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Reichel K, Herklotz V, Smolka A, Nybom H, Kellner A, De Riek J, Smulders MJM, Wissemann V, Ritz CM. Untangling the hedge: Genetic diversity in clonally and sexually transmitted genomes of European wild roses, Rosa L. PLoS One 2023; 18:e0292634. [PMID: 37797054 PMCID: PMC10553836 DOI: 10.1371/journal.pone.0292634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023] Open
Abstract
While European wild roses are abundant and widely distributed, their morphological taxonomy is complicated and ambiguous. In particular, the polyploid Rosa section Caninae (dogroses) is characterised by its unusual meiosis, causing simultaneous clonal and sexual transmission of sub-genomes. This hemisexual reproduction, which often co-occurs with vegetative reproduction, defies the standard definition of species boundaries. We analysed seven highly polymorphic microsatellite loci, scored for over 2 600 Rosa samples of differing ploidy, collected across Europe within three independent research projects. Based on their morphology, these samples had been identified as belonging to 21 dogrose and five other native rose species. We quantified the degree of clonality within species and at individual sampling sites. We then compared the genetic structure within our data to current rose morpho-systematics and searched for hemisexually co-inherited sets of alleles at individual loci. We found considerably fewer copies of identical multi-locus genotypes in dogroses than in roses with regular meiosis, with some variation recorded among species. While clonality showed no detectable geographic pattern, some genotypes appeared to be more widespread. Microsatellite data confirmed the current classification of subsections, but they did not support most of the generally accepted dogrose microspecies. Under canina meiosis, we found co-inherited sets of alleles as expected, but could not distinguish between sexually and clonally inherited sub-genomes, with only some of the detected allele combinations being lineage-specific.
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Affiliation(s)
- Katja Reichel
- Institute of Biology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Berlin, Germany
| | - Veit Herklotz
- Department of Botany, Senckenberg Museum for Natural History Görlitz, Senckenberg–Member of the Leibniz Association, Görlitz, Germany
| | - Alisia Smolka
- Institute of Biology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Berlin, Germany
- Department of Botany, Senckenberg Museum for Natural History Görlitz, Senckenberg–Member of the Leibniz Association, Görlitz, Germany
| | - Hilde Nybom
- Department of Plant Breeding, Balsgård, Swedish University of Agricultural Sciences, Kristianstad, Sweden
| | - Alexandra Kellner
- Institute of Botany, Systematic Botany Group, Justus-Liebig-University, Gießen, Germany
| | - Jan De Riek
- Flanders Research Institute for Agricultural, Fisheries and Food Research (ILVO), Plant Sciences Unit, Melle, Belgium
| | | | - Volker Wissemann
- Institute of Botany, Systematic Botany Group, Justus-Liebig-University, Gießen, Germany
| | - Christiane M. Ritz
- Department of Botany, Senckenberg Museum for Natural History Görlitz, Senckenberg–Member of the Leibniz Association, Görlitz, Germany
- International Institute (IHI) Zittau, Chair of Biodiversity of Higher Plants, Technical University Dresden, Zittau, Germany
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Jian H, Zhao L, Zhang H, Ma C, Wang Q, Yan H, Qiu X, Zhou N, Zhang T. Phylogeography and Population Genetics of Rosa chinensis var. s pontanea and R. lucidissima Complex, the Important Ancestor of Modern Roses. FRONTIERS IN PLANT SCIENCE 2022; 13:851396. [PMID: 35668800 PMCID: PMC9163990 DOI: 10.3389/fpls.2022.851396] [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: 01/09/2022] [Accepted: 04/14/2022] [Indexed: 05/28/2023]
Abstract
Rosa chinensis var. spontanea and R. lucidissima complex are the morphologically very similar key ancestors of modern roses with high importance in rose research and breeding. Although widely distributed in subtropical central and southwestern China, these two taxa are highly endangered. We sampled a total of 221 specimens and 330 DNA samples from 25 populations across the two taxa's whole range. Leaf morphological traits were compared. Two chloroplast DNA intergenic spacers (trnG-trnS, petL-psbE) and ITS were used for population genetics and phylogenetic study to delimit the boundary between the two taxa, assess the genetic variation, uncover the possible evolutionary mechanism responsible for the differentiation within the complex, and make the conservation recommendations. The complex exhibited high levels of genetic variation (h TcpDNA = 0.768, h TITS = 0.726) and high population differentiation even over small geographic distance. We suggest R. chinensis var. spontanea and R. lucidissma be treated as independent taxa, and the northern populations around and within the Sichuan Basin being R. chinensis var. spontanea, having broader leaflets and paler full-blooming flowers, while those in the middle and southern Yunnan-Guizhou Plateau and the adjacent regions being R. lucidissma, having narrower leaflets and darker full-blooming flowers. Transitional areas between the southeastern Sichuan Basin and northeastern Guizhou are the contact or the hybridization zone of the two taxa. Ancestral haplotypes of the complex (R. lucidissma) evolved at about 1.21-0.86 Mya in southeastern Yunnan-Guizhou Plateau and its adjacent regions and survived there during the Quaternary Oscillation. Ancestral haplotypes of R. chinensis var. spontanea deviated from R. lucidissma at about 0.022-0.031 Mya at the transitional areas (Daloushan and Wulingshan Mountains) between the northeastern edge of Yunnan-Guizhou Plaeteau and the southeastern border of Sichuan Basin, where they survived the LGM. The evolution of the complex included spatial isolation and inter-species hybridization. The complex's endangered status might be the result of over-exploitation for its ornamental and medical value, or due to reforestation of some originally open habitats. We provide specific recommendations for the two taxa's in situ and ex situ conservation.
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Affiliation(s)
- Hongying Jian
- National Engineering Research Center for Ornamental Horticulture/Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Ling Zhao
- School of Landscape Architecture and Horticulture Science, Southwest Forestry University, Kunming, China
| | - Hao Zhang
- National Engineering Research Center for Ornamental Horticulture/Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Changle Ma
- School of Landscape Architecture and Horticulture Science, Southwest Forestry University, Kunming, China
| | - Qigang Wang
- National Engineering Research Center for Ornamental Horticulture/Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Huijun Yan
- National Engineering Research Center for Ornamental Horticulture/Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xianqin Qiu
- National Engineering Research Center for Ornamental Horticulture/Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Ningning Zhou
- National Engineering Research Center for Ornamental Horticulture/Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Ting Zhang
- National Engineering Research Center for Ornamental Horticulture/Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
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Veluru A, Bhat KV, Raju DVS, Prasad KV, Tolety J, Bharadwaj C, Mitra SVACR, Banyal N, Singh KP, Panwar S. Characterization of Indian bred rose cultivars using morphological and molecular markers for conservation and sustainable management. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:95-106. [PMID: 32158123 PMCID: PMC7036390 DOI: 10.1007/s12298-019-00735-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/27/2019] [Accepted: 11/19/2019] [Indexed: 05/25/2023]
Abstract
Rose (Rosa × hybrid L.) is one of the most important commercial ornamental crops cultivated worldwide for its beauty, fragrance and nutraceutical values. Characterization of rose germplasm provides precise information about the extent of diversity present among the cultivars. It also helps in cultivar identification, intellectual property right protection, variety improvement and genetic diversity conservation. In the present study, 109 Indian bred rose cultivars were characterized using 59 morphological and 48 SSR markers. Out of 48 SSRs used, 31 markers exhibited polymorphism and 96 alleles were identified with an average of 3.9 alleles per locus. Nei's expected heterozygosity value of each locus ranged from 0.08 (with SSR ABRII/RPU32) to 0.78 (SSR Rh58). The similarity coefficient values ranged from 0.42 to 0.90 which indicated presence of moderated diversity among Indian cultivars. The neighbor-joining tree based on morphological data grouped the cultivars into two major clusters and several minor clusters based on their morphological resemblance. However, UPGMA dendrogram constructed using matching coefficient values grouped the cultivars into eight different clusters. Interpopulation analysis revealed higher genetic similarities between Hybrid Tea and Floribunda cultivars. An analysis for presence of population sub-structure grouped the Indian cultivars into eight different genetic groups. Analysis of molecular variance revealed apportioning of 97.59% of the variation to within subgroup diversity and 3.07% to between the cultivar groups. We have demonstrated here successful utilization of robust SSR to distinguish cultivars and assess genetic diversity among Indian bred rose cultivars. The information provided here is useful for cultivar identification and protection, cultivar improvement and genetic diversity conservation.
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Affiliation(s)
- Aparna Veluru
- 1Division of Floriculture and Landscape Architecture, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
| | | | | | | | - Janakiram Tolety
- 3Assistant Director General, Horticulture, KAB-II, Indian Council of Agricultural Research, New Delhi, 110 012 India
| | - Chellapilla Bharadwaj
- 5Division of Genetics, ICAR- Indian Agricultural Research Institute, New Delhi, 110 012 India
| | | | - Namita Banyal
- 1Division of Floriculture and Landscape Architecture, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
| | - Kanwar Pal Singh
- 1Division of Floriculture and Landscape Architecture, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
| | - Sapna Panwar
- 1Division of Floriculture and Landscape Architecture, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
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Almeida MC, Pina ES, Hernandes C, Zingaretti SM, Taleb-Contini SH, Salimena FRG, Slavov SN, Haddad SK, França SC, Pereira AMS, Bertoni BW. Genetic diversity and chemical variability of Lippia spp. (Verbenaceae). BMC Res Notes 2018; 11:725. [PMID: 30314442 PMCID: PMC6186075 DOI: 10.1186/s13104-018-3839-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 10/09/2018] [Indexed: 11/21/2022] Open
Abstract
Background The genus Lippia comprises 150 species, most of which have interesting medicinal properties. Lippia sidoides (syn. L. origanoides) exhibits strong antimicrobial activity and is included in the phytotherapy program implemented by the Brazilian Ministry of Health. Since species of Lippia are morphologically very similar, conventional taxonomic methods are sometimes insufficient for the unambiguous identification of plant material that is required for the production of certified phytomedicines. Therefore, genetic and chemical analysis with chemotype identification will contribute to a better characterization of Lippia species. Methods Amplified Length Polymorphism and Internal Transcribed Spacer molecular markers were applied to determine the plants’ genetic variability, and the chemical variability of Lippia spp. was determined by essential oil composition. Results Amplified Length Polymorphism markers were efficient in demonstrating the intra and inter-specific genetic variability of the genus and in separating the species L. alba, L. lupulina and L. origanoides into distinct groups. Phylogenetic analysis using Amplified Length Polymorphism and markers produced similar results and confirmed that L. alba and L. lupulina shared a common ancestor that differ from L. origanoides. Carvacrol, endo-fenchol and thymol were the most relevant chemical descriptors. Conclusion Based on the phylogenetic analysis it is proposed that L. grata should be grouped within L. origanoides due to its significant genetic similarity. Although Amplified Length Polymorphism and Internal Transcribed Spacer markers enabled the differentiation of individuals, the genotype selection for the production of certified phytomedicines must also consider the chemotype classification that reflects their real medicinal properties. Electronic supplementary material The online version of this article (10.1186/s13104-018-3839-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Milene C Almeida
- Departamento de Biotecnologia, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Ediedia S Pina
- Departamento de Biotecnologia, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Camila Hernandes
- Hospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil
| | - Sonia M Zingaretti
- Departamento de Biotecnologia, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Silvia H Taleb-Contini
- Departamento de Biotecnologia, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Fátima R G Salimena
- Departamento de Botânica, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Svetoslav N Slavov
- Hemocentro de Ribeirão Preto, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Simone K Haddad
- Hemocentro de Ribeirão Preto, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Suzelei C França
- Departamento de Biotecnologia, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Ana M S Pereira
- Departamento de Biotecnologia, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Bianca W Bertoni
- Departamento de Biotecnologia, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil.
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Investigating the genetic diversity and differentiation patterns in the Penstemon scariosus species complex under different sample sizes using AFLPs and SSRs. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1103-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Xin T, Huang W, De Riek J, Zhang S, Ahmed S, Van Huylenbroeck J, Long C. Genetic diversity, population structure, and traditional culture of Camellia reticulata. Ecol Evol 2017; 7:8915-8926. [PMID: 29152187 PMCID: PMC5677478 DOI: 10.1002/ece3.3340] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 07/03/2017] [Accepted: 07/20/2017] [Indexed: 11/30/2022] Open
Abstract
Camellia reticulata is an arbor tree that has been cultivated in southwestern China by various sociolinguistic groups for esthetic purposes as well as to derive an edible seed oil. This study examined the influence of management, socio‐economic factors, and religion on the genetic diversity patterns of Camellia reticulata utilizing a combination of ethnobotanical and molecular genetic approaches. Semi‐structured interviews and key informant interviews were carried out with local communities in China's Yunnan Province. We collected plant material (n = 190 individuals) from five populations at study sites using single‐dose AFLP markers in order to access the genetic diversity within and between populations. A total of 387 DNA fragments were produced by four AFLP primer sets. All DNA fragments were found to be polymorphic (100%). A relatively high level of genetic diversity was revealed in C. reticulata samples at both the species (Hsp = 0.3397, Isp = 0.5236) and population (percentage of polymorphic loci = 85.63%, Hpop = 0.2937, Ipop = 0.4421) levels. Findings further revealed a relatively high degree of genetic diversity within C. reticulata populations (Analysis of Molecular Variance = 96.31%). The higher genetic diversity within populations than among populations of C. reticulata from different geographies is likely due to the cultural and social influences associated with its long cultivation history for esthetic and culinary purposes by diverse sociolinguistic groups. This study highlights the influence of human management, socio‐economic factors, and other cultural variables on the genetic and morphological diversity of C. reticulata at a regional level. Findings emphasize the important role of traditional culture on the conservation and utilization of plant genetic diversity.
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Affiliation(s)
- Tong Xin
- College of Life and Environmental Sciences Minzu University of China Beijing China
| | - Weijuan Huang
- College of Life and Environmental Sciences Minzu University of China Beijing China
| | - Jan De Riek
- Plant Sciences Unit Institute for Agricultural and Fisheries Research Melle Belgium
| | - Shuang Zhang
- College of Life and Environmental Sciences Minzu University of China Beijing China
| | - Selena Ahmed
- Department of Health & Human Development Montana State University Bozeman MT USA
| | | | - Chunlin Long
- College of Life and Environmental Sciences Minzu University of China Beijing China.,Kunming Institute of Botany Chinese Academy of Sciences Kunming China
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Herklotz V, Ritz CM. Multiple and asymmetrical origin of polyploid dog rose hybrids (Rosa L. sect. Caninae (DC.) Ser.) involving unreduced gametes. ANNALS OF BOTANY 2017; 120:209-220. [PMID: 28028016 PMCID: PMC5737388 DOI: 10.1093/aob/mcw217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 09/14/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Polyploidy and hybridization are important factors for generating diversity in plants. The species-rich dog roses ( Rosa sect. Caninae ) originated by allopolyploidy and are characterized by unbalanced meiosis producing polyploid egg cells (usually 4 x ) and haploid sperm cells (1 x ). In extant natural stands species hybridize spontaneously, but the extent of natural hybridization is unknown. The aim of the study was to document the frequency of reciprocal hybridization between the subsections Rubigineae and Caninae with special reference to the contribution of unreduced egg cells (5 x ) producing 6 x offspring after fertilization with reduced (1 x ) sperm cells. We tested whether hybrids arose by independent multiple events or via a single or few incidences followed by a subsequent spread of hybrids. METHODS Population genetics of 45 mixed stands of dog roses across central and south-eastern Europe were analysed using microsatellite markers and flow cytometry. Hybrids were recognized by the presence of diagnostic alleles and multivariate statistics were used to display the relationships between parental species and hybrids. KEY RESULTS Among plants classified to subsect. Rubigineae , 32 % hybridogenic individuals were detected but only 8 % hybrids were found in plants assigned to subsect. Caninae . This bias between reciprocal crossings was accompanied by a higher ploidy level in Rubigineae hybrids, which originated more frequently by unreduced egg cells. Genetic patterns of hybrids were strongly geographically structured, supporting their independent origin. CONCLUSIONS The biased crossing barriers between subsections are explained by the facilitated production of unreduced gametes in subsect. Rubigineae . Unreduced egg cells probably provide the highly homologous chromosome sets required for correct chromosome pairing in hybrids. Furthermore, the higher frequency of Rubigineae hybrids is probably influenced by abundance effects because the plants of subsect. Caninae are much more abundant and thus provide large quantities of pollen. Hybrids are formed spontaneously, leading to highly diverse mixed stands, which are insufficiently characterized by the actual taxonomy.
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Affiliation(s)
- V. Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Am Museum 1, D-02826 Görlitz, Germany
| | - C. M. Ritz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Am Museum 1, D-02826 Görlitz, Germany
- For correspondence. E-mail
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8
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Winkler M, Escobar García P, Gattringer A, Sonnleitner M, Hülber K, Schönswetter P, Schneeweiss GM. A novel method to infer the origin of polyploids from Amplified Fragment Length Polymorphism data reveals that the alpine polyploid complex of Senecio carniolicus (Asteraceae) evolved mainly via autopolyploidy. Mol Ecol Resour 2017; 17:877-892. [PMID: 27978605 DOI: 10.1111/1755-0998.12641] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 11/24/2016] [Accepted: 12/06/2016] [Indexed: 11/30/2022]
Abstract
Despite its evolutionary and ecological relevance, the mode of polyploid origin has been notoriously difficult to be reconstructed from molecular data. Here, we present a method to identify the putative parents of polyploids and thus to infer the mode of their origin (auto- vs. allopolyploidy) from Amplified Fragment Length Polymorphism (AFLP) data. To this end, we use Cohen's d of distances between in silico polyploids, generated within a priori defined scenarios of origin from a priori delimited putative parental entities (e.g. taxa, genetic lineages), and natural polyploids. Simulations show that the discriminatory power of the proposed method increases mainly with increasing divergence between the lower-ploid putative ancestors and less so with increasing delay of polyploidization relative to the time of divergence. We apply the new method to the Senecio carniolicus aggregate, distributed in the European Alps and comprising two diploid, one tetraploid and one hexaploid species. In the eastern part of its distribution, the S. carniolicus aggregate was inferred to comprise an autopolyploid series, whereas for western populations of the tetraploid species, an allopolyploid origin involving the two diploid species was the most likely scenario. Although this suggests that the tetraploid species has two independent origins, other evidence (ribotype distribution, morphology) is consistent with the hypothesis of an autopolyploid origin with subsequent introgression by the second diploid species. Altogether, identifying the best among alternative scenarios using Cohen's d can be straightforward, but particular scenarios, such as allopolyploid origin vs. autopolyploid origin with subsequent introgression, remain difficult to be distinguished.
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Affiliation(s)
- Manuela Winkler
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria.,GLORIA Co-ordination, Center for Global Change and Sustainability, University of Natural Resources and Life Sciences Vienna (BOKU) & Institute for Interdisciplinary Mountain Research, Austrian Academy of Sciences, Silbergasse 30/3, Vienna, A-1190, