and reproductive development of Solanaceae plants. PLANT COMMUNICATIONS 2023:100595. [PMID: 36966360 PMCID: PMC10363554 DOI: 10.1016/j.xplc.2023.100595] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/02/2023] [Accepted: 03/22/2023] [Indexed: 06/18/2023]
Abstract
Solanaceae, the nightshade family, have ∼2700 species, including the important crops potato and tomato, ornamentals, and medicinal plants. Several sequenced Solanaceae genomes show evidence for whole-genome duplication (WGD), providing an excellent opportunity to investigate WGD and its impacts. Here, we generated 93 transcriptomes/genomes and combined them with 87 public datasets, for a total of 180 Solanaceae species representing all four subfamilies and 14 of 15 tribes. Nearly 1700 nuclear genes from these transcriptomic/genomic datasets were used to reconstruct a highly resolved Solanaceae phylogenetic tree with six major clades. The Solanaceae tree supports four previously recognized subfamilies (Goetzeioideae, Cestroideae, Nicotianoideae, and Solanoideae) and the designation of three other subfamilies (Schizanthoideae, Schwenckioideae, and Petunioideae), with the placement of several previously unassigned genera. We placed a Solanaceae-specific whole-genome triplication (WGT1) at ∼81 million years ago (mya), before the divergence of Schizanthoideae from other Solanaceae subfamilies at ∼73 mya. In addition, we detected two gene duplication bursts (GDBs) supporting proposed WGD events and four other GDBs. An investigation of the evolutionary histories of homologs of carpel and fruit developmental genes in 14 gene (sub)families revealed that 21 gene clades have retained gene duplicates. These were likely generated by the Solanaceae WGT1 and may have promoted fleshy fruit development. This study presents a well-resolved Solanaceae phylogeny and a new perspective on retained gene duplicates and carpel/fruit development, providing an improved understanding of Solanaceae evolution.
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Affiliation(s)
- Jie Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuangzu Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China
| | - Weibin Xu
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuangzu Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China
| | - Junwen Zhai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yi Hu
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Jing Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Caifei Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yiyong Zhao
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Lin Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | | | - Hong Ma
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, State College, PA 16802, USA.
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China.
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Feng X, Yu Q, Zeng J, He X, Ma W, Ge L, Liu W. Comprehensive Analysis of the INDETERMINATE DOMAIN (IDD) Gene Family and Their Response to Abiotic Stress in Zea mays. Int J Mol Sci 2023; 24:ijms24076185. [PMID: 37047154 PMCID: PMC10094743 DOI: 10.3390/ijms24076185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/20/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Transcription factors (TFs) are important regulators of numerous gene expressions due to their ability to recognize and combine cis-elements in the promoters of target genes. The INDETERMINATE DOMAIN (IDD) gene family belongs to a subfamily of C2H2 zinc finger proteins and has been identified only in terrestrial plants. Nevertheless, little study has been reported concerning the genome-wide analysis of the IDD gene family in maize. In total, 22 ZmIDD genes were identified, which can be distributed on 8 chromosomes in maize. On the basis of evolutionary relationships and conserved motif analysis, ZmIDDs were categorized into three clades (1, 2, and 3), each owning 4, 6, and 12 genes, respectively. We analyzed the characteristics of gene structure and found that 3 of the 22 ZmIDD genes do not contain an intron. Cis-element analysis of the ZmIDD promoter showed that most ZmIDD genes possessed at least one ABRE or MBS cis-element, and some ZmIDD genes owned the AuxRR-core, TCA-element, TC-rich repeats, and LTR cis-element. The Ka:Ks ratio of eight segmentally duplicated gene pairs demonstrated that the ZmIDD gene families had undergone a purifying selection. Then, the transcription levels of ZmIDDs were analyzed, and they showed great differences in diverse tissues as well as abiotic stresses. Furthermore, regulatory networks were constructed through the prediction of ZmIDD-targeted genes and miRNAs, which can inhibit the transcription of ZmIDDs. In total, 6 ZmIDDs and 22 miRNAs were discovered, which can target 180 genes and depress the expression of 9 ZmIDDs, respectively. Taken together, the results give us valuable information for studying the function of ZmIDDs involved in plant development and climate resilience in maize.
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Cheng S, Jia M, Su L, Liu X, Chu Q, He Z, Zhou X, Lu W, Jiang C. Genome-Wide Identification of the MADS-Box Gene Family during Male and Female Flower Development in Chayote (Sechium edule). Int J Mol Sci 2023; 24:ijms24076114. [PMID: 37047083 PMCID: PMC10094161 DOI: 10.3390/ijms24076114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 02/25/2023] [Accepted: 03/14/2023] [Indexed: 04/14/2023] Open
Abstract
The MADS-box gene plays an important role in plant growth and development. As an important vegetable of Cucurbitaceae, chayote has great edible and medicinal value. So far, there is little molecular research on chayote, and there are no reports on the MADS-box transcription factor of chayote. In this study, the MADS-box gene family of chayote was analyzed for the first time, and a total of 70 MADS-box genes were identified, including 14 type I and 56 type II MICK MADS genes. They were randomly distributed on 13 chromosomes except for chromosome 11. The light response element, hormone response element and abiotic stress response element were found in the promoter region of 70 MADS genes, indicating that the MADS gene can regulate the growth and development of chayote, resist abiotic stress, and participate in hormone response; GO and KEGG enrichment analysis also found that SeMADS genes were mainly enriched in biological regulation and signal regulation, which further proved the important role of MADS-box gene in plant growth and development. The results of collinearity showed that segmental duplication was the main driving force of MADS gene expansion in chayote. RNA-seq showed that the expression levels of SeMADS06, SeMADS13, SeMADS26, SeMADS28, SeMADS36 and SeMADS37 gradually increased with the growth of chayote, indicating that these genes may be related to the development of root tubers of 'Tuershao'. The gene expression patterns showed that 12 SeMADS genes were specifically expressed in the male flower in 'Tuershao' and chayote. In addition, SeMADS03 and SeMADS52 may be involved in regulating the maturation of male flowers of 'Tuershao' and chayote. SeMADS21 may be the crucial gene in the development stage of the female flower of 'Tuershao'. This study laid a theoretical foundation for the further study of the function of the MADS gene in chayote in the future.
