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Molitor C, Kurowski TJ, Fidalgo de Almeida PM, Kevei Z, Spindlow DJ, Chacko Kaitholil SR, Iheanyichi JU, Prasanna HC, Thompson AJ, Mohareb FR. A chromosome-level genome assembly of Solanum chilense, a tomato wild relative associated with resistance to salinity and drought. FRONTIERS IN PLANT SCIENCE 2024; 15:1342739. [PMID: 38525148 PMCID: PMC10957597 DOI: 10.3389/fpls.2024.1342739] [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: 11/22/2023] [Accepted: 02/12/2024] [Indexed: 03/26/2024]
Abstract
Introduction Solanum chilense is a wild relative of tomato reported to exhibit resistance to biotic and abiotic stresses. There is potential to improve tomato cultivars via breeding with wild relatives, a process greatly accelerated by suitable genomic and genetic resources. Methods In this study we generated a high-quality, chromosome-level, de novo assembly for the S. chilense accession LA1972 using a hybrid assembly strategy with ~180 Gbp of Illumina short reads and ~50 Gbp long PacBio reads. Further scaffolding was performed using Bionano optical maps and 10x Chromium reads. Results The resulting sequences were arranged into 12 pseudomolecules using Hi-C sequencing. This resulted in a 901 Mbp assembly, with a completeness of 95%, as determined by Benchmarking with Universal Single-Copy Orthologs (BUSCO). Sequencing of RNA from multiple tissues resulting in ~219 Gbp of reads was used to annotate the genome assembly with an RNA-Seq guided gene prediction, and for a de novo transcriptome assembly. This chromosome-level, high-quality reference genome for S. chilense accession LA1972 will support future breeding efforts for more sustainable tomato production. Discussion Gene sequences related to drought and salt resistance were compared between S. chilense and S. lycopersicum to identify amino acid variations with high potential for functional impact. These variants were subsequently analysed in 84 resequenced tomato lines across 12 different related species to explore the variant distributions. We identified a set of 7 putative impactful amino acid variants some of which may also impact on fruit development for example the ethylene-responsive transcription factor WIN1 and ethylene-insensitive protein 2. These variants could be tested for their ability to confer functional phenotypes to cultivars that have lost these variants.
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Affiliation(s)
- Corentin Molitor
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
| | - Tomasz J. Kurowski
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
| | | | - Zoltan Kevei
- Soil, Agrifood and Biosciences, Cranfield University, Wharley End, United Kingdom
| | - Daniel J. Spindlow
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
| | - Steffimol R. Chacko Kaitholil
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
| | - Justice U. Iheanyichi
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
| | - H. C. Prasanna
- Division of Vegetable Crops, ICAR-Indian Institute of Horticultural Research, Bangalore, India
| | - Andrew J. Thompson
- Soil, Agrifood and Biosciences, Cranfield University, Wharley End, United Kingdom
| | - Fady R. Mohareb
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
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Shi TL, Ma HY, Wang X, Liu H, Yan XM, Tian XC, Li ZC, Bao YT, Chen ZY, Zhao SW, Xiang Q, Jia KH, Nie S, Guan W, Mao JF. Differential gene expression and potential regulatory network of fatty acid biosynthesis during fruit and leaf development in yellowhorn ( Xanthoceras sorbifolium), an oil-producing tree with significant deployment values. FRONTIERS IN PLANT SCIENCE 2024; 14:1297817. [PMID: 38312356 PMCID: PMC10834690 DOI: 10.3389/fpls.2023.1297817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/22/2023] [Indexed: 02/06/2024]
Abstract
Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.
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Affiliation(s)
- Tian-Le Shi
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hai-Yao Ma
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xinrui Wang
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hui Liu
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xue-Mei Yan
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xue-Chan Tian
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhi-Chao Li
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yu-Tao Bao
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhao-Yang Chen
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shi-Wei Zhao
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Qiuhong Xiang
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kai-Hua Jia
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji’nan, China
| | - Shuai Nie
- Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High-Quality Rice in Southern China (Co-construction by Ministry and Province), Rice Research Institute, Guangzhou, China
- Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangzhou, China
| | - Wenbin Guan
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jian-Feng Mao
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
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Zhao X, Zhao Z, Cheng S, Wang L, Luo Z, Ai C, Liu Z, Liu P, Wang L, Wang J, Liu M, Li Y, Liu M. ZjWRKY23 and ZjWRKY40 Promote Fruit Size Enlargement by Targeting and Downregulating Cytokinin Oxidase/Dehydrogenase 5 Expression in Chinese Jujube. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18046-18058. [PMID: 37957030 DOI: 10.1021/acs.jafc.3c04377] [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: 11/21/2023]
Abstract
Fruit size is crucial for fruit trees, as it contributes to both quality and yield. However, the underlying mechanism of fruit size regulation remains largely unknown. Taking advantage of using a fruit double-sized bud mutant of Chinese jujube, "Jinkuiwang" and its wild type, "Jinsixiaozao", we carried out a comprehensive study on the mechanism of fruit size development in jujube. Using weighted gene coexpression network analyses, a number of candidate regulators for fruit size including those involved in hormonal signaling pathways, transcription factors, and heat shock proteins were identified. A hub gene named cytokinin oxidase/dehydrogenase 5 (ZjCKX5), responsible for cytokinin degradation, was found to play a negative role in regulating fruit size development, and overexpressing ZjCKX5 in tomato and Arabidopsis resulted in much smaller fruits and dwarf plants. Furthermore, another two hub genes, ZjWRKY23 and ZjWRKY40 transcription factors, were found to participate in fruit size regulation by targeting and downregulating the ZjCKX5 expression. Overexpressing ZjWRKY23 or ZjWRKY40 in tomato led to much larger fruits and promoted plant architecture. Based on these results, a molecular framework for jujube fruit size regulation, namely, ZjWRKY-ZjCKX5 module, was proposed. This study provides a new insight into the molecular networks underlying fruit size regulation.
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Affiliation(s)
- Xuan Zhao
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Zixuan Zhao
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Shasha Cheng
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Lihu Wang
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, Hebei 056038, China
| | - Zhi Luo
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Changfeng Ai
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Zhiguo Liu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Ping Liu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Lili Wang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Jiurui Wang
- College of Forestry, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Mengzhen Liu
- City Administration of Zhongjie Industrial Park in Cangzhou Bohai New Area, Cangzhou, Hebei 061108, China
| | - Yong Li
- City Administration of Zhongjie Industrial Park in Cangzhou Bohai New Area, Cangzhou, Hebei 061108, China
| | - Mengjun Liu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
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Qi X, Liu L, Liu C, Song L, Dong Y, Chen L, Li M. Sweet cherry AP2/ERF transcription factor, PavRAV2, negatively modulates fruit size by directly repressing PavKLUH expression. PHYSIOLOGIA PLANTARUM 2023; 175:e14065. [PMID: 38148242 DOI: 10.1111/ppl.14065] [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: 07/27/2023] [Revised: 09/12/2023] [Accepted: 10/13/2023] [Indexed: 12/28/2023]
Abstract
For sweet cherry, fruit size is one of the main targets in breeding programs owing to the high market value of larger fruits. KLUH/CYP78A5 is an important regulator of seed/fruit size in several plant species, but its molecular mechanism is largely unknown. In this study, we characterized the function of PavKLUH in the regulation of sweet cherry fruit size. The ectopic overexpression of PavKLUH in Arabidopsis increased the size of its siliques and seeds, whereas virus-induced gene silencing of PavKLUH in sweet cherry significantly decreased fruit size by restricting mesocarp cell expansion. We screened out an AP2/ERF transcription factor containing a B3-like domain, designated as PavRAV2, which was able to physically interact with PavKLUH promoter in a yeast one-hybrid (Y1H) system. In Y1H assays, electrophoretic mobility shift assays, and dual-luciferase reporter analyses, PavRAV2 directly bound to the promoter of PavKLUH in vitro and in vivo, and suppressed PavKLUH expression. Silencing of PavRAV2 resulted in enlarged fruit as a result of enhanced mesocarp cell expansion. Together, our results provide new insights into signaling pathways related to fruit size, and outline a possible mechanism for how the RAV transcription factor directly regulates CYP78A family members to influence fruit size and development.
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Affiliation(s)
- Xiliang Qi
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- National Horticultural Germplasm Resources Center, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Lifeng Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- National Horticultural Germplasm Resources Center, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Congli Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- National Horticultural Germplasm Resources Center, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Lulu Song
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- National Horticultural Germplasm Resources Center, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Yuanxin Dong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- National Horticultural Germplasm Resources Center, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Lei Chen
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- National Horticultural Germplasm Resources Center, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Ming Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- National Horticultural Germplasm Resources Center, Chinese Academy of Agricultural Sciences, Zhengzhou, China
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Peng Z, Li H, Liu G, Jia W, Fu D. NAC transcription factor NOR-like1 regulates tomato fruit size. PLANTA 2023; 258:9. [PMID: 37256357 DOI: 10.1007/s00425-023-04166-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/24/2023] [Indexed: 06/01/2023]
Abstract
MAIN CONCLUSION NOR-like1 regulates tomato fruit size by targeting SlARF9, SlGRAS2, SlFW3.2, and SlFW11.3 genes involved in cell division and cell expansion. Fruit size is an important agricultural character that determines the yield of crops. Here, we found that NAC transcription factor NOR-like1 regulated fruit size by regulating cell layer number and cell area in tomato. Over-expressing NOR-like1 gene in tomato reduced fruit weight and size, whereas the knock-out of NOR-like1 increased fruit weight and size. At the molecular level, NOR-like1 binds to the promoter of SlGRAS2, SlFW3.2, and SlFW11.3 to repress their transcription, while it also binds to the promoter of ARF9 to activate its transcription. Overall, these results expand the biological function of NOR-like1 and deepen our understanding of the transcriptional network that regulates tomato fruit size.
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Affiliation(s)
- Zhenzhen Peng
- Laboratory of Fruit Biology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Hongli Li
- Laboratory of Fruit Biology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Gangshuai Liu
- Laboratory of Fruit Biology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Wen Jia
- Laboratory of Fruit Biology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Daqi Fu
- Laboratory of Fruit Biology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
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Transcriptome and Co-Expression Network Analysis Reveals the Molecular Mechanism of Rice Root Systems in Response to Low-Nitrogen Conditions. Int J Mol Sci 2023; 24:ijms24065290. [PMID: 36982364 PMCID: PMC10048922 DOI: 10.3390/ijms24065290] [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: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Nitrogen is an important nutrient for plant growth and essential metabolic processes. Roots integrally obtain nutrients from soil and are closely related to the growth and development of plants. In this study, the morphological analysis of rice root tissues collected at different time points under low-nitrogen and normal nitrogen conditions demonstrated that, compared with normal nitrogen treatment, the root growth and nitrogen use efficiency (NUE) of rice under low-nitrogen treatment were significantly improved. To better understand the molecular mechanisms of the rice root system’s response to low-nitrogen conditions, a comprehensive transcriptome analysis of rice seedling roots under low-nitrogen and control conditions was conducted in this study. As a result, 3171 differentially expressed genes (DEGs) were identified. Rice seedling roots enhance NUE and promote root development by regulating the genes related to nitrogen absorption and utilization, carbon metabolism, root growth and development, and phytohormones, thereby adapting to low-nitrogen conditions. A total of 25,377 genes were divided into 14 modules using weighted gene co-expression network analysis (WGCNA). Two modules were significantly associated with nitrogen absorption and utilization. A total of 8 core genes and 43 co-expression candidates related to nitrogen absorption and utilization were obtained in these two modules. Further studies on these genes will contribute to the understanding of low-nitrogen adaptation and nitrogen utilization mechanisms in rice.
