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Liu C, Wang J, Ko YZ, Shiao MS, Wang Y, Sun J, Yuan Q, Wang L, Chiang YC, Guo L. Genetic diversities in wild and cultivated populations of the two closely-related medical plants species, Tripterygium Wilfordii and T. Hypoglaucum (Celastraceae). BMC PLANT BIOLOGY 2024; 24:195. [PMID: 38493110 PMCID: PMC10944624 DOI: 10.1186/s12870-024-04826-x] [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: 10/02/2023] [Accepted: 02/15/2024] [Indexed: 03/18/2024]
Abstract
BACKGROUND The sustainable supply of medicinal plants is important, and cultivating and domesticating them has been suggested as an optimal strategy. However, this can lead to a loss of genetic diversity. Tripterygium wilfordii Hook. f. is a medicinal plant commonly used in traditional Chinese medicine, but its wild populations are dwindling due to excessive harvesting. To protect the species and meet the increasing demand, it is urgent to cultivate it on a large scale. However, distinguishing between T. wilfordii and T. hypoglaucum, two similar species with different medicinal properties, is challenging. Therefore, it is crucial to understand the genetic diversity and population structure of these species for their sustainable utilization. RESULTS In this study, we investigated the genetic diversity and population structure of the two traditional medicinal semiwoody vines plant species, Tripterygium wilfordii and T. hypoglaucum, including wild and cultivated populations using chloroplast DNA (cpDNA) sequences and microsatellite loci. Our results indicated that the two species maintain a high level of genetic divergence, indicating possible genetic bases for the different contents of bioactive compounds of the two species. T. wilfordii showed lower genetic diversity and less subdivided population structures of both markers than T. hypoglaucum. The potential factors in shaping these interesting differences might be differentiated pollen-to-seed migration rates, interbreeding, and history of population divergence. Analyses of cpDNA and microsatellite loci supported that the two species are genetically distinct entities. In addition, a significant reduction of genetic diversity was observed for cultivated populations of the two species, which mainly resulted from the small initial population size and propagated vegetative practice during their cultivation. CONCLUSION Our findings indicate significant genetic divergence between T. wilfordii and T. hypoglaucum. The genetic diversity and population structure analyses provide important insights into the sustainable cultivation and utilization of these medicinal plants. Accurate identification and conservation efforts are necessary for both species to ensure the safety and effectiveness of crude drug use. Our study also highlighted the importance of combined analyses of different DNA markers in addressing population genetics of medicinal plants because of the contrasts of inheritance and rates of gene flow. Large-scale cultivation programs should consider preserving genetic diversity to enhance the long-term sustainability of T. wilfordii and T. hypoglaucum. Our study proposed that some populations showed higher genetic diversity and distinctness, which can be considered with priority for conservation and as the sources for future breeding and genetic improvement.
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Affiliation(s)
- Chao Liu
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jingyi Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Ya-Zhu Ko
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Meng-Shin Shiao
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Yiheng Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jiahui Sun
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Qingjun Yuan
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Lisong Wang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, 332900, China.
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung City, Taiwan.
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung City, Taiwan.
- The Multidisciplinary and Data Science Research Center(MDSRC), National Sun Yat-sen University, Kaohsiung, 804, Taiwan.
| | - Lanping Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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Weeden NF, Lavin M, Abbo S, Coyne CJ, McPhee K. A hypervariable intron of the STAYGREEN locus provides excellent discrimination among Pisum fulvum accessions and reveals evidence for a relatively recent hybridization event with Pisum sativum. FRONTIERS IN PLANT SCIENCE 2023; 14:1233280. [PMID: 37692437 PMCID: PMC10492584 DOI: 10.3389/fpls.2023.1233280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023]
Abstract
An analysis of 82 non-synonymous Pisum fulvum accessions for sequence variation in a fragment of the STAYGREEN (SGR) locus revealed 57 alleles, most of which differed in indel structure. Eight additional P. fulvum accessions, each supposedly synonymous with a different accession of the initial group, were also analyzed. In every case the paired synonymous accessions possessed the same SGR sequence but varied slightly for a 6-trait morphological phenotype, indicating that SGR sequence is a much more reliable indicator of accession identity than is a morphological characterization. SGR sequence analysis confirmed our previous finding that P. fulvum accessions separate into two allele groups. This division was not supported by results of previous studies that were based on sequences distributed across the entire genome, suggesting that the division may have been produced by selection at a nearby locus and that the SGR phylogeny may not be good indicator of overall relationships within the species. One P. fulvum accession, PI 595941 (=JI1796), displayed an SGR sequence outside the variation typical of the species. Instead, its allele resembled alleles limited to a set of Pisum sativum landraces from the Middle East, suggesting hybridization between ancestors of PI 595941 and some primitive form of domesticated P. sativum. With one exception from the extreme northwest corner of Israel, P. fulvum accessions collected north of latitude 35.5° N were fixed for alleles from group A. These northern accessions also displayed greatly reduced SGR sequence diversity compared to group A accessions collected from other regions, suggesting that the northern populations may represent recent extensions of the range of the species. Group B accessions were distributed from Lake Tiberias south and were generally sympatric with the southern group A accessions. Although group B accessions occupied a smaller area than group A, the SGR sequence diversity in this group (28 alleles in 33 accessions) exceeded that for group A.