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Affiliation(s)
- Shaobo Cheng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingyue Jia
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Lihong Su
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuanxuan Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Qianwen Chu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhongqun He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoting Zhou
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Wei Lu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Chengyao Jiang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
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Wang X, Huang Q, Shen Z, Baron GC, Li X, Lu X, Li Y, Chen W, Xu L, Lv J, Li W, Zong Y, Guo W. Genome-Wide Identification and Analysis of the MADS-Box Transcription Factor Genes in Blueberry ( Vaccinium spp.) and Their Expression Pattern during Fruit Ripening. PLANTS (BASEL, SWITZERLAND) 2023; 12:1424. [PMID: 37050050 PMCID: PMC10096547 DOI: 10.3390/plants12071424] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/08/2023] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
MADS-box is a class of transcriptional regulators that are ubiquitous in plants and plays important roles in the process of plant growth and development. Identification and analysis of blueberry MADS-box genes can lay a foundation for their function investigations. In the present study, 249 putative MADS-box genes were identified in the blueberry genome. Those MADS-box genes were distributed on 47 out of 48 chromosomes. The phylogenetic and evolutionary analyses showed that blueberry MADS-box genes were divided into 131 type I members and 118 type II members. The type I genes contained an average of 1.89 exons and the type II genes contained an average of 7.83 exons. Motif analysis identified 15 conserved motifs, of which 4 were related to the MADS domain and 3 were related to the K-box domain. A variety of cis-acting elements were found in the promoter region of the blueberry MADS-box gene, indicating that the MADS-box gene responded to various hormones and environmental alterations. A total of 243 collinear gene pairs were identified, most of which had a Ka/Ks value of less than 1. Nine genes belonging to SEP, AP3/PI, and AGL6 subfamilies were screened based on transcriptomic data. The expression patterns of those nine genes were also verified using quantitative PCR, suggesting that VcMADS6, VcMADS35, VcMADS44, VcMADS58, VcMADS125, VcMADS188, and VcMADS212 had potential functions in blueberry fruit ripening. The results of this study provide references for an in-depth understanding of the biological function of the blueberry MADS-box genes and the mechanism of blueberry fruit ripening.
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Affiliation(s)
- Xuxiang Wang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Qiaoyu Huang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Zhuli Shen
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | | | - Xiaoyi Li
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xiaoying Lu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Yongqiang Li
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Provincial Key Laboratory of Plant Biotechnology, Jinhua 321004, China
| | - Wenrong Chen
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Provincial Key Laboratory of Plant Biotechnology, Jinhua 321004, China
| | - Lishan Xu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Provincial Key Laboratory of Plant Biotechnology, Jinhua 321004, China
| | - Jinchao Lv
- Zhejiang Jinguo Environmental Protection Technology Company Limited, Jinhua 321000, China
| | - Wenjian Li
- Zhejiang Jinguo Environmental Protection Technology Company Limited, Jinhua 321000, China
| | - Yu Zong
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Provincial Key Laboratory of Plant Biotechnology, Jinhua 321004, China
| | - Weidong Guo
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Provincial Key Laboratory of Plant Biotechnology, Jinhua 321004, China
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Genome-Wide Identification and Expression of the Paulownia fortunei MADS-Box Gene Family in Response to Phytoplasma Infection. Genes (Basel) 2023; 14:genes14030696. [PMID: 36980968 PMCID: PMC10048600 DOI: 10.3390/genes14030696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023] Open
Abstract
Paulownia witches’ broom (PaWB), caused by phytoplasmas, is the most devastating infectious disease of Paulownia. Although a few MADS-box transcription factors have been reported to be involved in the formation of PaWB, there has been little investigation into all of the MADS-box gene family in Paulownia. The objective of this study is to identify the MADS-box gene family in Paulownia fortunei on a genome-wide scale and explore their response to PaWB infection. Bioinformatics software were used for identification, characterization, subcellular localization, phylogenetic analysis, the prediction of conserved motifs, gene structures, cis-elements, and protein-protein interaction network construction. The tissue expression profiling of PfMADS-box genes was analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). Transcriptome data and the protein interaction network prediction were combined to screen the genes associated with PaWB formation. We identified 89 MADS-box genes in the P. fortunei genome and categorized them into 14 subfamilies. The comprehensive analysis showed that segment duplication events had significant effects on the evolution of the PfMADS-box gene family; the motif distribution of proteins in the same subfamily are similar; development-related, phytohormone-responsive, and stress-related cis-elements were enriched in the promoter regions. The tissue expression pattern of PfMADS-box genes suggested that they underwent subfunctional differentiation. Three genes, PfMADS3, PfMADS57, and PfMADS87, might be related to the occurrence of PaWB. These results will provide a valuable resource to explore the potential functions of PfMADS-box genes and lay a solid foundation for understanding the roles of PfMADS-box genes in paulownia–phytoplasma interactions.
