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Okay A, Kırlıoğlu T, Durdu YŞ, Akdeniz SŞ, Büyük İ, Aras ES. Omics approaches to understand the MADS-box gene family in common bean (Phaseolus vulgaris L.) against drought stress. PROTOPLASMA 2024; 261:709-724. [PMID: 38240857 PMCID: PMC11196313 DOI: 10.1007/s00709-024-01928-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/09/2024] [Indexed: 06/25/2024]
Abstract
MADS-box genes are known to play important roles in diverse aspects of growth/devolopment and stress response in several plant species. However, no study has yet examined about MADS-box genes in P. vulgaris. In this study, a total of 79 PvMADS genes were identified and classified as type I and type II according to the phylogenetic analysis. While both type I and type II PvMADS classes were found to contain the MADS domain, the K domain was found to be present only in type II PvMADS proteins, in agreement with the literature. All chromosomes of the common bean were discovered to contain PvMADS genes and 17 paralogous gene pairs were identified. Only two of them were tandemly duplicated gene pairs (PvMADS-19/PvMADS-23 and PvMADS-20/PvMADS-24), and the remaining 15 paralogous gene pairs were segmentally duplicated genes. These duplications were found to play an important role in the expansion of type II PvMADS genes. Moreover, the RNAseq and RT-qPCR analyses showed the importance of PvMADS genes in response to drought stress in P. vulgaris.
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Affiliation(s)
- Aybüke Okay
- Department of Biology, Faculty of Science, Ankara University, Ankara, 06100, Turkey
| | - Tarık Kırlıoğlu
- Department of Biology, Faculty of Science, Ankara University, Ankara, 06100, Turkey
| | - Yasin Şamil Durdu
- Department of Biology, Faculty of Science, Ankara University, Ankara, 06100, Turkey
| | - Sanem Şafak Akdeniz
- Kalecik Vocational School Plant Protection Program, Ankara University, Ankara, 06100, Turkey
| | - İlker Büyük
- Department of Biology, Faculty of Science, Ankara University, Ankara, 06100, Turkey.
- Department of Biology, Faculty of Science, Ankara University, Block A, Emniyet, Dögol Cd. 6A, Yenimahalle, Ankara, 06560, Turkey.
| | - E Sümer Aras
- Department of Biology, Faculty of Science, Ankara University, Ankara, 06100, Turkey.
- Department of Biology, Faculty of Science, Ankara University, Block A, Emniyet, Dögol Cd. 6A, Yenimahalle, Ankara, 06560, Turkey.
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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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Yang J, Chen R, Liu W, Xiang X, Fan C. Genome-Wide Characterization and Phylogenetic and Stress Response Expression Analysis of the MADS-Box Gene Family in Litchi ( Litchi chinensis Sonn.). Int J Mol Sci 2024; 25:1754. [PMID: 38339030 PMCID: PMC10855657 DOI: 10.3390/ijms25031754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
The MADS-box protein is an important transcription factor in plants and plays an important role in regulating the plant abiotic stress response. In this study, a total of 94 MADS-box genes were predicted in the litchi genome, and these genes were widely distributed on all the chromosomes. The LcMADS-box gene family was divided into six subgroups (Mα, Mβ, Mγ, Mδ, MIKC, and UN) based on their phylogenetical relationships with Arabidopsis, and the closely linked subgroups exhibited more similarity in terms of motif distribution and intron/exon numbers. Transcriptome analysis indicated that LcMADS-box gene expression varied in different tissues, which can be divided into universal expression and specific expression. Furthermore, we further validated that LcMADS-box genes can exhibit different responses to various stresses using quantitative real-time PCR (qRT-PCR). Moreover, physicochemical properties, subcellular localization, collinearity, and cis-acting elements were also analyzed. The findings of this study provide valuable insights into the MADS-box gene family in litchi, specifically in relation to stress response. The identification of hormone-related and stress-responsive cis-acting elements in the MADS-box gene promoters suggests their involvement in stress signaling pathways. This study contributes to the understanding of stress tolerance mechanisms in litchi and highlights potential regulatory mechanisms underlying stress responses.
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Affiliation(s)
| | | | | | | | - Chao Fan
- Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (J.Y.)
