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Gong S, Gan H, Chu J, Wang Z, Sun J. A chromosome-level genome assembly provides insights into the local adaptation of Tamarix austromongolica in the Yellow River Basin, China. DNA Res 2024; 31:dsae021. [PMID: 38946223 PMCID: PMC11306577 DOI: 10.1093/dnares/dsae021] [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: 02/18/2024] [Revised: 06/06/2024] [Accepted: 06/29/2024] [Indexed: 07/02/2024] Open
Abstract
Tamarix austromongolica is endemic to the Yellow River Basin and has adapted to diverse ecological settings in the region, including the arid areas of northwestern China and the saline soil regions of the Yellow River Delta. However, the genetic basis of its local adaptation remains unclear. We report a chromosome-level assembly of the T. austromongolica genome based on PacBio high-fidelity sequencing and Hi-C technology. The 12 pseudochromosomes cover 98.44% of the 1.32 Gb assembly, with a contig N50 of 52.57 Mb and a BUSCO score of 98.2%. The genome comprises 913.6 Mb (68.83%) of repetitive sequences and 22,374 protein-coding genes. Genome evolution analyses suggest that genes under positive selection and significantly expanded gene families have facilitated T. austromongolica's adaptability to diverse environmental factors and high resistance to diseases. Using genotyping-by-sequencing, we conducted population structure and selection analyses of 114 samples from 15 sites. Two genetic groups were identified, and 114 and 289 candidate genes were assigned to the populations of the northwestern and eastern parts of the Yellow River, respectively. Furthermore, we discovered numerous candidate genes associated with high-altitude adaptability and salt tolerance. This research provides valuable genomic resources for the evolutionary study and genetic breeding of tamarisk.
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Affiliation(s)
- Shuai Gong
- Coastal Forestry Research Center of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Honghao Gan
- Coastal Forestry Research Center of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Jianmin Chu
- Coastal Forestry Research Center of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou 015200, PR China
| | - Zhaoshan Wang
- Coastal Forestry Research Center of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Jia Sun
- Coastal Forestry Research Center of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
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2
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Jo S, El-Demerdash A, Owen C, Srivastava V, Wu D, Kikuchi S, Reed J, Hodgson H, Harkess A, Shu S, Plott C, Jenkins J, Williams M, Boston LB, Lacchini E, Qu T, Goossens A, Grimwood J, Schmutz J, Leebens-Mack J, Osbourn A. Unlocking saponin biosynthesis in soapwort. Nat Chem Biol 2024:10.1038/s41589-024-01681-7. [PMID: 39043959 DOI: 10.1038/s41589-024-01681-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 06/18/2024] [Indexed: 07/25/2024]
Abstract
Soapwort (Saponaria officinalis) is a flowering plant from the Caryophyllaceae family with a long history of human use as a traditional source of soap. Its detergent properties are because of the production of polar compounds (saponins), of which the oleanane-based triterpenoid saponins, saponariosides A and B, are the major components. Soapwort saponins have anticancer properties and are also of interest as endosomal escape enhancers for targeted tumor therapies. Intriguingly, these saponins share common structural features with the vaccine adjuvant QS-21 and, thus, represent a potential alternative supply of saponin adjuvant precursors. Here, we sequence the S. officinalis genome and, through genome mining and combinatorial expression, identify 14 enzymes that complete the biosynthetic pathway to saponarioside B. These enzymes include a noncanonical cytosolic GH1 (glycoside hydrolase family 1) transglycosidase required for the addition of D-quinovose. Our results open avenues for accessing and engineering natural and new-to-nature pharmaceuticals, drug delivery agents and potential immunostimulants.
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Affiliation(s)
- Seohyun Jo
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Amr El-Demerdash
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK
- Department of Chemistry, Faculty of Sciences, Mansoura University, Mansoura, Egypt
| | - Charlotte Owen
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Vikas Srivastava
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK
- Department of Botany, School of Life Sciences, Central University of Jammu, Jammu, India
| | - Dewei Wu
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Shingo Kikuchi
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK
| | - James Reed
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Hannah Hodgson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Shengqiang Shu
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Plott
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | | | - Elia Lacchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Tongtong Qu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Centre for Plant Systems Biology, Ghent, Belgium
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, GA, USA
| | - Anne Osbourn
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, UK.
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Zheng SH, Diao YC, Du J, Li JT, Zhao S, Liu MJ, Lin HC, Zeng Y, Wang JY. Genomics and resequencing of Fagopyrum dibotrys from different geographic regions reveals species evolution and genetic diversity. FRONTIERS IN PLANT SCIENCE 2024; 15:1380157. [PMID: 38919820 PMCID: PMC11196786 DOI: 10.3389/fpls.2024.1380157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024]
Abstract
Fagopyrum dibotrys, belonging to the family Polygonaceae and genus Fagopyrum, is used in traditional Chinese medicine and is rich in beneficial components, such as flavonoids. As its abundant medicinal value has become increasingly recognized, its excessive development poses a considerable challenge to wild germplasm resources, necessitating artificial cultivation and domestication. Considering these factors, a high-quality genome of F. dibotrys was assembled and the evolutionary relationships within Caryophyllales were compared, based on which 58 individual samples of F. dibotrys were re-sequenced. We found that the samples could be categorized into three purebred populations and regions distributed at distinct elevations. Our varieties were cultivated from the parental populations of the subpopulation in central Yunnan. F. dibotrys is speculated to have originated in the high-altitude Tibetan Plateau region, and that its combination with flavonoids can protect plants against ultraviolet radiation; this infers a subpopulation with a high accumulation of flavonoids. This study assembled a high-quality genome and provided a theoretical foundation for the future introduction, domestication, and development of cultivated varieties of F. dibotrys.
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Affiliation(s)
- Si-hao Zheng
- China National Traditional Chinese Medicine Co., Ltd, Beijing, China
| | - Yong-chao Diao
- China National Traditional Chinese Medicine Co., Ltd, Beijing, China
| | - Jie Du
- China National Traditional Chinese Medicine Co., Ltd, Beijing, China
| | - Jin-tong Li
- China Traditional Chinese Medicine Seed&Seeding, Co., Ltd, Beijing, China
| | - Sha Zhao
- China National Traditional Chinese Medicine Co., Ltd, Beijing, China
| | - Mei-juan Liu
- China National Traditional Chinese Medicine Co., Ltd, Beijing, China
| | - Hui-cai Lin
- China Traditional Chinese Medicine Seed&Seeding, Co., Ltd, Beijing, China
| | - Yan Zeng
- China National Traditional Chinese Medicine Co., Ltd, Beijing, China
| | - Ji-yong Wang
- China National Traditional Chinese Medicine Co., Ltd, Beijing, China
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Zhang T, Wang Y, Wu S, Tian E, Yang C, Zhou Z, Yan X, Wang P. Chemoproteomics reveals the epoxidase enzyme for the biosynthesis of camptothecin in Ophiorrhiza pumila. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1044-1047. [PMID: 38095243 DOI: 10.1111/jipb.13594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/10/2023] [Indexed: 01/19/2024]
Abstract
The downstream biosynthetic route of camptothecin has remained unclear for more than half a century. Here, we discovered a P450 enzyme involved in camptothecin biosynthesis from plant by chemoproteomics, which lays the foundation for synthesis of camptothecin and highlights the effectiveness of chemoproteomic profiling for discovering unknown enzymes.
