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Caizergues AE, Santangelo JS, Ness RW, Angeoletto F, Anstett DN, Anstett J, Baena-Diaz F, Carlen EJ, Chaves JA, Comerford MS, Dyson K, Falahati-Anbaran M, Fellowes MDE, Hodgins KA, Hood GR, Iñiguez-Armijos C, Kooyers NJ, Lázaro-Lobo A, Moles AT, Munshi-South J, Paule J, Porth IM, Santiago-Rosario LY, Whitney KS, Tack AJM, Johnson MTJ. Does urbanisation lead to parallel demographic shifts across the world in a cosmopolitan plant? Mol Ecol 2024; 33:e17311. [PMID: 38468155 DOI: 10.1111/mec.17311] [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: 08/15/2023] [Revised: 12/08/2023] [Accepted: 01/30/2024] [Indexed: 03/13/2024]
Abstract
Urbanisation is occurring globally, leading to dramatic environmental changes that are altering the ecology and evolution of species. In particular, the expansion of human infrastructure and the loss and fragmentation of natural habitats in cities is predicted to increase genetic drift and reduce gene flow by reducing the size and connectivity of populations. Alternatively, the 'urban facilitation model' suggests that some species will have greater gene flow into and within cities leading to higher diversity and lower differentiation in urban populations. These alternative hypotheses have not been contrasted across multiple cities. Here, we used the genomic data from the GLobal Urban Evolution project (GLUE), to study the effects of urbanisation on non-adaptive evolutionary processes of white clover (Trifolium repens) at a global scale. We found that white clover populations presented high genetic diversity and no evidence of reduced Ne linked to urbanisation. On the contrary, we found that urban populations were less likely to experience a recent decrease in effective population size than rural ones. In addition, we found little genetic structure among populations both globally and between urban and rural populations, which showed extensive gene flow between habitats. Interestingly, white clover displayed overall higher gene flow within urban areas than within rural habitats. Our study provides the largest comprehensive test of the demographic effects of urbanisation. Our results contrast with the common perception that heavily altered and fragmented urban environments will reduce the effective population size and genetic diversity of populations and contribute to their isolation.
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Affiliation(s)
- Aude E Caizergues
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - James S Santangelo
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA
| | - Rob W Ness
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Fabio Angeoletto
- Programa de Pós-Graduação em Gestão e Tecnologia Ambiental da Universidade Federal de Rondonópolis, Rondonópolis, Brasil
| | - Daniel N Anstett
- Department of Plant Biology, Department of Entomology, Plant Resilience Institute, Michigan State University, East Lansing, Michigan, USA
| | - Julia Anstett
- Genomic Sciences and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Elizabeth J Carlen
- Living Earth Collaborative, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jaime A Chaves
- Universidad San Francisco de Quito, Ecuador, Quito
- San Francisco State University, San Francisco, California, USA
| | - Mattheau S Comerford
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, USA
| | | | | | | | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Glen Ray Hood
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Carlos Iñiguez-Armijos
- Laboratorio de Ecología Tropical y Servicios Ecosistémicos (EcoSs-Lab), Universidad Técnica Particular de Loja, Loja, Ecuador
| | | | - Adrián Lázaro-Lobo
- Biodiversity Research Institute (IMIB), CSIC-University of Oviedo-Principality of Asturias, Mieres, Spain
| | - Angela T Moles
- Evolution & Ecology Research Centre, UNSW-University of New South Wales, Sydney, New South Wales, Australia
| | - Jason Munshi-South
- Department of Biology and Louis Calder Center, Fordham University, New York City, New York, USA
| | - Juraj Paule
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Ilga M Porth
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Luis Y Santiago-Rosario
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Kaitlin Stack Whitney
- Science, Technology & Society Department, Rochester Institute of Technology, Rochester, New York, USA
| | - Ayko J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Marc T J Johnson
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
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Gogoi A, Munda S, Paw M, Begum T, Siddiqui MH, Gaafar ARZ, Kesawat MS, Lal M. Molecular genetic divergence analysis amongst high curcumin lines of Golden Crop (Curcuma longa L.) using SSR marker and use in trait-specific breeding. Sci Rep 2023; 13:19690. [PMID: 37952010 PMCID: PMC10640617 DOI: 10.1038/s41598-023-46779-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 11/04/2023] [Indexed: 11/14/2023] Open
Abstract
Curcuma longa L., is recognized worldwide as a medicinally and economically important plant species due to its curcumin content which is an industrially important compound. In this study, a total of 329 accessions were collected from four states of India and planted in the experimental farm of CSIR-NEIST, Jorhat, India, in augmented design. Among these, 152 high curcumin (> 1.50%) accessions were screened for molecular divergence study using 39 SSR primers. The primers showed the most efficient outcome with 2-8 allele/ loci and a total 163 number of alleles with 100% polymorphism. Cluster analysis revealed the construction of three clusters, out of which one cluster was geographically dependent, and germplasm was particularly from Assam state. Jaccard's pairwise coefficient showed maximum genetic dissimilarity of (0.75) between accession RRLJCL 3 and RRLJCL 126, indicating high variation as it was from two different states viz Arunachal Pradesh and Nagaland respectively and minimum genetic dissimilarity of (0.09) between RRLJCL 58 and RRLJCL 59 indicating significantly less variation as the two accessions were from same state, i.e., Arunachal Pradesh. Analysis of Molecular Variance (AMOVA) revealed high molecular variation within the population (87%) and significantly less variation among the population (13%). Additionally, Neighbour Joining dendrogram, Principal Component Analysis (PCA), and bar plot structure revealed similar clustering of germplasm. This diversity assessment will help in selecting the trait-specific genotypes, crop improvement program, conservation of gene pool, marker-assisted breeding, and quantitative trait loci identification. Moreover, to the best of our knowledge, it is the first molecular diversity report among 152 high curcumin lines of C. longa from North East India using 39 SSR primers.
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Affiliation(s)
- Anindita Gogoi
- Academy of Scientific and Industrial Research, Ghaziabad, UP, 201002, India
- CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India
| | - Sunita Munda
- CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India
| | - Manabi Paw
- CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India
| | - Twahira Begum
- CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India.
| | - Manzer H Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Abdel-Rhman Z Gaafar
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Mahipal Singh Kesawat
- Institute for Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Mohan Lal
- Academy of Scientific and Industrial Research, Ghaziabad, UP, 201002, India.
- CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India.
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Li M, Zhang X, Zhang T, Bai Y, Chen C, Guo D, Guo C, Shu Y. Genome-wide analysis of the WRKY genes and their important roles during cold stress in white clover. PeerJ 2023; 11:e15610. [PMID: 37456899 PMCID: PMC10348312 DOI: 10.7717/peerj.15610] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/31/2023] [Indexed: 07/18/2023] Open
Abstract
Background White clover (Trifolium repens L) is a high-quality forage grass with a high protein content, but it is vulnerable to cold stress, which can negatively affect its growth and development. WRKY transcription factor is a family of plant transcription factors found mainly in higher plants and plays an important role in plant growth, development, and stress response. Although WRKY transcription factors have been studied extensively in other plants, it has been less studied in white clover. Methods and Results In the present research, we have performed a genome-wide analysis of the WRKY gene family of white clover, in total, there were 145 members of WRKY transcription factors identified in white clover. The characterization of the TrWRKY genes was detailed, including conserved motif analysis, phylogenetic analysis, and gene duplication analysis, which have provided a better understanding of the structure and evolution of the TrWRKY genes in white clover. Meanwhile, the genetic regulation network (GRN) containing TrWRKY genes was reconstructed, and Gene Ontology (GO) annotation analysis of these function genes showed they contributed to regulation of transcription process, response to wounding, and phosphorylay signal transduction system, all of which were important processes in response to abiotic stress. To determine the TrWRKY genes function under cold stress, the RNA-seq dataset was analyzed; most of TrWRKY genes were highly upregulated in response to cold stress, particularly in the early stages of cold stress. These results were validated by qRT-PCR experiment, implying they are involved in various gene regulation pathways in response to cold stress. Conclusion The results of this study provide insights that will be useful for further functional analyses of TrWRKY genes in response to biotic or abiotic stresses in white clover. These findings are likely to be useful for further research on the functions of TrWRKY genes and their role in response to cold stress, which is important to understand the molecular mechanism of cold tolerance in white clover and improve its cold tolerance.