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Nan J, An J, Yang Y, Zhao G, Yang X, Liu H, Han B. Genome-wide identification of the MADS-box gene family in Avena sativa and its role in photoperiod-insensitive oat. PeerJ 2024; 12:e16759. [PMID: 38274325 PMCID: PMC10809983 DOI: 10.7717/peerj.16759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/13/2023] [Indexed: 01/27/2024] Open
Abstract
Background Traditional spring-summer sown oat is a typical long-day crop that cannot head under short-day conditions. The creation of photoperiod-insensitive oats overcomes this limitation. MADS-box genes are a class of transcription factors involved in plant flowering signal transduction regulation. Previous transcriptome studies have shown that MADS-box genes may be related to the oat photoperiod. Methods Putative MADS-box genes were identified in the whole genome of oat. Bioinformatics methods were used to analyze their classification, conserved motifs, gene structure, evolution, chromosome localization, collinearity and cis-elements. Ten representative genes were further screened via qRT‒PCR analysis under short days. Results In total, sixteen AsMADS genes were identified and grouped into nine subfamilies. The domains, conserved motifs and gene structures of all AsMADS genes were conserved. All members contained light-responsive elements. Using the photoperiod-insensitive oat MENGSIYAN4HAO (MSY4) and spring-summer sown oat HongQi2hao (HQ2) as materials, qRT‒PCR analysis was used to analyze the AsMADS gene at different panicle differentiation stages under short-day conditions. Compared with HQ2, AsMADS3, AsMADS8, AsMADS11, AsMADS13, and AsMADS16 were upregulated from the initial stage to the branch differentiation stage in MSY4, while AsMADS12 was downregulated. qRT‒PCR analysis was also performed on the whole panicle differentiation stages in MSY4 under short-day conditions, the result showed that the expression levels of AsMADS9 and AsMADS11 gradually decreased. Based on the subfamily to which these genes belong, the above results indicated that AsMADS genes, especially SVP, SQUA and Mα subfamily members, regulated panicle development in MSY4 by responding to short-days. This work provides a foundation for revealing the function of the AsMADS gene family in the oat photoperiod pathway.
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Affiliation(s)
- Jinsheng Nan
- Inner Mongolia Agricultural University, Key Lab of Germplasm Innovation and Utlization of Triticeae Crop at Universities of Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Jianghong An
- Inner Mongolia Agricultural University, Key Lab of Germplasm Innovation and Utlization of Triticeae Crop at Universities of Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Inner Mongolia Academy of Agriculture and Animal Husbandry Science, Hohhot, Inner Mongolia, China
| | - Yan Yang
- Inner Mongolia Agricultural University, Key Lab of Germplasm Innovation and Utlization of Triticeae Crop at Universities of Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Guofen Zhao
- Inner Mongolia Agricultural University, Key Lab of Germplasm Innovation and Utlization of Triticeae Crop at Universities of Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Xiaohong Yang
- Zhangjiakou Academy of Agricultural Sciences, Zhangjiakou, HeBei Province, China
| | - Huiyan Liu
- Inner Mongolia Agricultural University, Key Lab of Germplasm Innovation and Utlization of Triticeae Crop at Universities of Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Bing Han
- Inner Mongolia Agricultural University, Key Lab of Germplasm Innovation and Utlization of Triticeae Crop at Universities of Inner Mongolia Autonomous Region, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
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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: 1.0] [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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Wang F, Zhou Z, Zhu L, Gu Y, Guo B, Lv C, Zhu J, Xu R. Genome-wide analysis of the MADS-box gene family involved in salt and waterlogging tolerance in barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1178065. [PMID: 37229117 PMCID: PMC10203460 DOI: 10.3389/fpls.2023.1178065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/07/2023] [Indexed: 05/27/2023]
Abstract
MADS-box transcription factors are crucial members of regulatory networks underlying multiple developmental pathways and abiotic stress regulatory networks in plants. Studies on stress resistance-related functions of MADS-box genes are very limited in barley. To gain insight into this gene family and elucidate their roles in salt and waterlogging stress resistance, we performed genome-wide identification, characterization and expression analysis of MADS-box genes in barley. A whole-genome survey of barley revealed 83 MADS-box genes, which were categorized into type I (Mα, Mβ and Mγ) and type II (AP1, SEP1, AGL12, STK, AGL16, SVP and MIKC*) lineages based on phylogeny, protein motif structure. Twenty conserved motifs were determined and each HvMADS contained one to six motifs. We also found tandem repeat duplication was the driven force for HvMADS gene family expansion. Additionally, the co-expression regulatory network of 10 and 14 HvMADS genes was predicted in response to salt and waterlogging stress, and we proposed HvMADS11,13 and 35 as candidate genes for further exploration of the functions in abiotic stress. The extensive annotations and transcriptome profiling reported in this study ultimately provides the basis for MADS functional characterization in genetic engineering of barley and other gramineous crops.