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The B-Type Cyclin CYCB1-1 Regulates Embryonic Development and Seed Size in Maize. Int J Mol Sci 2022; 23:ijms23115907. [PMID: 35682593 PMCID: PMC9180882 DOI: 10.3390/ijms23115907] [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: 04/29/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 02/06/2023] Open
Abstract
Progress through the cell cycle is a critical process during plant embryo and seed development and its progression is regulated by cyclins. Despite extensive study of cyclins in other systems, their role in embryo and seed development of maize is unclear. In this study, we demonstrate that ZmCYCB1-1 overexpression significantly accelerated embryo growth and increased seed size. In situ hybridization and toluidine blue staining indicated that ZmCYCB1-1 was highly expressed in the plumule of embryos, and the cells of the plumule were smaller, denser, and more regularly arranged in ZmCYCB1-1 overexpression plants. Overexpression of ZmCYCB1-1 in maize also resulted in an increased ear length and enhanced kernel weight by increasing kernel width. Transcriptome analysis indicated that the overexpression of ZmCYCB1-1 affected several different metabolic pathways, including photosynthesis in embryos and leaves, and lipid metabolism in leaves. Conversely, knocking out ZmCYCB1-1 resulted in plants with slow growth. Our results suggest that ZmCYCB1-1 regulates embryo growth and seed size, making it an ideal target for efforts aimed at maize yield improvement.
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Maeda S, Sasaki K, Kaku H, Kanda Y, Ohtsubo N, Mori M. Overexpression of Rice BSR2 Confers Disease Resistance and Induces Enlarged Flowers in Torenia fournieri Lind. Int J Mol Sci 2022; 23:ijms23094735. [PMID: 35563126 PMCID: PMC9102792 DOI: 10.3390/ijms23094735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/18/2022] [Accepted: 04/23/2022] [Indexed: 11/16/2022] Open
Abstract
Plant pathogens evade basal defense systems and attack different organs and tissues of plants. Genetic engineering of plants with genes that confer resistance against pathogens is very effective in pathogen control. Conventional breeding for disease resistance in ornamental crops is difficult and lagging relative to that in non-ornamental crops due to an inadequate number of disease-resistant genes. Therefore, genetic engineering of these plants with defense-conferring genes is a practical approach. We used rice BSR2 encoding CYP78A15 for developing transgenic Torenia fournieri Lind. lines. The overexpression of BSR2 conferred resistance against two devastating fungal pathogens, Rhizoctonia solani and Botrytis cinerea. In addition, BSR2 overexpression resulted in enlarged flowers with enlarged floral organs. Histological observation of the petal cells suggested that the enlargement in the floral organs could be due to the elongation and expansion of the cells. Therefore, the overexpression of BSR2 confers broad-spectrum disease resistance and induces the production of enlarged flowers simultaneously. Therefore, this could be an effective strategy for developing ornamental crops that are disease-resistant and economically more valuable.
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Affiliation(s)
- Satoru Maeda
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NIAS), Tsukuba 305-8602, Japan; (S.M.); (H.K.); (Y.K.)
| | - Katsutomo Sasaki
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NIVFS), Tsukuba 305-0852, Japan; (K.S.); (N.O.)
| | - Hisatoshi Kaku
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NIAS), Tsukuba 305-8602, Japan; (S.M.); (H.K.); (Y.K.)
- JICA Tsukuba Center, Tsukuba 305-0074, Japan
| | - Yasukazu Kanda
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NIAS), Tsukuba 305-8602, Japan; (S.M.); (H.K.); (Y.K.)
| | - Norihiro Ohtsubo
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NIVFS), Tsukuba 305-0852, Japan; (K.S.); (N.O.)
| | - Masaki Mori
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NIAS), Tsukuba 305-8602, Japan; (S.M.); (H.K.); (Y.K.)