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Affiliation(s)
- Tong Zhang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular, Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular, Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Shiwen Wu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular, Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Ernuo Tian
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular, Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengshuai Yang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular, Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular, Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xing Yan
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular, Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pingping Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular, Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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Sala-Cholewa K, Tomasiak A, Nowak K, Piński A, Betekhtin A. DNA methylation analysis of floral parts revealed dynamic changes during the development of homostylous Fagopyrum tataricum and heterostylous F. esculentum flowers. BMC PLANT BIOLOGY 2024; 24:448. [PMID: 38783206 PMCID: PMC11112930 DOI: 10.1186/s12870-024-05162-w] [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: 03/30/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Proper flower development is essential for plant reproduction, a crucial aspect of the plant life cycle. This process involves precisely coordinating transcription factors, enzymes, and epigenetic modifications. DNA methylation, a ubiquitous and heritable epigenetic mechanism, is pivotal in regulating gene expression and shaping chromatin structure. Fagopyrum esculentum demonstrates anti-hypertensive, anti-diabetic, anti-inflammatory, cardio-protective, hepato-protective, and neuroprotective properties. However, the heteromorphic heterostyly observed in F. esculentum poses a significant challenge in breeding efforts. F. tataricum has better resistance to high altitudes and harsh weather conditions such as drought, frost, UV-B radiation damage, and pests. Moreover, F. tataricum contains significantly higher levels of rutin and other phenolics, more flavonoids, and a balanced amino acid profile compared to common buckwheat, being recognised as functional food, rendering it an excellent candidate for functional food applications. RESULTS This study aimed to compare the DNA methylation profiles between the Pin and Thrum flower components of F. esculentum, with those of self-fertile species of F. tataricum, to understand the potential role of this epigenetic mechanism in Fagopyrum floral development. Notably, F. tataricum flowers are smaller than those of F. esculentum (Pin and Thrum morphs). The decline in DNA methylation levels in the developed open flower components, such as petals, stigmas and ovules, was consistent across both species, except for the ovule in the Thrum morph. Conversely, Pin and Tartary ovules exhibited a minor decrease in DNA methylation levels. The highest DNA methylation level was observed in Pin stigma from closed flowers, and the most significant decrease was in Pin stigma from open flowers. In opposition, the nectaries of open flowers exhibited higher levels of DNA methylation than those of closed flowers. The decrease in DNA methylation might correspond with the downregulation of genes encoding methyltransferases. CONCLUSIONS Reduced overall DNA methylation and the expression of genes associated with these epigenetic markers in fully opened flowers of both species may indicate that demethylation is necessary to activate the expression of genes involved in floral development.
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Affiliation(s)
- Katarzyna Sala-Cholewa
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska St, Katowice, 40-032, Poland.
| | - Alicja Tomasiak
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska St, Katowice, 40-032, Poland
| | - Katarzyna Nowak
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska St, Katowice, 40-032, Poland
| | - Artur Piński
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska St, Katowice, 40-032, Poland
| | - Alexander Betekhtin
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska St, Katowice, 40-032, Poland.
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Nie M, Li L, He C, Lu J, Guo H, Li X, Jiang M, Zhan R, Sun W, Yin J, Wu Q. Genome-wide identification, subcellular localization, and expression analysis of the phosphatidyl ethanolamine-binding protein family reveals the candidates involved in flowering and yield regulation of Tartary buckwheat ( Fagopyrum tataricum). PeerJ 2024; 12:e17183. [PMID: 38560476 PMCID: PMC10979741 DOI: 10.7717/peerj.17183] [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: 11/28/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Background PEBP (phosphatidyl ethanolamine-binding protein) is widely found in eukaryotes including plants, animals and microorganisms. In plants, the PEBP family plays vital roles in regulating flowering time and morphogenesis and is highly associated to agronomic traits and yields of crops, which has been identified and characterized in many plant species but not well studied in Tartary buckwheat (Fagopyrum tataricum Gaertn.), an important coarse food grain with medicinal value. Methods Genome-wide analysis of FtPEBP gene family members in Tartary buckwheat was performed using bioinformatic tools. Subcellular localization analysis was performed by confocal microscopy. The expression levels of these genes in leaf and inflorescence samples were analyzed using qRT-PCR. Results Fourteen Fagopyrum tataricum PEBP (FtPEBP) genes were identified and divided into three sub-clades according to their phylogenetic relationships. Subcellular localization analysis of the FtPEBP proteins in tobacco leaves indicated that FT- and TFL-GFP fusion proteins were localized in both the nucleus and cytoplasm. Gene structure analysis showed that most FtPEBP genes contain four exons and three introns. FtPEBP genes are unevenly distributed in Tartary buckwheat chromosomes. Three tandem repeats were found among FtFT5/FtFT6, FtMFT1/FtMFT2 and FtTFL4/FtTFL5. Five orthologous gene pairs were detected between F. tataricum and F. esculentum. Seven light-responsive, nine hormone-related and four stress-responsive elements were detected in FtPEBPs promoters. We used real-time PCR to investigate the expression levels of FtPEBPs among two flowering-type cultivars at floral transition time. We found FtFT1/FtFT3 were highly expressed in leaf and young inflorescence of early-flowering type, whereas they were expressed at very low levels in late-flowering type cultivars. Thus, we deduced that FtFT1/FtFT3 may be positive regulators for flowering and yield of Tartary buckwheat. These results lay an important foundation for further studies on the functions of FtPEBP genes which may be utilized for yield improvement.
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Affiliation(s)
- Mengping Nie
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Li Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Cailin He
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Jing Lu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Huihui Guo
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Xiao'an Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Mi Jiang
- Key Laboratory of Wheat Crop Research in Ganzi Academy of Agricultural Sciences, Ganzi Academy of Agricultural Sciences, Ganzi, Sichuan, China
| | - Ruiling Zhan
- Key Laboratory of Wheat Crop Research in Ganzi Academy of Agricultural Sciences, Ganzi Academy of Agricultural Sciences, Ganzi, Sichuan, China
| | - Wenjun Sun
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Junjie Yin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qi Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
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Zhao H, Wang L, Jia Y, Zhao J, Li C, Chen H, Wu H, Wu Q. Accumulation of the bitter substance quercetin mediated by the overexpression of a novel seed-specific gene FtRDE2 in Tartary buckwheat. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108402. [PMID: 38310726 DOI: 10.1016/j.plaphy.2024.108402] [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: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/06/2024]
Abstract
Tartary buckwheat (Fagopyrum tataricum) is frequently employed as a resource to develop health foods, owing to its abundant flavonoids such as rutin. However, the consumption of Tartary buckwheat (TB) is limited in food products due to the strong bitterness induced by the hydrolysis of rutin into quercetin. This transformation is facilitated by the degrading enzyme (RDE). While multiple RDE isoenzymes exist in TB, the superior coding gene of FtRDEs has not been fully explored, which hinders the breeding of TB varieties with minimal bitterness. Here, we found that FtRDE2 is the most abundant enzyme in RDE crude extracts, and its corresponding gene is specifically expressed in TB seeds. Results showed that FtRDE2 has strong rutin hydrolysis activity. Overexpression of FtRDE2 not only significantly promoted rutin hydrolysis and quercetin accumulation but also dramatically upregulated genes involved in the early phase of flavonoid synthesis (FtPAL1、FtC4H1、Ft4CL1, FtCHI1) and anthocyanin metabolism (FtDFR1). These findings elucidate the role of FtRDE2, emphasizing it as an endogenous factor contributing to the bitterness in TB and its involvement in the metabolic regulatory network. Moreover, correlation analysis revealed a positive relationship between the catalytic activity of RDE extracts and the expression level of FtRDE2 during seed germination. In summary, our results suggest that FtRDE2 can serve as a promising candidate for the molecular breeding of a TB variety with minimal bitterness.
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Affiliation(s)
- Haixia Zhao
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an, 625014, Sichuan Province, China
| | - Lijiao Wang
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an, 625014, Sichuan Province, China
| | - Yujie Jia
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an, 625014, Sichuan Province, China
| | - Jiali Zhao
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an, 625014, Sichuan Province, China
| | - Chenglei Li
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an, 625014, Sichuan Province, China
| | - Hui Chen
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an, 625014, Sichuan Province, China
| | - Huala Wu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an, 625014, Sichuan Province, China; Xichang University, 615013, Xichang, Sichuan, China.
| | - Qi Wu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an, 625014, Sichuan Province, China
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Zhang H, He Q, Xing L, Wang R, Wang Y, Liu Y, Zhou Q, Li X, Jia Z, Liu Z, Miao Y, Lin T, Li W, Du H. The haplotype-resolved genome assembly of autotetraploid rhubarb Rheum officinale provides insights into its genome evolution and massive accumulation of anthraquinones. PLANT COMMUNICATIONS 2024; 5:100677. [PMID: 37634079 PMCID: PMC10811376 DOI: 10.1016/j.xplc.2023.100677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 06/05/2023] [Accepted: 08/24/2023] [Indexed: 08/28/2023]
Abstract
Rheum officinale, a member of the Polygonaceae family, is an important medicinal plant that is widely used in traditional Chinese medicine. Here, we report a 7.68-Gb chromosome-scale assembly of R. officinale with a contig N50 of 3.47 Mb, which was clustered into 44 chromosomes across four homologous groups. Comparative genomics analysis revealed that transposable elements have made a significant contribution to its genome evolution, gene copy number variation, and gene regulation and expression, particularly of genes involved in metabolite biosynthesis, stress resistance, and root development. We placed the recent autotetraploidization of R. officinale at ∼0.58 mya and analyzed the genomic features of its homologous chromosomes. Although no dominant monoploid genomes were observed at the overall expression level, numerous allele-differentially-expressed genes were identified, mainly with different transposable element insertions in their regulatory regions, suggesting that they functionally diverged after polyploidization. Combining genomics, transcriptomics, and metabolomics, we explored the contributions of gene family amplification and tetraploidization to the abundant anthraquinone production of R. officinale, as well as gene expression patterns and differences in anthraquinone content among tissues. Our report offers unprecedented genomic resources for fundamental research on the autopolyploid herb R. officinale and guidance for polyploid breeding of herbs.
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Affiliation(s)
- Hongyu Zhang
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Qiang He
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Longsheng Xing
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Ruyu Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Yu Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Yu Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Qinghong Zhou
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Xuanzhao Li
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Zheng Jia
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Ze Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Yuqing Miao
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Tao Lin
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Wei Li
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Huilong Du
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China.
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Pipan B, Sinkovič L, Neji M, Janovská D, Zhou M, Meglič V. Agro-Morphological and Molecular Characterization Reveal Deep Insights in Promising Genetic Diversity and Marker-Trait Associations in Fagopyrum esculentum and Fagopyrum tataricum. PLANTS (BASEL, SWITZERLAND) 2023; 12:3321. [PMID: 37765484 PMCID: PMC10534386 DOI: 10.3390/plants12183321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/08/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023]
Abstract
Characterisation of genetic diversity is critical to adequately exploit the potential of germplasm collections and identify important traits for breeding programs and sustainable crop improvement. Here, we characterised the phenotypic and genetic diversity of a global collection of the two cultivated buckwheat species Fagopyrum esculentum and Fagopyrum tataricum (190 and 51 accessions, respectively) using 37 agro-morphological traits and 24 SSR markers. A wide range of variation was observed in both species for most of the traits analysed. The two species differed significantly in most traits, with traits related to seeds and flowering contributing most to differentiation. The accessions of each species were divided into three major phenoclusters with no clear geographic clustering. At the molecular level, the polymorphic SSR markers were highly informative, with an average polymorphic information content (PIC) of over 0.65 in both species. Genetic diversity, as determined by Nei's expected heterozygosity (He), was high (He = 0.77 and He = 0.66, respectively) and differed significantly between species (p = 0.03) but was homogeneously distributed between regions, confirming the lack of genetic structure as determined by clustering approaches. The weak genetic structure revealed by the phenotypic and SSR data and the low fixation indices in both species suggested frequent seed exchange and extensive cultivation and selection. In addition, 93 and 140 significant (p < 0.05) marker-trait associations (MTAs) were identified in both species using a general linear model and a mixed linear model, most of which explained >20% of the phenotypic variation in associated traits. Core collections of 23 and 13 phenotypically and genetically diverse accessions, respectively, were developed for F. esculentum and F. tataricum. Overall, the data analysed provided deep insights into the agro-morphological and genetic diversity and genetic relationships among F. esculentum and F. tataricum accessions and pointed to future directions for genomics-based breeding programs and germplasm management.
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Affiliation(s)
- Barbara Pipan
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetocva ulica 17, SI-1000 Ljubljana, Slovenia; (L.S.); (M.N.); (V.M.)
| | - Lovro Sinkovič
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetocva ulica 17, SI-1000 Ljubljana, Slovenia; (L.S.); (M.N.); (V.M.)
| | - Mohamed Neji
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetocva ulica 17, SI-1000 Ljubljana, Slovenia; (L.S.); (M.N.); (V.M.)
| | - Dagmar Janovská
- Gene Bank, Crop Research Institute, Drnovská 507, 161 06 Prague, Czech Republic;
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 420, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China;
| | - Vladimir Meglič
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetocva ulica 17, SI-1000 Ljubljana, Slovenia; (L.S.); (M.N.); (V.M.)
