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Chen W, Jiang B, Zeng H, Liu Z, Chen W, Zheng S, Wu J, Lou H. Molecular regulatory mechanisms of staminate strobilus development and dehiscence in Torreya grandis. PLANT PHYSIOLOGY 2024; 195:534-551. [PMID: 38365225 DOI: 10.1093/plphys/kiae081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/06/2023] [Accepted: 12/24/2023] [Indexed: 02/18/2024]
Abstract
Gymnosperms are mostly dioecious, and their staminate strobili undergo a longer developmental period than those of angiosperms. However, the underlying molecular mechanisms remain unclear. This study aimed to identify key genes and pathways involved in staminate strobilus development and dehiscence in Torreya grandis. Through weighted gene co-expression network analysis (WGCNA), we identified fast elongation-related genes enriched in carbon metabolism and auxin signal transduction, whereas dehiscence-related genes were abundant in alpha-linolenic acid metabolism and the phenylpropanoid pathway. Based on WGCNA, we also identified PHYTOCHROME-INTERACTING FACTOR4 (TgPIF4) as a potential regulator for fast elongation of staminate strobilus and 2 WRKY proteins (TgWRKY3 and TgWRKY31) as potential regulators for staminate strobilus dehiscence. Multiple protein-DNA interaction analyses showed that TgPIF4 directly activates the expression of TRANSPORT INHIBITOR RESPONSE2 (TgTIR2) and NADP-MALIC ENZYME (TgNADP-ME). Overexpression of TgPIF4 significantly promoted staminate strobilus elongation by elevating auxin signal transduction and pyruvate content. TgWRKY3 and TgWRKY31 bind to the promoters of the lignin biosynthesis gene PHENYLALANINE AMMONIA-LYASE (TgPAL) and jasmonic acid metabolism gene JASMONATE O-METHYLTRANSFERASE (TgJMT), respectively, and directly activate their transcription. Overexpression of TgWRKY3 and TgWRKY31 in the staminate strobilus led to early dehiscence, accompanied by increased lignin and methyl jasmonate levels, respectively. Collectively, our findings offer a perspective for understanding the growth of staminate strobili in gymnosperms.
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Affiliation(s)
- Weijie Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Baofeng Jiang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Hao Zeng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Zhihui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Wenchao Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Shan Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Heqiang Lou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
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Feng YY, Du H, Huang KY, Ran JH, Wang XQ. Reciprocal expression of MADS-box genes and DNA methylation reconfiguration initiate bisexual cones in spruce. Commun Biol 2024; 7:114. [PMID: 38242964 PMCID: PMC10799047 DOI: 10.1038/s42003-024-05786-6] [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: 07/27/2023] [Accepted: 01/05/2024] [Indexed: 01/21/2024] Open
Abstract
The naturally occurring bisexual cone of gymnosperms has long been considered a possible intermediate stage in the origin of flowers, but the mechanisms governing bisexual cone formation remain largely elusive. Here, we employed transcriptomic and DNA methylomic analyses, together with hormone measurement, to investigate the molecular mechanisms underlying bisexual cone development in the conifer Picea crassifolia. Our study reveals a "bisexual" expression profile in bisexual cones, especially in expression patterns of B-class, C-class and LEAFY genes, supporting the out of male model. GGM7 could be essential for initiating bisexual cones. DNA methylation reconfiguration in bisexual cones affects the expression of key genes in cone development, including PcDAL12, PcDAL10, PcNEEDLY, and PcHDG5. Auxin likely plays an important role in the development of female structures of bisexual cones. This study unveils the potential mechanisms responsible for bisexual cone formation in conifers and may shed light on the evolution of bisexuality.
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Affiliation(s)
- Yuan-Yuan Feng
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Du
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Kai-Yuan Huang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jin-Hua Ran
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiao-Quan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, 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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Zhou P, Wang Z, Li Y, Zhou Q. Identification and Expression of the MADS-box Gene Family in Different Versions of the Ginkgo biloba Genome. PLANTS (BASEL, SWITZERLAND) 2023; 12:3334. [PMID: 37765498 PMCID: PMC10535167 DOI: 10.3390/plants12183334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023]
Abstract
MADS-box transcription factors play important roles in many organisms. These transcription factors are involved in processes such as the formation of the flower organ structure and the seed development of plants. Ginkgo biloba has two genome versions (version 2019 and version 2021), and there is no analysis or comparison of the MADS-box gene family in these two genomes. In this study, 26 and 20 MADS-box genes were identified from the two genomes of Ginkgo, of which 12 pairs of genes reached more than 80% similarity. According to our phylogenetic analysis results, we divided these genes into type I (Mα and Mγ subfamilies) and type II (MIKC and Mδ subfamilies) members. We found that both sets of genomes lacked the Mβ gene, while the MIKC gene was the most numerous. Further analysis of the gene structure showed that the MIKC genes in the two genomes had extralong introns (≥20 kb); these introns had different splicing patterns, and their expression might be more abundant. The gene expression analysis proved that GbMADS genes were expressed to varying degrees in eight Ginkgo biological tissues. Type II GbMADS genes not only were found to be related to female flower bud differentiation and development but also are important in seed development. Therefore, MADS-box genes may play important roles in the development of Ginkgo reproductive organs, which may suggest a genetic role in sexual differentiation. This study further contributes to the research on MADS-box genes and provides new insights into sex determination in Ginkgo.
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Affiliation(s)
- Pengyan Zhou
- Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (P.Z.); (Y.L.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China;
| | - Zesen Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China;
| | - Yingang Li
- Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (P.Z.); (Y.L.)
| | - Qi Zhou
- Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (P.Z.); (Y.L.)
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Dai Y, Wang Y, Zeng L, Jia R, He L, Huang X, Zhao H, Liu D, Zhao H, Hu S, Gao L, Guo A, Xia W, Ji C. Genomic and Transcriptomic Insights into the Evolution and Divergence of MIKC-Type MADS-Box Genes in Carica papaya. Int J Mol Sci 2023; 24:14039. [PMID: 37762345 PMCID: PMC10531014 DOI: 10.3390/ijms241814039] [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: 07/03/2023] [Revised: 09/02/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
MIKC-type MADS-box genes, also known as type II genes, play a crucial role in regulating the formation of floral organs and reproductive development in plants. However, the genome-wide identification and characterization of type II genes as well as a transcriptomic survey of their potential roles in Carica papaya remain unresolved. Here, we identified and characterized 24 type II genes in the C. papaya genome, and investigated their evolutional scenario and potential roles with a widespread expression profile. The type II genes were divided into thirteen subclades, and gene loss events likely occurred in papaya, as evidenced by the contracted member size of most subclades. Gene duplication mainly contributed to MIKC-type gene formation in papaya, and the duplicated gene pairs displayed prevalent expression divergence, implying the evolutionary significance of gene duplication in shaping the diversity of type II genes in papaya. A large-scale transcriptome analysis of 152 samples indicated that different subclasses of these genes showed distinct expression patterns in various tissues, biotic stress response, and abiotic stress response, reflecting their divergent functions. The hub-network of male and female flowers and qRT-PCR suggested that TT16-3 and AGL8 participated in male flower development and seed germination. Overall, this study provides valuable insights into the evolution and functions of MIKC-type genes in C. papaya.
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Affiliation(s)
- Yunsu Dai
- Sanya Nanfan Research Institution of Hainan University, Sanya 572025, China; (Y.D.); (Y.W.); (D.L.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
| | - Yu Wang
- Sanya Nanfan Research Institution of Hainan University, Sanya 572025, China; (Y.D.); (Y.W.); (D.L.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
| | - Liwang Zeng
- Key Laboratory of Applied Research on Tropical Crop Information Technology of Hainan Province, Institute of Scientific and Technical Information, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Ruizong Jia
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
| | - Linwen He
- College of Marine Science, Hainan University, Haikou 570228, China;
| | - Xueying Huang
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- College of Marine Science, Hainan University, Haikou 570228, China;
| | - Hui Zhao
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
| | - Difa Liu
- Sanya Nanfan Research Institution of Hainan University, Sanya 572025, China; (Y.D.); (Y.W.); (D.L.)
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Haixu Zhao
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
| | - Shuai Hu
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
| | - Ling Gao
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Anping Guo
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
| | - Wei Xia
- Sanya Nanfan Research Institution of Hainan University, Sanya 572025, China; (Y.D.); (Y.W.); (D.L.)
| | - Changmian Ji
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
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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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Identifying Genes Associated with Female Flower Development of Phellodendron amurense Rupr. Using a Transcriptomics Approach. Genes (Basel) 2023; 14:genes14030661. [PMID: 36980934 PMCID: PMC10048520 DOI: 10.3390/genes14030661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023] Open
Abstract
Phellodendron amurense Rupr., a species of Rutaceae, is a nationally protected and valuable medicinal plant. It is generally considered to be dioecious. With the discovery of monoecious P. amurense, the phenomenon that its sex development is regulated by epigenetics has been revealed, but the way epigenetics affects the sex differentiation of P. amurense is still unclear. In this study, we investigated the effect of DNA methylation on the sexual development of P. amurense. The young inflorescences of male plants were treated with the demethylation agent 5-azaC, and the induced female flowers were obtained. The induced female flowers’ morphological functions and transcriptome levels were close to those of normally developed plants. Genes associated with the development of female flowers were studied by comparing the differences in transcriptome levels between the male and female flowers. Referring to sex-related genes reported in other plants, 188 candidate genes related to the development of female flowers were obtained, including sex-regulating genes, genes related to the formation and development of sexual organs, genes related to biochemical pathways, and hormone-related genes. RPP0W, PAL3, MCM2, MCM6, SUP, PIN1, AINTEGUMENTA, AINTEGUMENTA-LIKE6, AGL11, SEUSS, SHI-RELATED SEQUENCE 5, and ESR2 were preliminarily considered the key genes for female flower development. This study has demonstrated that epigenetics was involved in the sex regulation of P. amurense, with DNA methylation as one of its regulatory modes. Moreover, some candidate genes related to the sexual differentiation of P. amurense were obtained with analysis. These results are of great significance for further exploring the mechanism of sex differentiation of P. amurense and studying of sex differentiation of plants.
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Ye S, Ding W, Bai W, Lu J, Zhou L, Ma X, Zhu Q. Application of a novel strong promoter from Chinese fir ( Cunninghamia lanceolate) in the CRISPR/Cas mediated genome editing of its protoplasts and transgenesis of rice and poplar. FRONTIERS IN PLANT SCIENCE 2023; 14:1179394. [PMID: 37152166 PMCID: PMC10157052 DOI: 10.3389/fpls.2023.1179394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 03/27/2023] [Indexed: 05/09/2023]
Abstract
Novel constitutive promoters are essential for plant biotechnology. Although in angiosperms, a number of promoters were applied in monocots or dicots genetic engineering, only a few promoters were used in gymnosperm. Here we identified two strong promoters (Cula11 and Cula08) from Chinese fir (C. lanceolate) by screening the transcriptomic data and preliminary promoter activity assays in tobacco. By using the newly established Chinese fir protoplast transient expression technology that enables in vivo molecular biology studies in its homologous system, we compared the activities of Cula11 and Cula08 with that of the commonly used promoters in genetic engineering of monocots or dicots, such as CaM35S, CmYLCV, and ZmUbi, and our results revealed that Cula11 and Cula08 promoters have stronger activities in Chinese fir protoplasts. Furthermore, the vector containing Cas gene driven by Cula11 promoter and sgRNA driven by the newly isolated CulaU6b polyIII promoters were introduced into Chinese fir protoplasts, and CRISPR/Cas mediated gene knock-out event was successfully achieved. More importantly, compared with the commonly used promoters in the genetic engineering in angiosperms, Cula11 promoter has much stronger activity than CaM35S promoter in transgenic poplar, and ZmUbi promoter in transgenic rice, respectively, indicating its potential application in poplar and rice genetic engineering. Overall, the novel putative constitutive gene promoters reported here will have great potential application in gymnosperm and angiosperm biotechnology, and the transient gene expression system established here will serve as a useful tool for the molecular and genetic analyses of Chinese fir genes.
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Affiliation(s)
| | | | | | | | | | | | - Qiang Zhu
- *Correspondence: Xiangqing Ma, ; Qiang Zhu,
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9
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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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10
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Wang Y, Yang T, Li Y, Hou J, He J, Ma N, Zhou X. Genome-wide identification and expression analysis of MIKC C genes in rose provide insight into their effects on flower development. FRONTIERS IN PLANT SCIENCE 2022; 13:1059925. [PMID: 36407632 PMCID: PMC9666904 DOI: 10.3389/fpls.2022.1059925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
The MIKCC-type gene family plays important roles in plant growth, development, and tolerance of biotic and abiotic stress, especially during floral organ differentiation. However, there have been no studies of MIKCC-type genes in rose, and functional differentiation of family members has not been explored. In this study, we identified 42 MIKCC-type genes in rose, classified the genes into 12 subfamilies, and constructed a phylogenetic tree. We performed expression analysis of these genes, and found that expression patterns correlated with the predicted subfamily, indicating that the features of MIKCC-type genes were broadly conserved during evolution. Collinear analysis of MIKCC genes among Rosaceae species confirmed the occurrence of whole genome duplications (WGD) and revealed some species-specific MIKCC genes. Transcriptome analysis showed that the expression of some MIKCC-type genes responded to low temperatures (4°C, 24 h) during flower organ differentiation. These conserved, duplicated, and novel expression patterns of MIKCC-type genes may have facilitated the adaptation of rose to various internal and external environmental changes. The results of this study provide a theoretical basis for future functional analysis of the MIKCC genes in rose and investigation of the evolutionary pattern of the MIKCC gene family in the Rosaceae genome.
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11
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Wang Z, Cai Q, Xia H, Han B, Li M, Wang Y, Zhu M, Jiao C, Wang D, Zhu J, Yuan W, Zhu D, Xu C, Wang H, Zhou M, Zhang X, Shi J, Chen J. Genome-Wide Identification and Comparative Analysis of WOX Genes in Four Euphorbiaceae Species and Their Expression Patterns in Jatropha curcas. Front Genet 2022; 13:878554. [PMID: 35846114 PMCID: PMC9280045 DOI: 10.3389/fgene.2022.878554] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/22/2022] [Indexed: 11/18/2022] Open
Abstract
The WUSCHEL-related homeobox (WOX) proteins are widely distributed in plants and play important regulatory roles in growth and development processes such as embryonic development and organ development. Here, series of bioinformatics methods were utilized to unravel the structural basis and genetic hierarchy of WOX genes, followed by regulation of the WOX genes in four Euphorbiaceae species. A genome-wide survey identified 59 WOX genes in Hevea brasiliensis (H. brasiliensis: 20 genes), Jatropha curcas (J. curcas: 10 genes), Manihot esculenta (M. esculenta: 18 genes), and Ricinus communis (R. communis: 11 genes). The phylogenetic analysis revealed that these WOX members could be clustered into three close proximal clades, such as namely ancient, intermediate and modern/WUS clades. In addition, gene structures and conserved motif analyses further validated that the WOX genes were conserved within each phylogenetic clade. These results suggested the relationships among WOX members in the four Euphorbiaceae species. We found that WOX genes in H. brasiliensis and M. esculenta exhibit close genetic relationship with J. curcas and R. communis. Additionally, the presence of various cis-acting regulatory elements in the promoter of J. curcas WOX genes (JcWOXs) reflected distinct functions. These speculations were further validated with the differential expression profiles of various JcWOXs in seeds, reflecting the importance of two JcWOX genes (JcWOX6 and JcWOX13) during plant growth and development. Our quantitative real-time PCR (qRT-PCR) analysis demonstrated that the JcWOX11 gene plays an indispensable role in regulating plant callus. Taken together, the present study reports the comprehensive characteristics and relationships of WOX genes in four Euphorbiaceae species, providing new insights into their characterization.
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Affiliation(s)
- Zhanjun Wang
- College of Life Sciences, Hefei Normal University, Hefei, China
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Qianwen Cai
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Haimeng Xia
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Bingqing Han
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Minhui Li
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Yue Wang
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Minhui Zhu
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Chunyan Jiao
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Dandan Wang
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Junjie Zhu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Wenya Yuan
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Di Zhu
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Congcong Xu
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Hongyan Wang
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Minghui Zhou
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Xie Zhang
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- *Correspondence: Jinhui Chen,
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