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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: 2.0] [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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Ye LX, Luo MM, Wang Z, Bai FX, Luo X, Gao L, Peng J, Chen QH, Zhang L. Genome-wide analysis of MADS-box gene family in kiwifruit (Actinidia chinensis var. chinensis) and their potential role in floral sex differentiation. Front Genet 2022; 13:1043178. [PMID: 36468015 PMCID: PMC9714460 DOI: 10.3389/fgene.2022.1043178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022] Open
Abstract
Kiwifruit (Actinidia chinensis Planch.) is a functionally dioecious plant, which displays diverse morphology in male and female flowers. MADS-box is an ancient and huge gene family that plays a key role in plant floral organ differentiation. In this study, we have identified 89 MADS-box genes from A. chinensis Red 5 genome. These genes are distributed on 26 chromosomes and are classified into type I (21 genes) and type II (68 genes). Overall, type II AcMADS-box genes have more complex structures than type I with more exons, protein domains, and motifs, indicating that type II genes may have more diverse functions. Gene duplication analysis showed that most collinearity occurred in type II AcMADS-box genes, which was consistent with a large number of type II genes. Analysis of cis-acting elements in promoters showed that AcMADS-box genes are mainly associated with light and phytohormone responsiveness. The expression profile of AcMADS-box genes in different tissues showed that most genes were highly expressed in flowers. Further, the qRT-PCR analysis of the floral organ ABCDE model-related genes in male and female flowers revealed that AcMADS4, AcMADS56, and AcMADS70 were significantly expressed in female flowers. It indicated that those genes may play an important role in the sex differentiation of kiwifruit. This work provided a comprehensive analysis of the AcMADS-box genes and may help facilitate our understanding of the sex differentiation regulatory mechanism in kiwifruit.
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Affiliation(s)
- Li-Xia Ye
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Min-Min Luo
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
- College of Horticulture and Gardening, Yangtze University, Jingzhou, China
| | - Zhi Wang
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Fu-Xi Bai
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Xuan Luo
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Lei Gao
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Jue Peng
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Qing-Hong Chen
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
- *Correspondence: Qing-Hong Chen, ; Lei Zhang,
| | - Lei Zhang
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
- *Correspondence: Qing-Hong Chen, ; Lei Zhang,
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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: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
The MADS-box gene family plays a crucial role in multiple developmental processes of plants, especially in floral organ specification and the regulation of fruit development and ripening. Juglans mandshurica is a precious fruit material whose quality and yield are determined by floral organ development. The molecular mechanism of J. mandshurica female and male flower development depending on MADS-box genes remains unclear. In our study, 67 JmMADS genes were identified and unevenly distributed on 15 of 16 J. mandshurica chromosomes. These genes were divided into two types [type I (Mα, Mγ, Mδ) and type II (MIKC)]. The gene structure and motif analyses showed that most genes belonging to the same type had similar gene structures and conserved motifs. The analysis of syntenic relationships showed that MADS-box genes in J. mandshurica, J. sigillata, and J. regia exhibited the highest homology and great collinearity. Analysis of cis-acting elements showed that JmMADS gene promoter regions contained light, stress and hormone response cis-acting elements. The gene expression patterns demonstrated that 30 and 26 JmMADS genes were specifically expressed in the female and male flowers, respectively. In addition, 12 selected genes common to J. mandshurica female and male flowers were significantly upregulated at the mature stage and were used to validate the reliability of the transcriptome data using quantitative real-time PCR. This comprehensive and systematic analysis of J. mandshurica MADS-box genes lays a foundation for future studies on MADS-box gene family functions.
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Affiliation(s)
- Hanxi Li
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
| | - Yuxi Li
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xinxin Zhang
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Kewei Cai
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yan Li
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
| | - Qingcheng Wang
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Guanzheng Qu
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Rui Han
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
| | - Xiyang Zhao
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
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Identification of MADS-Box Transcription Factors in Iris laevigata and Functional Assessment of IlSEP3 and IlSVP during Flowering. Int J Mol Sci 2022; 23:ijms23179950. [PMID: 36077350 PMCID: PMC9456522 DOI: 10.3390/ijms23179950] [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: 07/26/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
Iris laevigata is ideal for gardening and landscaping in northeast China because of its beautiful flowers and strong cold resistance. However, the short length of flowering time (2 days for individual flowers) greatly limits its applications. Molecular breeding and engineering hold high potential for producing I. laevigata of desirable flowering properties. A prerequisite is to identify and characterize key flowering control genes, the identity of which remains largely unknown in I. laevigata due to the lack of genome information. To fill this knowledge gap, we used sequencing data of the I. laevigata transcriptome to identify MADS-box gene-encoding transcription factors that have been shown to play key roles in developmental processes, including flowering. Our data revealed 41 putative MADS-box genes, which consisted of 8 type I (5 Mα and 3 Mβ, respectively) and 33 type II members (2 MIKC* and 31 MIKCC, respectively). We then selected IlSEP3 and IlSVP for functional studies and found that both are localized to the nucleus and that they interact physically in vitro. Ectopic expression of IlSEP3 in Arabidopsis resulted in early flowering (32 days) compared to that of control plants (36 days), which could be mediated by modulating the expression of FT, SOC1, AP1, SVP, SPL3, VRN1, and GA20OX. By contrast, plants overexpressing IlSVP were phenotypically similar to that of wild type. Our functional validation of IlSEP3 was consistent with the notion that SEP3 promotes flowering in multiple plant species and indicated that IlSEP3 regulates flowering in I. laevigata. Taken together, this work provided a systematic identification of MADS-box genes in I. laevigata and demonstrated that the flowering time of I. laevigata can be genetically controlled by altering the expression of key MADS-box genes.
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