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Qi T, Tang T, Zhou Q, Yang W, Hassan MJ, Cheng B, Nie G, Li Z, Peng Y. Optimization of Protocols for the Induction of Callus and Plant Regeneration in White Clover ( Trifolium repens L.). Int J Mol Sci 2023; 24:11260. [PMID: 37511020 PMCID: PMC10378747 DOI: 10.3390/ijms241411260] [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: 06/14/2023] [Revised: 07/02/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
White clover is a widely grown temperate legume forage with high nutritional value. Research on the functional genomics of white clover requires a stable and efficient transformation system. In this study, we successfully induced calluses from the cotyledons and leaves of 10 different white clover varieties. The results showed that the callus formation rate in the cotyledons did not vary significantly among the varieties, but the highest callus formation rate was observed in 'Koala' leaves. Subsequently, different concentrations of antioxidants and hormones were tested on the browning rate and differentiation ability of the calluses, respectively. The results showed that the browning rate was the lowest on MS supplemented with 20 mg L-1 AgNO3 and 25 mg L-1 VC, respectively, and the differentiation rate was highest on MS supplemented with 1 mg L-1 6-BA, 1 mg L-1 KT and 0.5 mg L-1 NAA. In addition, the transformation system for Agrobacterium tumefaciens-mediated transformation of 4-day-old leaves was optimized to some extent and obtained a positive callus rate of 8.9% using green fluorescent protein (GFP) as a marker gene. According to our data, by following this optimized protocol, the transformation efficiency could reach 2.38%. The results of this study will provide the foundation for regenerating multiple transgenic white clover from a single genetic background.
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Affiliation(s)
- Tiangang Qi
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tao Tang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qinyu Zhou
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Weiqiang Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Muhammad Jawad Hassan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Bizhen Cheng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhou Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Peng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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Vaishnav K, Tiwari V, Durgapal A, Meena B, Rana TS. Estimation of genetic diversity and population genetic structure in Gymnema sylvestre (Retz.) R. Br. ex Schult. populations using DAMD and ISSR markers. J Genet Eng Biotechnol 2023; 21:42. [PMID: 37022506 PMCID: PMC10079795 DOI: 10.1186/s43141-023-00497-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/20/2023] [Indexed: 04/07/2023]
Abstract
BACKGROUND Gymnema sylvestre (Retz.) R. Br. ex Schult. is a well-known medicinal plant against diabetes in India. There is as such no organized cultivation in India, and the plant is still being collected from the wild for their therapeutic uses. It is, therefore, important to estimate the genetic diversity and population genetic structure of G. sylvestre to ascertain the genetically diverse germplasm. The present study, therefore, was undertaken to analyze the genetic variability in 118 accessions belonging to 11 wild populations of G. sylvestre using directed amplification of minisatellite-region DNA (DAMD) and inter simple sequence repeats (ISSR). RESULTS The present genetic analyses of 11 populations with 25 markers (8 DAMD and 17 ISSR) revealed significant genetic diversity (H = 0.26, I = 0.40, PPL = 80.89%) at a species level, while the average genetic diversity at the population level was low. Among the 11 populations studied, PCH and UTK populations showed maximum genetic diversity, followed by KNR and AMB, while TEL population revealed the lowest genetic diversity. AMOVA and Gst values (0.18) revealed that most of the genetic variations are found within populations and very less among populations, and higher gene flow (Nm = 2.29) was found to be responsible for the genetic homogenization of the populations. The clustering pattern resulting from the UPGMA dendrogram was in congruence with STRUCTURE and PCoA, segregating all the 11 populations into two main genetic clusters: cluster I (populations of North and Central India) and cluster II (populations of South India). The clustering patterns obtained from all three statistical methods indicate that the genetic structure in G. sylvestre populations corresponds to the geographical diversity of the populations and represents a strong genetic structure. CONCLUSION The genetically diverse populations identified during the present study could be a potential genetic resource for further prospecting and conserving this important plant resource.
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Affiliation(s)
- Kanchana Vaishnav
- Molecular Systematics Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, Uttar Pradesh, India
- Maharana Pratap Government Degree College, Nanakmatta, Udham Singh Nagar, Kumaun University, Nainital, 263001, Uttarakhand, India
| | - Vandana Tiwari
- Molecular Systematics Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, Uttar Pradesh, India
| | - Anjala Durgapal
- Maharana Pratap Government Degree College, Nanakmatta, Udham Singh Nagar, Kumaun University, Nainital, 263001, Uttarakhand, India
| | - Baleshwar Meena
- CSIR-Traditional Knowledge Digital Library Unit, New Delhi, 110067, India
| | - T S Rana
- Molecular Systematics Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, Uttar Pradesh, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India.
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Zhang X, Yang H, Li M, Chen C, Bai Y, Guo D, Guo C, Shu Y. Time-course RNA-seq analysis provides an improved understanding of genetic regulation in response to cold stress from white clover ( Trifolium repens L.). BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2108339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Affiliation(s)
- Xueqi Zhang
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, PR China
| | - Huanhuan Yang
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, PR China
| | - Manman Li
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, PR China
| | - Chao Chen
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, PR China
| | - Yan Bai
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, PR China
| | - Donglin Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, PR China
| | - Changhong Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, PR China
| | - Yongjun Shu
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, PR China
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Ma S, Zhao J, Su W, Zheng J, Zhang S, Zhao W, Su S. Transcriptome-derived SSR markers for DNA fingerprinting and inter-populations genetic diversity assessment of Atractylodes chinensis. THE NUCLEUS 2022. [DOI: 10.1007/s13237-022-00398-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
Abstract
AbstractAtractylodes chinensis (fam. Asteraceae) is an important medicinal plant due to its unique pharmacological activity. The species is widely distributed in most areas of northern China. It is difficult to identify different populations of A. chinensis due to their similarity in characteristics. This study was the first investigation to date that assessed the genetic diversity of A. chinensis from different geographical counties of northern China using simple sequence repeat (SSR) markers. Of the 106 SSR primers in the clusters classified in the sesquiterpenoid biosynthesis pathway in the transcriptomic database of A. chinensis, ten with high polymorphism were used to analyze the inter-populations genetic diversity and construct DNA fingerprinting of 19 A. chinensis populations. A total of 78 alleles were detected, with an average number of 6.5 alleles per primer. The PIC value ranged from 0.4748 to 0.8918 with a mean of 0.6265. The neighbor-joining tree was used to classify 19 populations of A. chinensis into three clusters. DNA fingerprinting was performed according to these ten SSR markers. The results revealed that geographic origin is not exactly related to genetic diversity, as populations belonging to different provinces are grouped in the same cluster. The results of this study confirm that SSR markers are effective for genetic diversity analysis. The inter-populations genetic diversity and fingerprinting of A. chinensis in this study could provide a scientific basis for species identification and selective breeding.
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Lu Y, Chen J, Chen B, Liu Q, Zhang H, Yang L, Chao Z, Tian E. High genetic diversity and low population differentiation of a medical plant Ficus hirta Vahl., uncovered by microsatellite loci: implications for conservation and breeding. BMC PLANT BIOLOGY 2022; 22:334. [PMID: 35820829 PMCID: PMC9277808 DOI: 10.1186/s12870-022-03734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Wuzhimaotao (Radix Fici Hirtae) originates from the dry root of Ficus hirta (Moraceae), which is widely known as a medical and edible plant distributed in South China. As the increasing demand for Wuzhimaotao, the wild F. hirta has been extremely reduced during the past years. It is urgent to protect and rationally develop the wild resources of F. hirta for its sustainable utilization. However, a lack of genetic background of F. hirta makes it difficult to plan conservation and breeding strategies for this medical plant. In the present study, a total of 414 accessions of F. hirta from 7 provinces in southern China were evaluated for the population genetics using 9 polymorphic SSR markers. RESULTS A mean of 17.1 alleles per locus was observed. The expected heterozygosity (He) varied from 0.142 to 0.861 (mean = 0.706) in nine SSR loci. High genetic diversity (He = 0.706, ranged from 0.613 to 0.755) and low genetic differentiation among populations (G'ST = 0.147) were revealed at population level. In addition, analysis of molecular variance (AMOVA) indicated that the principal molecular variance existed within populations (96.2%) was significantly higher than that among populations (3.8%). Meanwhile, the three kinds of clustering methods analysis (STRUCTURE, PCoA and UPGMA) suggested that the sampled populations were clustered into two main genetic groups (K = 2). Mantel test showed a significant correlation between geographic and genetic distance among populations (R2 = 0.281, P < 0.001). Pollen flow, seed flow and/or geographical barriers might be the main factors that formed the current genetic patterns of F. hirta populations. CONCLUSIONS This is a comprehensive study of genetic diversity and population structure of F. hirta in southern China. We revealed the high genetic diversity and low population differentiation in this medicinal plant and clarified the causes of its current genetic patterns. Our study will provide novel insights into the exploitation and conservation strategies for F. hirta.
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Affiliation(s)
- Yi Lu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Jianling Chen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Bing Chen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Qianqian Liu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China
| | - Hanlin Zhang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Liyuan Yang
- Department of Landscape Plants and Ornamental Horticulture, College of Landscape Architecture, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, People's Republic of China.
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, People's Republic of China.
| | - Zhi Chao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China.
| | - Enwei Tian
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China.
- Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou, 510515, China.
- Guangdong Provincial Engineering Laboratory of Chinese Medicine Preparation Technology, Guangzhou, 510515, China.
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Mursyidin DH, Makruf MI, Badruzsaufari, Noor A. Molecular diversity of exotic durian (Durio spp.) germplasm: a case study of Kalimantan, Indonesia. J Genet Eng Biotechnol 2022; 20:39. [PMID: 35230532 PMCID: PMC8888783 DOI: 10.1186/s43141-022-00321-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/18/2022] [Indexed: 02/06/2023]
Abstract
Background Durian of Indonesia, specifically Durio zibethinus, is a potential agricultural commodity for domestic and international markets. However, its quality is still less competitive or significantly lower to fulfill the export market, compared to a similar one from other countries. This study aimed to determine and analyze the genetic diversity and relationship of the exotic durian (Durio spp.) germplasm originally from Kalimantan, Indonesia, using the rbcL marker. Results Based on this marker, the durian germplasm has a low genetic diversity (π%=0.24). It may strongly correspond with the variability sites or mutation present in the region. In this case, the rbcL region of the durian germplasm has generated 23 variable sites with a transition/transversion (Ti/Tv) bias value of 1.00. However, following the phylogenetic and principal component analyses, this germplasm is separated into four main clades and six groups, respectively. In this case, D. zibethinus was very closely related to D. exleyanus. Meanwhile, D. lowianus and D. excelsus were the farthest. In further analysis, 29 durians were very closely related, and the farthest was shown by Durian Burung (D. acutifolius) and Kalih Haliyang (D. kutejensis) as well as Pampaken Burung Kecil (D. kutejensis) and Durian Burung (D. acutifolius) with a divergence coefficient of 0.011. The Pearson correlation analysis confirms that 20 pairs of individual durians have a strong relation, shown by, e.g., Maharawin Hamak and Durian Burung as well as Mantuala Batu Hayam and Durian Burung Besar. Conclusion While the durian has a low genetic diversity, the phylogenetic analyses revealed that this germplasm originally from Kalimantan, Indonesia, shows unique relationships. These findings may provide a beneficial task in supporting the durian genetic conservation and breeding practices in the future, locally and globally.
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Li Z, Yun L, Gao Z, Wang T, Ren X, Zhao Y. EST-SSR Primer Development and Genetic Structure Analysis of Psathyrostachys juncea Nevski. FRONTIERS IN PLANT SCIENCE 2022; 13:837787. [PMID: 35295628 PMCID: PMC8919075 DOI: 10.3389/fpls.2022.837787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/07/2022] [Indexed: 05/14/2023]
Abstract
Psathyrostachys juncea is a perennial forage grass which plays an important role in soil and water conservation and ecological maintenance in cold and dry areas of temperate regions. In P. juncea, a variety of biotic and abiotic stress related genes have been used in crop improvement, indicating its agronomic, economic, forage, and breeding value. To date, there have been few studies on the genetic structure of P. juncea. Here, the genetic diversity and population structure of P. juncea were analyzed by EST-SSR molecular markers to evaluate the genetic differentiation related to tillering traits in P. juncea germplasm resources. The results showed that 400 simple sequence repeat (SSR) loci were detected in 2,020 differentially expressed tillering related genes. A total of 344 scored bands were amplified using 103 primer pairs, out of which 308 (89.53%) were polymorphic. The Nei's gene diversity of 480 individuals was between 0.092 and 0.449, and the genetic similarity coefficient was between 0.5008 and 0.9111, with an average of 0.6618. Analysis of molecular variance analysis showed that 93% of the variance was due to differences within the population, and the remaining 7% was due to differences among populations. Psathyrostachys juncea materials were clustered into five groups based on population genetic structure, principal coordinate analysis and unweighted pair-group method with arithmetic means (UPGMA) analysis. The results were similar between clustering methods, but a few individual plants were distributed differently by the three models. The clustering results, gene diversity and genetic similarity coefficients showed that the overall genetic relationship of P. juncea individuals was relatively close. A Mantel test, UPGMA and structural analysis also showed a significant correlation between genetic relationship and geographical distribution. These results provide references for future breeding programs, genetic improvement and core germplasm collection of P. juncea.
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Affiliation(s)
- Zhen Li
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Lan Yun
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Grassland Resources Ministry of Education, Hohhot, China
| | - Zhiqi Gao
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Tian Wang
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaomin Ren
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Yan Zhao
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
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