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Genome-Wide Identification and Characterization of Copper Chaperone for Superoxide Dismutase (CCS) Gene Family in Response to Abiotic Stress in Soybean. Int J Mol Sci 2023; 24:ijms24065154. [PMID: 36982229 PMCID: PMC10048983 DOI: 10.3390/ijms24065154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/10/2023] Open
Abstract
Copper Chaperone For Superoxide Dismutase (CCS) genes encode copper chaperone for Superoxide dismutase (SOD) and dramatically affect the activity of SOD through regulating copper delivery from target to SOD. SOD is the effective component of the antioxidant defense system in plant cells to reduce oxidative damage by eliminating Reactive oxygen species (ROS), which are produced during abiotic stress. CCS might play an important role in abiotic stress to eliminate the damage caused by ROS, however, little is known about CCS in soybean in abiotic stress regulation. In this study, 31 GmCCS gene family members were identified from soybean genome. These genes were classified into 4 subfamilies in the phylogenetic tree. Characteristics of 31 GmCCS genes including gene structure, chromosomal location, collinearity, conserved domain, protein motif, cis-elements, and tissue expression profiling were systematically analyzed. RT-qPCR was used to analyze the expression of 31 GmCCS under abiotic stress, and the results showed that 5 GmCCS genes(GmCCS5, GmCCS7, GmCCS8, GmCCS11 and GmCCS24) were significantly induced by some kind of abiotic stress. The functions of these GmCCS genes in abiotic stress were tested using yeast expression system and soybean hairy roots. The results showed that GmCCS7/GmCCS24 participated in drought stress regulation. Soybean hairy roots expressing GmCCS7/GmCCS24 showed improved drought stress tolerance, with increased SOD and other antioxidant enzyme activities. The results of this study provide reference value in-depth study CCS gene family, and important gene resources for the genetic improvement of soybean drought stress tolerance.
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Gene Structural Specificity and Expression of MADS-Box Gene Family in Camellia chekiangoleosa. Int J Mol Sci 2023; 24:ijms24043434. [PMID: 36834845 PMCID: PMC9960327 DOI: 10.3390/ijms24043434] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
MADS-box genes encode transcription factors that affect plant growth and development. Camellia chekiangoleosa is an oil tree species with ornamental value, but there have been few molecular biological studies on the developmental regulation of this species. To explore their possible role in C. chekiangoleosa and lay a foundation for subsequent research, 89 MADS-box genes were identified across the whole genome of C. chekiangoleosa for the first time. These genes were present on all the chromosomes and were found to have expanded by tandem duplication and fragment duplication. Based on the results of a phylogenetic analysis, the 89 MADS-box genes could be divided into either type I (38) or type II (51). Both the number and proportion of the type II genes were significantly greater than those of Camellia sinensis and Arabidopsis thaliana, indicating that C. chekiangoleosa type II genes experienced a higher duplication rate or a lower loss rate. The results of both a sequence alignment and a conserved motif analysis suggest that the type II genes are more conserved, meaning that they may have originated and differentiated earlier than the type I genes did. At the same time, the presence of extra-long amino acid sequences may be an important feature of C. chekiangoleosa. Gene structure analysis revealed the number of introns of MADS-box genes: twenty-one type I genes had no introns, and 13 type I genes contained only 1~2 introns. The type II genes have far more introns and longer introns than the type I genes do. Some MIKCC genes have super large introns (≥15 kb), which are rare in other species. The super large introns of these MIKCC genes may indicate richer gene expression. Moreover, the results of a qPCR expression analysis of the roots, flowers, leaves and seeds of C. chekiangoleosa showed that the MADS-box genes were expressed in all those tissues. Overall, compared with that of the type I genes, the expression of the type II genes was significantly higher. The CchMADS31 and CchMADS58 genes (type II) were highly expressed specifically in the flowers, which may in turn regulate the size of the flower meristem and petals. CchMADS55 was expressed specifically in the seeds, which might affect seed development. This study provides additional information for the functional characterization of the MADS-box gene family and lays an important foundation for in-depth study of related genes, such as those involved in the development of the reproductive organs of C. chekiangoleosa.
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Song M, Zhang Y, Jia Q, Huang S, An R, Chen N, Zhu Y, Mu J, Hu S. Systematic analysis of MADS-box gene family in the U's triangle species and targeted mutagenesis of BnaAG homologs to explore its role in floral organ identity in Brassica napus. FRONTIERS IN PLANT SCIENCE 2023; 13:1115513. [PMID: 36714735 PMCID: PMC9878456 DOI: 10.3389/fpls.2022.1115513] [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: 12/04/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
MADS-box transcription factors play an important role in regulating floral organ development and participate in environmental responses. To date, the MADS-box gene family has been widely identified in Brassica rapa (B. rapa), Brassica oleracea (B. oleracea), and Brassica napus (B. napus); however, there are no analogous reports in Brassica nigra (B. nigra), Brassica juncea (B. juncea), and Brassica carinata (B. carinata). In this study, a whole-genome survey of the MADS-box gene family was performed for the first time in the triangle of U species, and a total of 1430 MADS-box genes were identified. Based on the phylogenetic relationship and classification of MADS-box genes in Arabidopsis thaliana (A. thaliana), 1430 MADS-box genes were categorized as M-type subfamily (627 genes), further divided into Mα, Mβ, Mγ, and Mδ subclades, and MIKC-type subfamily (803 genes), further classified into 35 subclades. Gene structure and conserved protein motifs of MIKC-type MADS-box exhibit diversity and specificity among different subclades. Comparative analysis of gene duplication events and syngenic gene pairs among different species indicated that polyploidy is beneficial for MIKC-type gene expansion. Analysis of transcriptome data within diverse tissues and stresses in B. napus showed tissue-specific expression of MIKC-type genes and a broad response to various abiotic stresses, particularly dehydration stress. In addition, four representative floral organ mutants (wtl, feml, aglf-2, and aglf-1) in the T0 generation were generated by editing four AGAMOUS (BnaAG) homoeologs in B. napus that enriched the floral organ variant phenotype. In brief, this study provides useful information for investigating the function of MADS-box genes and contributes to revealing the regulatory mechanisms of floral organ development in the genetic improvement of new varieties.
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Affiliation(s)
- Min Song
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Yanfeng Zhang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Qingli Jia
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Shuhua Huang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Ran An
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Nana Chen
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Yantao Zhu
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Jianxin Mu
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Shengwu Hu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
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Genome-Wide Analysis of the Mads-Box Transcription Factor Family in Solanum melongena. Int J Mol Sci 2023; 24:ijms24010826. [PMID: 36614267 PMCID: PMC9821028 DOI: 10.3390/ijms24010826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/17/2022] [Accepted: 12/29/2022] [Indexed: 01/09/2023] Open
Abstract
The MADS-box transcription factors are known to be involved in several aspects of plant growth and development, especially in floral organ specification. However, little is known in eggplant. Here, 120 eggplant MADS-box genes were identified and categorized into type II (MIKCC and MIKC*) and type I (Mα, Mβ, and Mγ) subfamilies based on phylogenetic relationships. The exon number in type II SmMADS-box genes was greater than that in type I SmMADS-box genes, and the K-box domain was unique to type II MADS-box TFs. Gene duplication analysis revealed that segmental duplications were the sole contributor to the expansion of type II genes. Cis-elements of MYB binding sites related to flavonoid biosynthesis were identified in three SmMADS-box promoters. Flower tissue-specific expression profiles showed that 46, 44, 38, and 40 MADS-box genes were expressed in the stamens, stigmas, petals, and pedicels, respectively. In the flowers of SmMYB113-overexpression transgenic plants, the expression levels of 3 SmMADS-box genes were co-regulated in different tissues with the same pattern. Correlation and protein interaction predictive analysis revealed six SmMADS-box genes that might be involved in the SmMYB113-regulated anthocyanin biosynthesis pathway. This study will aid future studies aimed at functionally characterizing important members of the MADS-box gene family.
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Sánchez-Sánchez M, Carrillo-Tripp J, Aispuro-Hernández E, Quintana-Obregón EA, Martínez-Téllez MÁ. Understanding tobamovirus-plant interactions: implications for breeding resistance to tomato brown rugose fruit virus. JOURNAL OF PLANT PATHOLOGY 2023; 105:83-94. [PMCID: PMC9734318 DOI: 10.1007/s42161-022-01287-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/21/2022] [Indexed: 11/07/2024]
Abstract
The genus Tobamovirus comprises a group of single-stranded RNA viruses that affect a wide variety of vegetables of economic importance. Tobamoviruses express a series of proteins that interact with the plant’s cellular machinery, allowing viral infection; during incompatible interactions, active defense is mediated by host proteins encoded by resistance genes. The genes conferring viral resistance and tolerance in non-susceptible hosts have been studied for their ability to transfer desired resistance traits to different crops. The N gene from Nicotiana spp., the repertoire of Tm genes in Solanum spp., the L locus from Capsicum spp., and TOM genes are the most studied genetic sequences for understanding resistance to tobamoviruses. Through classical plant breeding and genetic engineering techniques, it has been possible to introgress these resistance genes (R ) into new species. However, new reports highlight the ability of tobamoviruses to overcome R -mediated defense. One of the most notorious recent cases is the tomato brown rugose fruit virus (ToBRFV). The main characteristic of ToBRFV is its capacity to overcome the resistance mediated by the Tm-2 2 gene, resulting in a limited repertoire of options to combat the virus. To defeat emerging viruses, it is necessary to apply the knowledge from other tobamoviruses-host relationships and use new technologies such as genome-wide association studies (GWAS) to understand and associate the architecture of resistance genes present in the Solanaceae family for the benefit of plant breeding. Although new genomic tools such as CRISPR systems open the possibility of coping with viral diseases, there are no commercial ToBRFV-resistant tomato varieties. Hence, the world’s leading seed suppliers compete to develop and bring these varieties to market.
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Affiliation(s)
- Mario Sánchez-Sánchez
- Laboratorio de Fisiología Vegetal, Centro de Investigación en Alimentación y Desarrollo A.C., Carretera Gustavo Enrique Astiazarán Rosas, No. 46, Col. La Victoria, 83304 Hermosillo, Sonora México
| | - Jimena Carrillo-Tripp
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, 22860 Ensenada, Baja California México
| | - Emmanuel Aispuro-Hernández
- Laboratorio de Fisiología Vegetal, Centro de Investigación en Alimentación y Desarrollo A.C., Carretera Gustavo Enrique Astiazarán Rosas, No. 46, Col. La Victoria, 83304 Hermosillo, Sonora México
| | - Eber Addí Quintana-Obregón
- CONACYT-Centro de Investigación en Alimentación y Desarrollo A.C., Carretera Gustavo Enrique Astiazarán Rosas, No. 46, Col. La Victoria, 83304 Hermosillo, Sonora México
| | - Miguel Ángel Martínez-Téllez
- Laboratorio de Fisiología Vegetal, Centro de Investigación en Alimentación y Desarrollo A.C., Carretera Gustavo Enrique Astiazarán Rosas, No. 46, Col. La Victoria, 83304 Hermosillo, Sonora México
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Zhang X, Wang X, Pan L, Guo W, Li Y, Wang W. Genome-wide identification and expression analysis of MADS-box transcription factors reveal their involvement in sex determination of hardy rubber tree ( Eucommia ulmoides oliv.). Front Genet 2023; 14:1138703. [PMID: 36896236 PMCID: PMC9988917 DOI: 10.3389/fgene.2023.1138703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/06/2023] [Indexed: 02/23/2023] Open
Abstract
Eucommia ulmoides is a famous rubber-producing and medicinal tree species that produces unisexual flowers on separate individuals from the earliest stage of stamen/pistil primordium formation. To explore the genetic regulation pathway of sex in E. ulmoides, comprehensive genome-wide analyses and tissue-/sex-specific transcriptome comparisons of MADS-box transcription factors were performed for the first time in this work. Quantitative real-time PCR technique was employed to further validate the expression of genes that are assigned to floral organ ABCDE model. A total of 66 non-redundant E. ulmoides MADS-box (EuMADS) genes were identified, they were classified into Type I (M-type, 17 genes) and Type II (MIKC, 49 genes). Complex protein-motif composition, exon-intron structure and phytohormone-response cis-elements were detected in MIKC-EuMADS genes. Furthermore, 24 differentially-expressed EuMADS genes (DEGs) between male and female flowers, and two DEGs between male and female leaves were revealed. Amongst the 14 floral organ ABCDE model-related genes, there were 6 (A/B/C/E-class) and 5 (A/D/E-class) genes displayed male- and female-biased expression respectively. In particular, one B-class gene EuMADS39 and one A-class gene EuMADS65 were almost exclusively expressed in male trees, no matter in flower or leaf tissues. Collectively, these results suggested a critical role of MADS-box transcription factors in sex determination of E. ulmoides, which is conducive to decoding the molecular regulation mechanism of sex in E. ulmoides.
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Affiliation(s)
- Xianzhi Zhang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xinyi Wang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Linsi Pan
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wei Guo
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yongquan Li
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wencai Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
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Yang Z, Nie G, Feng G, Xu X, Li D, Wang X, Huang L, Zhang X. Genome-wide identification of MADS-box gene family in orchardgrass and the positive role of DgMADS114 and DgMADS115 under different abiotic stress. Int J Biol Macromol 2022; 223:129-142. [PMID: 36356860 DOI: 10.1016/j.ijbiomac.2022.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022]
Abstract
Abiotic stress, a major factor limit growth and productivity of major crops. Orchardgrass is one of the most important cool-season forage grasses in the world, and it is highly tolerant to abiotic stress. The MADS-box transcription factor family is one of the largest families in plants, and it plays vital roles in multiple biological processes. However, MADS-box transcription factors in orchardgrass, especially those involved in abiotic stress, have not yet been elucidated. Here, 123 DgMADS-box members were identified in orchardgrass and a detailed overview has been presented. Syntenic analysis indicated that the expansion of the DgMADS-box genes in orchardgrass is mainly dependent on tandem duplication events. Some DgMADS-box genes were induced by multiple abiotic stresses, indicating that these genes may play critical regulatory roles in orchardgrass response to various abiotic stresses. Heterologous expression showed that DgMADS114 and DgMADS115 could enhance stress tolerance of transgenic Arabidopsis, as revealed by longer root length or higher survival rates under PEG, NaCl, ABA, and heat stress. The results of this study provide a scientific basis for clarifying the functional characterization of MADS-box genes in orchardgrass in response to environmental stress can be further used to improve forages and crops via breeding programs.
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Affiliation(s)
- Zhongfu Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoheng Xu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Dandan Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xia Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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Larriba E, Nicolás-Albujer M, Sánchez-García AB, Pérez-Pérez JM. Identification of Transcriptional Networks Involved in De Novo Organ Formation in Tomato Hypocotyl Explants. Int J Mol Sci 2022; 23:16112. [PMID: 36555756 PMCID: PMC9788163 DOI: 10.3390/ijms232416112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Some of the hormone crosstalk and transcription factors (TFs) involved in wound-induced organ regeneration have been extensively studied in the model plant Arabidopsis thaliana. In previous work, we established Solanum lycopersicum "Micro-Tom" explants without the addition of exogenous hormones as a model to investigate wound-induced de novo organ formation. The current working model indicates that cell reprogramming and founder cell activation requires spatial and temporal regulation of auxin-to-cytokinin (CK) gradients in the apical and basal regions of the hypocotyl combined with extensive metabolic reprogramming of some cells in the apical region. In this work, we extended our transcriptomic analysis to identify some of the gene regulatory networks involved in wound-induced organ regeneration in tomato. Our results highlight a functional conservation of key TF modules whose function is conserved during de novo organ formation in plants, which will serve as a valuable resource for future studies.
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Genome-Wide Identification, Evolution, and Expression Characterization of the Pepper (Capsicum spp.) MADS-box Gene Family. Genes (Basel) 2022; 13:genes13112047. [PMID: 36360285 PMCID: PMC9690561 DOI: 10.3390/genes13112047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
MADS domain transcription factors play roles throughout the whole lifecycle of plants from seeding to flowering and fruit-bearing. However, systematic research into MADS-box genes of the economically important vegetable crop pepper (Capsicum spp.) is still lacking. We identified 174, 207, and 72 MADS-box genes from the genomes of C. annuum, C. baccatum, and C. chinense, respectively. These 453 MADS-box genes were divided into type I (Mα, Mβ, Mγ) and type II (MIKC* and MIKCC) based on their phylogenetic relationships. Collinearity analysis identified 144 paralogous genes and 195 orthologous genes in the three Capsicum species, and 70, 114, and 10 MADS-box genes specific to C. annuum, C. baccatum, and C. chinense, respectively. Comparative genomic analysis highlighted functional differentiation among homologous MADS-box genes during pepper evolution. Tissue expression analysis revealed three main expression patterns: highly expressed in roots, stems, leaves, and flowers (CaMADS93/CbMADS35/CcMADS58); only expressed in roots; and specifically expressed in flowers (CaMADS26/CbMADS31/CcMADS11). Protein interaction network analysis showed that type II CaMADS mainly interacted with proteins related to flowering pathway and flower organ development. This study provides the basis for an in-depth study of the evolutionary features and biological functions of pepper MADS-box genes.
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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: 5] [Impact Index Per Article: 1.7] [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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Mou Y, Yuan C, Sun Q, Yan C, Zhao X, Wang J, Wang Q, Shan S, Li C. MIKC-type MADS-box transcription factor gene family in peanut: Genome-wide characterization and expression analysis under abiotic stress. FRONTIERS IN PLANT SCIENCE 2022; 13:980933. [PMID: 36340369 PMCID: PMC9631947 DOI: 10.3389/fpls.2022.980933] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Peanut (Arachis hypogaea) is one of the most important economic crops around the world, especially since it provides vegetable oil and high-quality protein for humans. Proteins encoded by MADS-box transcription factors are widely involved in regulating plant growth and development as well as responses to abiotic stresses. However, the MIKC-type MADS-box TFs in peanut remains currently unclear. Hence, in this study, 166 MIKC-type MADS-box genes were identified in both cultivated and wild-type peanut genomes, which were divided into 12 subfamilies. We found a variety of development-, hormone-, and stress-related cis-acting elements in the promoter region of peanut MIKC-type MADS-box genes. The chromosomal distribution of peanut MADS-box genes was not random, and gene duplication contributed to the expansion of the MADS-box gene family. The interaction network of the peanut AhMADS proteins was established. Expression pattern analysis showed that AhMADS genes were specifically expressed in tissues and under abiotic stresses. It was further confirmed via the qRT-PCR technique that five selected AhMADS genes could be induced by abiotic and hormone treatments and presented different expressive profiles under various stresses. Taken together, these findings provide valuable information for the exploration of candidate genes in molecular breeding and further study of AhMADS gene functions.
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Zhu X, Wang B, Wang X, Wei X. Genome-wide identification, structural analysis and expression profiles of short internodes related sequence gene family in quinoa. Front Genet 2022; 13:961925. [PMID: 36072673 PMCID: PMC9443693 DOI: 10.3389/fgene.2022.961925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 07/01/2022] [Indexed: 11/27/2022] Open
Abstract
Based on the whole genome data information of Chenopodium quinoa Willd, the CqSRS gene family members were systematically identified and analyzed by bioinformatics methods, and the responses of CqSRS genes to NaCl (100 mmol/L), salicylic acid (200 umol/L) and low temperature (4°C) were detected by qRT-PCR. The results showed that a total of 10 SHI related sequence genes were identified in quinoa, and they were distributed on 9 chromosomes, and there were four pairs of duplicated genes. The number of amino acids encoded ranged from 143 aa to 370 aa, and the isoelectric point ranged from 4.81 to 8.90. The secondary structure was mainly composed of random coil (Cc). Most of the SRS gene encoding proteins were located in the cytoplasm (5 CqSRS). Phylogenetic analysis showed that the CqSRS genes were divided into three groups, and the gene structure showed that the number of exons of CqSRS was between two-five. Promoter analysis revealed that there are a total of 44 elements related to plant hormone response elements, light response elements, stress response elements and tissue-specific expression in the upstream regin of the gene. Protein interaction showed that all 10 CqSRS proteins appeared in the known protein interaction network diagram in Arabidopsis. Expression profile analysis showed that CqSRS genes had different expression patterns, and some genes had tissue-specific expression. qRT-PCR showed that all SRS family genes responded to ABA、NaCl、drought and low-temperature treatments, but the expression levels of different CqSRS genes were significantly different under various stresses. This study lays a foundation for further analyzed the function of CqSRS genes.
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Affiliation(s)
- Xiaolin Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Baoqiang Wang
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xian Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaohong Wei
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Xiaohong Wei,
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Duan K, Fu H, Fang D, Wang K, Zhang W, Liu H, Sahu SK, Chen X. Genome-Wide Analysis of the MADS-Box Gene Family in Holoparasitic Plants ( Balanophora subcupularis and Balanophora fungosa var. globosa). FRONTIERS IN PLANT SCIENCE 2022; 13:846697. [PMID: 35712591 PMCID: PMC9197559 DOI: 10.3389/fpls.2022.846697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
MADS-box is an important transcription factor family that is involved in the regulation of various stages of plant growth and development, especially flowering regulation and flower development. Being a holoparasitic plant, the body structure of Balanophoraceae has changed dramatically over time, and its vegetative and reproductive organs have been extensively modified, with rudimentary flower organs. Meanwhile, extraordinary gene losses have been identified in holoparasitic plants compared with autotrophs. Our study reveals that the MADS-box gene family contracted sharply in Balanophora subcupularis and Balanophora fungosa var. globosa, and some subfamilies were lost, exhibiting reduced redundancy in both. The genes that functioned in the transition from the vegetative to floral production stages suffered a significant loss, but the ABCE model genes remained intact. We further investigated genes related to flowering regulation in B. subcupularis and B. fungosa var. globosa, vernalization and autonomous ways of regulating flowering time remained comparatively integrated, while genes in photoperiod and circadian clock pathways were almost lost. Convergent gene loss in flowering regulation occurred in Balanophora and another holoparasitic plant Sapria himalayana (Rafflesiaceae). The genome-wide analysis of the MADS-box gene family in Balanophora species provides valuable information for understanding the classification, gene loss pattern, and flowering regulation mechanism of MADS-box gene family in parasitic plants.
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Affiliation(s)
- Kunyu Duan
- Beijing Genomics Institute College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hui Fu
- Beijing Genomics Institute College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute, Shenzhen, China
| | - Kaimeng Wang
- Beijing Genomics Institute College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Wen Zhang
- China National GeneBank, Beijing Genomics Institute, Shenzhen, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute, Shenzhen, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute, Shenzhen, China
| | - Xiaoli Chen
- Beijing Genomics Institute College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute, Shenzhen, China
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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: 3.7] [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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Trubanová N, Shi J, Schilling S. Firming up your tomato: a natural promoter variation in a MADS-box gene is causing all-flesh tomatoes. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1-4. [PMID: 34986230 PMCID: PMC8730695 DOI: 10.1093/jxb/erab442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This article comments on: Liu L, Zhang K, Bai JR, Lu J, Lu X, Hu J, Pan C, He S, Yuan J, Zhang Y, Zhang M, Guo Y, Wang X, Huang Z, Du Y, Cheng F, Li J. 2022. All-flesh fruit in tomato is controlled by reduced expression dosage of AFF through a structural variant mutation in the promoter. Journal of Experimental Botany 73, 123–138.
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Affiliation(s)
- Nina Trubanová
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Ireland
| | - Jiaqi Shi
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Ireland
| | - Susanne Schilling
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Ireland
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Hou Q, Li S, Shang C, Wen Z, Cai X, Hong Y, Qiao G. Genome-wide characterization of chalcone synthase genes in sweet cherry and functional characterization of CpCHS1 under drought stress. FRONTIERS IN PLANT SCIENCE 2022; 13:989959. [PMID: 36061761 PMCID: PMC9437463 DOI: 10.3389/fpls.2022.989959] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/03/2022] [Indexed: 05/22/2023]
Abstract
Cherries are one of the important fruit trees. The growth of cherry is greatly affected by abiotic stresses such as drought, which hinders its development. Chalcone synthase (CHS, EC 2.3.1.74) is a crucial rate-limiting enzyme in the flavonoid biosynthetic pathway that plays an important role in regulating plant growth, development, and abiotic stress tolerance. In the current study, three genes encoding chalcone synthase were identified in the genome of sweet cherry (Prunus avium L.). The three genes contained fewer introns and showed high homology with CHS genes of other Rosaceae members. All members are predicted to localize in the cytoplasm. The conserved catalytic sites may be located at the Cys163, Phe214, His302, and Asn335 residues. These genes were differentially expressed during flower bud dormancy and fruit development. The total flavonoid content of Chinese cherry (Cerasus pseudocerasus Lindl.) was highest in the leaves and slightly higher in the pulp than in the peel. No significant difference in total flavonoid content was detected between aborted kernels and normally developing kernels. Overexpression of Chinese cherry CpCHS1 in tobacco improved the germination frequency of tobacco seeds under drought stress, and the fresh weight of transgenic seedlings under drought stress was higher than that of the wild type, and the contents of SOD, POD, CAT, and Pro in OE lines were significantly increased and higher than WT under drought stress. These results indicate cherry CHS genes are conserved and functionally diverse and will assist in elucidating the functions of flavonoid synthesis pathways in cherry and other Rosaceae species under drought stress.
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Affiliation(s)
- Qiandong Hou
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Shuang Li
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Chunqiong Shang
- College of Forestry, Institute for Forest Resources & Environment of Guizhou, Guizhou University, Guiyang, China
| | - Zhuang Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Xiaowei Cai
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Yi Hong
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Guang Qiao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- *Correspondence: Guang Qiao,
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Sun Y, Wen H, Tian Y, Mao X, Li X, Li J, Hu Y, Liu Y, Li J, Li Y. HSP90 and HSP70 Families in Lateolabrax maculatus: Genome-Wide Identification, Molecular Characterization, and Expression Profiles in Response to Various Environmental Stressors. Front Physiol 2021; 12:784803. [PMID: 34880782 PMCID: PMC8646100 DOI: 10.3389/fphys.2021.784803] [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: 09/28/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Heat shock proteins (HSPs) are a large class of highly conserved chaperons, which play important roles in response to elevated temperature and other environmental stressors. In the present study, 5 HSP90 genes and 17 HSP70 genes were systematically characterized in spotted seabass (Lateolabrax maculatus). The evolutionary footprint of HSP genes was revealed via the analysis of phylogeny, chromosome location, and gene copy numbers. In addition, the gene structure features and the putative distribution of heat shock elements (HSEs) and hypoxia response elements (HREs) in the promoter regions were analyzed. The protein-protein interaction (PPI) network analyses results indicated the potential transcriptional regulation between the heat shock factor 1 (HSF1) and HSPs and a wide range of interactions among HSPs. Furthermore, quantitative (q)PCR was performed to detect the expression profiles of HSP90 and HSP70 genes in gill, liver, and muscle tissues after heat stress, meanwhile, the expression patterns in gills under alkalinity and hypoxia stresses were determined by analyzing RNA-Seq datasets. Results showed that after heat stress, most of the examined HSP genes were significantly upregulated in a tissue-specific and time-dependent manners, and hsp90aa1.1, hsp90aa1.2, hsp70.1, and hsp70.2 were the most intense responsive genes in all three tissues. In response to alkalinity stress, 11 out of 13 significantly regulated HSP genes exhibited suppressed expression patterns. Alternatively, among the 12 hypoxia-responsive-expressed HSP genes, 7 genes showed induced expressions, while hsp90aa1.2, hsp70.1, and hsp70.2 had more significant upregulated changes after hypoxic challenge. Our findings provide the essential basis for further functional studies of HSP genes in response to abiotic stresses in spotted seabass.
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Affiliation(s)
- Yalong Sun
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Haishen Wen
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Yuan Tian
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Xuebin Mao
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Xiurong Li
- Quality and Safety Center of Agricultural and Livestock Products, Bayannaoer, China
| | - Junjie Li
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Yanbo Hu
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Yang Liu
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Jifang Li
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Yun Li
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
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Shao Z, He M, Zeng Z, Chen Y, Hanna AD, Zhu H. Genome-Wide Identification and Expression Analysis of the MADS-Box Gene Family in Sweet Potato [ Ipomoea batatas (L.) Lam]. Front Genet 2021; 12:750137. [PMID: 34868221 PMCID: PMC8636027 DOI: 10.3389/fgene.2021.750137] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
MADS-box gene, one of the largest transcription factor families in plants, is a class of transcription factors widely present in eukaryotes. It plays an important role in plant growth and development and participates in the growth and development of flowers and fruits. Sweet potato is the seventh most important food crop in the world. Its tuberous roots, stems, and leaves contain a large number of proteins, lipids, carotenoids, anthocyanins, conjugated phenolic acids, and minerals, which have high edible, forage, and medicinal value, and is also an important energy crop. At present, MADS-box genes in sweet potato have rarely been reported, and there has been no study on the genome-wide identification and classification of MADS-box genes in Ipomoea batatas. This study provided the first comprehensive analysis of sweet potato MADS-box genes. We identified 95 MADS-box genes, analyzed the structure and protein of sweet potato MADS-box genes, and categorized them based on phylogenetic analysis with Arabidopsis MADS-box proteins. Chromosomal localization indicated an unequal number of MADS-box genes in all 14 chromosomes except LG3, with more than 10 MADS-box genes located on chromosomes LG7, LG11, and LG15. The MADS domain and core motifs of the sweet potato MADS-box genes were identified by motif analysis. We identified 19 MADS-box genes with collinear relationships and analyzed duplication events. Cis-acting elements, such as light-responsive, auxin-responsive, drought-inducible, and MeJA-responsive elements, were found in the promoter region of the MADS-box genes in sweet potato, which further indicates the basis of MADS-box gene regulation in response to environmental changes and hormones. RNA-seq suggested that sweet potato MADS-box genes exhibit tissue-specific expression patterns, with 34 genes highly expressed in sweet potato flowers and fruits, and 19 genes highly expressed in the tuberous root, pencil root, or fibrous root. qRT-PCR again validated the expression levels of the 10 genes and found that IbMADS1, IbMADS18, IbMADS19, IbMADS79, and IbMADS90 were highly expressed in the tuberous root or fibrous root, and IbMADS18, IbMADS31, and IbMADS83 were highly expressed in the fruit. In this study, the molecular basis of MADS-box genes of sweet potato was analyzed from various angles. The effects of MADS-box genes on the growth and development of sweet potato were investigated, which may provide a certain theoretical basis for molecular breeding of sweet potato.
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Affiliation(s)
- Zhengwei Shao
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Minhong He
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Zhipeng Zeng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Yanzhu Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Amoanimaa-Dede Hanna
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Hongbo Zhu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
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Nezhdanova AV, Slugina MA, Dyachenko EA, Kamionskaya AM, Kochieva EZ, Shchennikova AV. Analysis of the structure and function of the tomato Solanum lycopersicum L. MADS-box gene SlMADS5. Vavilovskii Zhurnal Genet Selektsii 2021; 25:492-501. [PMID: 34595372 PMCID: PMC8453369 DOI: 10.18699/vj21.056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/12/2021] [Accepted: 05/18/2021] [Indexed: 12/01/2022] Open
Abstract
At all stages of f lowering, a decisive role is played by the family of MADS-domain transcription factors,
the combinatorial action of which is described by the ABCDE-model of f lower development. The current volume of
data suggests a high conservatism of ABCDE genes in angiosperms. The E-proteins SEPALLATA are the central hub of
the MADS-complexes, which determine the identity of the f loral organs. The only representative of the SEPALLATA3
clade in tomato Solanum lycopersicum L., SlMADS5, is involved in determining the identity of petals, stamens, and
carpels; however, data on the functions of the gene are limited. The study was focused on the SlMADS5 functional
characterization. Structural and phylogenetic analyses of SlMADS5 conf irmed its belonging to the SEP3 clade. An
in silico expression analysis revealed the absence of gene transcripts in roots, leaves, and shoot apical meristem,
and their presence in f lowers, fruits, and seeds at different stages of development. Two-hybrid analysis showed
the ability of SlMADS5 to activate transcription of the target gene and interact with TAGL1. Transgenic plants Nicotiana
tabacum L. with constitutive overexpression of SlMADS5 cDNA f lowered 2.2 times later than the control; plants
formed thickened leaves, 2.5–3.0 times thicker stems, 1.5–2.7 times shortened internodes, and 1.9 times fewer
f lowers and capsules than non-transgenic plants. The f lower structure did not differ from the control; however, the
corolla petals changed color from light pink to magenta. Analysis of the expression of SlMADS5 and the tobacco
genes NtLFY, NtAP1, NtWUS, NtAG, NtPLE, NtSEP1, NtSEP2, and NtSEP3 in leaves and apexes of transgenic and control
plants showed that SlMADS5 mRNA is present only in tissues of transgenic lines. The other genes analyzed were
highly expressed in the reproductive meristem of control plants. Gene transcripts were absent or were imperceptibly
present in the leaves and vegetative apex of the control, as well as in the leaves and apexes of transgenic lines.
The results obtained indicate the possible involvement of SlMADS5 in the regulation of f lower meristem development
and the pathway of anthocyanin biosynthesis in petals.
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Affiliation(s)
- A V Nezhdanova
- Institute of Bioengineering, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - M A Slugina
- Institute of Bioengineering, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - E A Dyachenko
- Institute of Bioengineering, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - A M Kamionskaya
- Institute of Bioengineering, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - E Z Kochieva
- Institute of Bioengineering, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - A V Shchennikova
- Institute of Bioengineering, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
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Alhindi T, Al-Abdallat AM. Genome-Wide Identification and Analysis of the MADS-Box Gene Family in American Beautyberry ( Callicarpa americana). PLANTS 2021; 10:plants10091805. [PMID: 34579338 PMCID: PMC8466759 DOI: 10.3390/plants10091805] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 12/27/2022]
Abstract
The MADS-box gene family encodes a number of transcription factors that play key roles in various plant growth and development processes from response to environmental cues to cell differentiation and organ identity, especially the floral organogenesis, as in the prominent ABCDE model of flower development. Recently, the genome of American beautyberry (Callicarpa americana) has been sequenced. It is a shrub native to the southern region of United States with edible purple-colored berries; it is a member of the Lamiaceae family, a family of medical and agricultural importance. Seventy-eight MADS-box genes were identified from 17 chromosomes of the C. americana assembled genome. Peptide sequences blast and analysis of phylogenetic relationships with MADS-box genes of Sesame indicum, Solanum lycopersicum, Arabidopsis thaliana, and Amborella trichopoda were performed. Genes were separated into 32 type I and 46 type II MADS-box genes. C. americana MADS-box genes were clustered into four groups: MIKCC, MIKC*, Mα-type, and Mγ-type, while the Mβ-type group was absent. Analysis of the gene structure revealed that from 1 to 15 exons exist in C. americana MADS-box genes. The number of exons in type II MADS-box genes (5–15) greatly exceeded the number in type I genes (1–9). The motif distribution analysis of the two types of MADS-box genes showed that type II MADS-box genes contained more motifs than type I genes. These results suggested that C. americana MADS-box genes type II had more complex structures and might have more diverse functions. The role of MIKC-type MADS-box genes in flower and fruit development was highlighted when the expression profile was analyzed in different organs transcriptomes. This study is the first genome-wide analysis of the C. americana MADS-box gene family, and the results will further support any functional and evolutionary studies of C. americana MADS-box genes and serve as a reference for related studies of other plants in the medically important Lamiaceae family.
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Affiliation(s)
- Tareq Alhindi
- Department of Biological Sciences, School of Science, The University of Jordan, Amman 11942, Jordan
- Correspondence:
| | - Ayed M. Al-Abdallat
- Department of Horticulture and Crop Science, School of Agriculture, The University of Jordan, Amman 11942, Jordan;
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