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Affiliation(s)
- N. F. Weeden
- Department of Plant Sciences & Plant Pathology, College of Agriculture, Montana State University, Bozeman, MT, United States
| | - M. Lavin
- Department of Plant Sciences & Plant Pathology, College of Agriculture, Montana State University, Bozeman, MT, United States
| | - S. Abbo
- The Robert H. Smith Faculty of Agriculture, Food and Environment, and the Jacob & Rachel Liss Chair in Agronomy at the Hebrew University of Jerusalem, Rehovot, Israel
| | - C. J. Coyne
- Plant Germplasm Introduction and Testing Research, Agricultural Research Service (USDA), Pullman, WA, United States
| | - K. McPhee
- Department of Plant Sciences & Plant Pathology, College of Agriculture, Montana State University, Bozeman, MT, United States
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Muniz AC, Lemos-Filho JP, Buzatti RSDO, Ribeiro PCC, Fernandes FM, Lovato MB. Genetic data improve the assessment of the conservation status based only on herbarium records of a Neotropical tree. Sci Rep 2019; 9:5693. [PMID: 30952869 PMCID: PMC6451013 DOI: 10.1038/s41598-019-41454-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 03/07/2019] [Indexed: 11/30/2022] Open
Abstract
Although there is a consensus among conservation biologists about the importance of genetic information, the assessment of extinction risk and conservation decision-making generally do not explicitly consider this type of data. Genetic data can be even more important in species where little other information is available. In this study, we investigated a poorly known legume tree, Dimorphandra exaltata, from the Brazilian Atlantic Forest, a hotspot for conservation. We coupled species distribution models and geospatial assessment based on herbarium records with population genetic analyses to evaluate its genetic status and extinction risk, and to suggest conservation measures. Dimorphandra exaltata shows low genetic diversity, inbreeding, and genetic evidence of decrease in population size, indicating that the species is genetically depleted. Geospatial assessment classified the species as Endangered. Species distribution models projected a decrease in range size in the near future (2050). The genetic status of the species suggests low adaptive potential, which compromises its chances of survival in the face of ongoing climatic change. Altogether, our coupled analyses show that the species is even more threatened than indicated by geospatial analyses alone. Thus, conservation measures that take into account genetic data and the impacts of climate change in the species should be implemented.
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Affiliation(s)
- André Carneiro Muniz
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, CP 486, Belo Horizonte, MG, 31270-901, Brazil
| | - José Pires Lemos-Filho
- Departamento de Botânica, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | | | - Priciane Cristina Correa Ribeiro
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, CP 486, Belo Horizonte, MG, 31270-901, Brazil
- Universidade Federal do Tocantins, Campus Universitário Araguaína, Araguaína, TO 77824-838, Brazil
| | - Fernando Moreira Fernandes
- Jardim Botânico da Fundação Municipal de Parques e Zoobotânica de Belo Horizonte, Coordination of Plano de Ação Nacional para a Conservação do faveiro-de-wilson, Belo Horizonte, Brazil
| | - Maria Bernadete Lovato
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, CP 486, Belo Horizonte, MG, 31270-901, Brazil.
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Burstin J, Salloignon P, Chabert-Martinello M, Magnin-Robert JB, Siol M, Jacquin F, Chauveau A, Pont C, Aubert G, Delaitre C, Truntzer C, Duc G. Genetic diversity and trait genomic prediction in a pea diversity panel. BMC Genomics 2015; 16:105. [PMID: 25765216 PMCID: PMC4355348 DOI: 10.1186/s12864-015-1266-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 01/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pea (Pisum sativum L.), a major pulse crop grown for its protein-rich seeds, is an important component of agroecological cropping systems in diverse regions of the world. New breeding challenges imposed by global climate change and new regulations urge pea breeders to undertake more efficient methods of selection and better take advantage of the large genetic diversity present in the Pisum sativum genepool. Diversity studies conducted so far in pea used Simple Sequence Repeat (SSR) and Retrotransposon Based Insertion Polymorphism (RBIP) markers. Recently, SNP marker panels have been developed that will be useful for genetic diversity assessment and marker-assisted selection. RESULTS A collection of diverse pea accessions, including landraces and cultivars of garden, field or fodder peas as well as wild peas was characterised at the molecular level using newly developed SNP markers, as well as SSR markers and RBIP markers. The three types of markers were used to describe the structure of the collection and revealed different pictures of the genetic diversity among the collection. SSR showed the fastest rate of evolution and RBIP the slowest rate of evolution, pointing to their contrasted mode of evolution. SNP markers were then used to predict phenotypes -the date of flowering (BegFlo), the number of seeds per plant (Nseed) and thousand seed weight (TSW)- that were recorded for the collection. Different statistical methods were tested including the LASSO (Least Absolute Shrinkage ans Selection Operator), PLS (Partial Least Squares), SPLS (Sparse Partial Least Squares), Bayes A, Bayes B and GBLUP (Genomic Best Linear Unbiased Prediction) methods and the structure of the collection was taken into account in the prediction. Despite a limited number of 331 markers used for prediction, TSW was reliably predicted. CONCLUSION The development of marker assisted selection has not reached its full potential in pea until now. This paper shows that the high-throughput SNP arrays that are being developed will most probably allow for a more efficient selection in this species.
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Affiliation(s)
- Judith Burstin
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
| | - Pauline Salloignon
- Clinical and Innovation Proteomic Platform (CLIPP), CHU Dijon, Université de Bourgogne, 1 rue du Professeur Marion, Dijon, 21000, France.
| | | | | | - Mathieu Siol
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
| | - Françoise Jacquin
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
| | - Aurélie Chauveau
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
- Present address: US EPGV, IG-CEA, Centre National de Génotypage, 2 rue Gaston Crémieux, Evry Cedex, 91057, France.
| | - Caroline Pont
- UMR GDEC, Plateforme Gentyane, Clermont Ferrand, 63100, France.
| | - Grégoire Aubert
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
| | - Catherine Delaitre
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
| | - Caroline Truntzer
- Clinical and Innovation Proteomic Platform (CLIPP), CHU Dijon, Université de Bourgogne, 1 rue du Professeur Marion, Dijon, 21000, France.
| | - Gérard Duc
- UMR1347, Agroecology, INRA, 17 rue de Sully, Dijon Cedex, 21065, France.
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Shi J, Huang S, Fu D, Yu J, Wang X, Hua W, Liu S, Liu G, Wang H. Evolutionary dynamics of microsatellite distribution in plants: insight from the comparison of sequenced brassica, Arabidopsis and other angiosperm species. PLoS One 2013; 8:e59988. [PMID: 23555856 PMCID: PMC3610691 DOI: 10.1371/journal.pone.0059988] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 02/24/2013] [Indexed: 11/19/2022] Open
Abstract
Despite their ubiquity and functional importance, microsatellites have been largely ignored in comparative genomics, mostly due to the lack of genomic information. In the current study, microsatellite distribution was characterized and compared in the whole genomes and both the coding and non-coding DNA sequences of the sequenced Brassica, Arabidopsis and other angiosperm species to investigate their evolutionary dynamics in plants. The variation in the microsatellite frequencies of these angiosperm species was much smaller than those for their microsatellite numbers and genome sizes, suggesting that microsatellite frequency may be relatively stable in plants. The microsatellite frequencies of these angiosperm species were significantly negatively correlated with both their genome sizes and transposable elements contents. The pattern of microsatellite distribution may differ according to the different genomic regions (such as coding and non-coding sequences). The observed differences in many important microsatellite characteristics (especially the distribution with respect to motif length, type and repeat number) of these angiosperm species were generally accordant with their phylogenetic distance, which suggested that the evolutionary dynamics of microsatellite distribution may be generally consistent with plant divergence/evolution. Importantly, by comparing these microsatellite characteristics (especially the distribution with respect to motif type) the angiosperm species (aside from a few species) all clustered into two obviously different groups that were largely represented by monocots and dicots, suggesting a complex and generally dichotomous evolutionary pattern of microsatellite distribution in angiosperms. Polyploidy may lead to a slight increase in microsatellite frequency in the coding sequences and a significant decrease in microsatellite frequency in the whole genome/non-coding sequences, but have little effect on the microsatellite distribution with respect to motif length, type and repeat number. Interestingly, several microsatellite characteristics seemed to be constant in plant evolution, which can be well explained by the general biological rules.
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Affiliation(s)
- Jiaqin Shi
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shunmou Huang
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, China
| | - Jinyin Yu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xinfa Wang
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Wei Hua
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shengyi Liu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Guihua Liu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hanzhong Wang
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- * E-mail:
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