- Correspondence: ; Tel.: +81-29-838-7008
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Li Q, Feng Q, Snouffer A, Zhang B, Rodríguez GR, van der Knaap E. Increasing Fruit Weight by Editing a Cis-Regulatory Element in Tomato KLUH Promoter Using CRISPR/Cas9. FRONTIERS IN PLANT SCIENCE 2022; 13:879642. [PMID: 35481139 PMCID: PMC9037380 DOI: 10.3389/fpls.2022.879642] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 03/07/2022] [Indexed: 06/01/2023]
Abstract
CRISPR/Cas-mediated genome editing is a powerful approach to accelerate yield enhancement to feed growing populations. Most applications focus on "negative regulators" by targeting coding regions and promoters to create nulls or weak loss-of-function alleles. However, many agriculturally important traits are conferred by gain-of-function alleles. Therefore, creating gain-of-function alleles for "positive regulators" by CRISPR will be of great value for crop improvement. CYP78A family members are the positive regulators of organ weight and size in crops. In this study, we engineered allelic variation by editing tomato KLUH promoter around a single-nucleotide polymorphism (SNP) that is highly associated with fruit weight. The SNP was located in a conserved putative cis-regulatory element (CRE) as detected by the homology-based prediction and the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq). Twenty-one mutant alleles with various insertion and deletion sizes were generated in the LA1589 background. Five mutant alleles (m2+4bp , m3+1bp , m5-1bp , m13-8bp , and m14-9bp ) showed a consistent increase in fruit weight and a significant decrease in the proportion of small fruits in all experimental evaluations. Notably, m2+4bp and m3+1bp homozygote significantly increase fruit weight by 10.7-15.7 and 8.7-16.3%, respectively. Further analysis of fruit weight based on fruit position on the inflorescence indicated that the five beneficial alleles increase the weight of all fruits along inflorescence. We also found that allele types and transcriptional changes of SlKLUH were poor predictors of the changes in fruit weight. This study not only provides a way of identifying conserved CRE but also highlights enormous potential for CRISPR/Cas-mediated cis-engineering of CYP78A members in yield improvement.
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Affiliation(s)
- Qiang Li
- College of Horticulture, Hebei Agricultural University, State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Baoding, China
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Qian Feng
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Ashley Snouffer
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Biyao Zhang
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Gustavo Rubén Rodríguez
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Cátedra de Genética, Facultad de Ciencias Agrarias UNR, Santa Fe, Argentina
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Horticulture, University of Georgia, Athens, GA, United States
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Peng Z, Zhao C, Li S, Guo Y, Xu H, Hu G, Liu Z, Chen X, Chen J, Lin S, Su W, Yang X. Integration of genomics, transcriptomics and metabolomics identifies candidate loci underlying fruit weight in loquat. HORTICULTURE RESEARCH 2022; 9:uhac037. [PMID: 35137085 PMCID: PMC9071381 DOI: 10.1093/hr/uhac037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/12/2022] [Accepted: 01/30/2022] [Indexed: 05/05/2023]
Abstract
Fruit weight is an integral part of fruit-quality traits and directly influences commodity values and economic returns of fruit crops. Despite its importance, the molecular mechanisms underlying fruit weight remain understudied, especially for perennial fruit tree crops such as cultivated loquat (Eriobotrya japonica Lindl.). Auxin is known to regulate fruit development, whereas its role and metabolism in fruit development remain obscure in loquat. In this study, we applied a multi-omics approach, integrating whole-genome resequencing-based quantitative trait locus (QTL) mapping with an F1 population, population genomics analysis using germplasm accessions, transcriptome analysis, and metabolic profiling to identify the genomic regions potentially associated with fruit weight in loquat. We identified three major loci associated with fruit weight, supported by both QTL mapping and comparative genomic analysis between small- and big-fruited loquat cultivars. Comparison between two genotypes with contrasting fruit weight performance through transcriptomic and metabolic profiling revealed an important role of auxin in regulating fruit development, especially at the fruit enlarging stage. The multi-omics approach identified two homologs of ETHYLENE INSENSITIVE 4 (EjEIN4) and TORNADO 1 (EjTRN1) as promising candidates controlling fruit weight. Moreover, three single nucleotide polymorphism (SNP) markers were closely associated with fruit weight. Results from this study provided insights from multiple perspectives into the genetic and metabolic controls of fruit weight in loquat. The candidate genomic regions, genes, and sequence variants will facilitate understanding the molecular basis of fruit weight and lay a foundation for future breeding and manipulation of fruit weight in loquat.
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Affiliation(s)
- Ze Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Chongbin Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Shuqing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Yihan Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Hongxia Xu
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Guibing Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Zongli Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Xiuping Chen
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China
| | - Junwei Chen
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Shunquan Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Wenbing Su
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China
| | - Xianghui Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
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11
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Genetic and Molecular Regulation Mechanisms in the Formation and Development of Vegetable Fruit Shape. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Vegetable crops have a long history of cultivation worldwide and rich germplasm resources. With its continuous development and progress, molecular biology technology has been applied to various fields of vegetable crop research. Fruit is an important organ in vegetable crops, and fruit shape can affect the yield and commercialization of vegetables. In nature, fruits show differences in size and shape. Based on fruit shape diversity, the growth direction and coordination mechanism of fruits remain unclear. In this review, we discuss the latest research on fruit shape. In addition, we compare the current theories on the molecular mechanisms that regulate fruit growth, size, and shape in different vegetable families.
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Durán-Medina Y, Ruiz-Cortés BE, Guerrero-Largo H, Marsch-Martínez N. Specialized metabolism and development: An unexpected friendship. CURRENT OPINION IN PLANT BIOLOGY 2021; 64:102142. [PMID: 34856480 DOI: 10.1016/j.pbi.2021.102142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 10/12/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Plants produce a myriad of metabolites. Some of them have been regarded for a long time as secondary or specialized metabolites and are considered to have functions mostly in defense and the adaptation of plants to their environment. However, in the last years, new research has shown that these metabolites can also have roles in the regulation of plant growth and development, some acting as signals, through the interaction with hormonal pathways, and some independently of them. These reports provide a glimpse of the functional possibilities that specialized metabolites present in the modulation of plant development and encourage more research in this direction.
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Affiliation(s)
- Yolanda Durán-Medina
- Biotecnology and Biochemistry Department, Centre for Research and Advanced Studies (CINVESTAV-IPN) Irapuato Unit, Mexico
| | - Beatriz Esperanza Ruiz-Cortés
- Biotecnology and Biochemistry Department, Centre for Research and Advanced Studies (CINVESTAV-IPN) Irapuato Unit, Mexico
| | - Herenia Guerrero-Largo
- Biotecnology and Biochemistry Department, Centre for Research and Advanced Studies (CINVESTAV-IPN) Irapuato Unit, Mexico
| | - Nayelli Marsch-Martínez
- Biotecnology and Biochemistry Department, Centre for Research and Advanced Studies (CINVESTAV-IPN) Irapuato Unit, Mexico.
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Wang L, Suo X, Liu Y, Liu C, Luo M. Sphingosine Promotes Embryo Biomass in Upland Cotton: A Biochemical and Transcriptomic Analysis. Biomolecules 2021; 11:525. [PMID: 33915924 PMCID: PMC8065874 DOI: 10.3390/biom11040525] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 12/21/2022] Open
Abstract
Sphingolipids are essential membrane components and signal molecules, but their regulatory role in cotton embryo growth is largely unclear. In this study, we evaluated the effects of treatment with the sphingolipid synthesis inhibitor fumonisin B1 (FB1), the serine palmityl transferase (SPT) inhibitor myriocin, the SPT sphingolipid product DHS (d18:0 dihydrosphingosine), and the post-hydroxylation DHS product PHS (t18:0 phytosphingosine) on embryo growth in culture, and performed comparative transcriptomic analysis on control and PHS-treated samples. We found that FB1 could inhibit cotton embryo development. At the five-day ovule/embryo developmental stage, PHS was the most abundant sphingolipid. An SPT enzyme inhibitor reduced the fresh weight of embryos, while PHS had the opposite effect. The transcriptomic analysis identified 2769 differentially expressed genes (1983 upregulated and 786 downregulated) in the PHS samples. A large number of transcription factors were highly upregulated, such as zinc finger, MYB, NAC, bHLH, WRKY, MADS, and GRF in PHS-treated samples compared to controls. The lipid metabolism and plant hormone (auxin, brassinosteroid, and zeatin) related genes were also altered. Our findings provide target metabolites and genes for cotton seed improvement.
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Affiliation(s)
- Li Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China; (L.W.); (Y.L.); (C.L.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiaodong Suo
- Key Laboratory of Biotechnology and Crop Quality Improvement of Ministry of Agriculture, Biotechnology Research Center, Southwest University, Chongqing 400716, China;
| | - Yujie Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China; (L.W.); (Y.L.); (C.L.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Chen Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China; (L.W.); (Y.L.); (C.L.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Ming Luo
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China; (L.W.); (Y.L.); (C.L.)
- Key Laboratory of Biotechnology and Crop Quality Improvement of Ministry of Agriculture, Biotechnology Research Center, Southwest University, Chongqing 400716, China;
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