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10
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Pinski A, Betekhtin A. Efficient Agrobacterium-mediated transformation and genome editing of Fagopyrum tataricum. FRONTIERS IN PLANT SCIENCE 2023; 14:1270150. [PMID: 37746024 PMCID: PMC10515086 DOI: 10.3389/fpls.2023.1270150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 08/28/2023] [Indexed: 09/26/2023]
Abstract
Fagopyrum tataricum (L.) Gaertn. is an exceptional crop known for its remarkable health benefits, high levels of beneficial polyphenols and gluten-free properties, making it highly sought-after as a functional food. Its self-fertilisation capability and adaptability to challenging environments further contribute to its potential as a sustainable agricultural option. To harness its unique traits, genetic transformation in F. tataricum is crucial. In this study, we optimised the Agrobacterium-mediated transformation protocol for F. tataricum callus, resulting in a transformation rate of regenerated plants of approximately 20%. The protocol's effectiveness was confirmed through successful GUS staining, GFP expression, and the generation of albino plants via FtPDS gene inactivation. These results validate the feasibility of genetic manipulation and highlight the potential for trait enhancement in F. tataricum.
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Affiliation(s)
- Artur Pinski
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Alexander Betekhtin
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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11
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Zhang K, He Y, Lu X, Shi Y, Zhao H, Li X, Li J, Liu Y, Ouyang Y, Tang Y, Ren X, Zhang X, Yang W, Sun Z, Zhang C, Quinet M, Luthar Z, Germ M, Kreft I, Janovská D, Meglič V, Pipan B, Georgiev MI, Studer B, Chapman MA, Zhou M. Comparative and population genomics of buckwheat species reveal key determinants of flavor and fertility. MOLECULAR PLANT 2023; 16:1427-1444. [PMID: 37649255 PMCID: PMC10512774 DOI: 10.1016/j.molp.2023.08.013] [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: 08/24/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 09/01/2023]
Abstract
Common buckwheat (Fagopyrum esculentum) is an ancient crop with a world-wide distribution. Due to its excellent nutritional quality and high economic and ecological value, common buckwheat is becoming increasingly important throughout the world. The availability of a high-quality reference genome sequence and population genomic data will accelerate the breeding of common buckwheat, but the high heterozygosity due to the outcrossing nature has greatly hindered the genome assembly. Here we report the assembly of a chromosome-scale high-quality reference genome of F. esculentum var. homotropicum, a homozygous self-pollinating variant of common buckwheat. Comparative genomics revealed that two cultivated buckwheat species, common buckwheat (F. esculentum) and Tartary buckwheat (F. tataricum), underwent metabolomic divergence and ecotype differentiation. The expansion of several gene families in common buckwheat, including FhFAR genes, is associated with its wider distribution than Tartary buckwheat. Copy number variation of genes involved in the metabolism of flavonoids is associated with the difference of rutin content between common and Tartary buckwheat. Furthermore, we present a comprehensive atlas of genomic variation based on whole-genome resequencing of 572 accessions of common buckwheat. Population and evolutionary genomics reveal genetic variation associated with environmental adaptability and floral development between Chinese and non-Chinese cultivated groups. Genome-wide association analyses of multi-year agronomic traits with the content of flavonoids revealed that Fh05G014970 is a potential major regulator of flowering period, a key agronomic trait controlling the yield of outcrossing crops, and that Fh06G015130 is a crucial gene underlying flavor-associated flavonoids. Intriguingly, we found that the gene translocation and sequence variation of FhS-ELF3 contribute to the homomorphic self-compatibility of common buckwheat. Collectively, our results elucidate the genetic basis of speciation, ecological adaptation, fertility, and unique flavor of common buckwheat, and provide new resources for future genomics-assisted breeding of this economically important crop.
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Affiliation(s)
- Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China
| | - Yuqi He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China
| | - Xiang Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China
| | - Yaliang Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China
| | - Hui Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China; College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaobo Li
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, China
| | - Jinlong Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China
| | - Yang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China
| | - Yinan Ouyang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China
| | - Yu Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China
| | - Xue Ren
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, China
| | - Xuemei Zhang
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, China
| | - Weifei Yang
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, China
| | - Zhaoxia Sun
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu 030801, Shanxi, China; Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, Taiyuan 030031, Shanxi, China
| | - Chunhua Zhang
- Tongliao Institute Agricultural and Animal Husbandry Sciences, Tongliao 028015, Inner Mongolia, China
| | - Muriel Quinet
- Groupe de Recherche en Physiologie Végétale (GRPV), Earth and Life Institute-Agronomy (ELI-A), Université Catholique de Louvain, Croix du Sud 4-5, boîte L7.07.13, B-1348, Louvain-la-Neuve, Belgium
| | - Zlata Luthar
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Mateja Germ
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Ivan Kreft
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; Nutrition Institute, Tržaška 40, 1000 Ljubljana, Slovenia
| | - Dagmar Janovská
- Gene Bank, Crop Research Institute, Drnovská 507, Prague 6, Czech Republic
| | - Vladimir Meglič
- Agricultural Institute of Slovenia, Hacquetova ulica, Ljubljana, Slovenia
| | - Barbara Pipan
- Agricultural Institute of Slovenia, Hacquetova ulica, Ljubljana, Slovenia
| | - Milen I Georgiev
- Laboratory of Metabolomics, Institute of Microbiology, Bulgarian Academy of Sciences, Plovdiv, Bulgaria; Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton SO17 1BJ, UK
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China.
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12
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Chen C, Zhang Y, Liu Y, Cui J, He X, Wu Y, Yue L, Zhang J, Ding M, Yi Z, Fang X. Joint QTL Mapping and Transcriptome Sequencing Analysis Reveal Candidate Seed-Shattering-Related Genes in Common Buckwheat. Int J Mol Sci 2023; 24:10013. [PMID: 37373161 DOI: 10.3390/ijms241210013] [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: 05/03/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Common buckwheat (Fagopyrum esculentum M.) is an important traditional miscellaneous grain crop. However, seed-shattering is a significant problem in common buckwheat. To investigate the genetic architecture and genetic regulation of seed-shattering in common buckwheat, we constructed a genetic linkage map using the F2 population of Gr (green-flower mutant and shattering resistance) and UD (white flower and susceptible to shattering), which included eight linkage groups with 174 loci, and detected seven QTLs of pedicel strength. RNA-seq analysis of pedicel in two parents revealed 214 differentially expressed genes DEGs that play roles in phenylpropanoid biosynthesis, vitamin B6 metabolism, and flavonoid biosynthesis. Weighted gene co-expression network analysis (WGCNA) was performed and screened out 19 core hub genes. Untargeted GC-MS analysis detected 138 different metabolites and conjoint analysis screened out 11 DEGs, which were significantly associated with differential metabolites. Furthermore, we identified 43 genes in the QTLs, of which six genes had high expression levels in the pedicel of common buckwheat. Finally, 21 candidate genes were screened out based on the above analysis and gene function. Our results provided additional knowledge for the identification and functions of causal candidate genes responsible for the variation in seed-shattering and would be an invaluable resource for the genetic dissection of common buckwheat resistance-shattering molecular breeding.
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Affiliation(s)
- Chuyi Chen
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Yuke Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Institute of Advanced Agricultural Sciences, Peking University, Weifang 261000, China
| | - Yang Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Jingbin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Xingxing He
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Yichao Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Linqing Yue
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Jian Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Mengqi Ding
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Zelin Yi
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Xiaomei Fang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
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13
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Pinski A, Zhou M, Betekhtin A. Editorial: Advances in buckwheat research. FRONTIERS IN PLANT SCIENCE 2023; 14:1190090. [PMID: 37143884 PMCID: PMC10152880 DOI: 10.3389/fpls.2023.1190090] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 04/11/2023] [Indexed: 05/06/2023]
Affiliation(s)
- Artur Pinski
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
- *Correspondence: Artur Pinski, ; Meiliang Zhou, ; Alexander Betekhtin,
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Artur Pinski, ; Meiliang Zhou, ; Alexander Betekhtin,
| | - Alexander Betekhtin
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
- *Correspondence: Artur Pinski, ; Meiliang Zhou, ; Alexander Betekhtin,
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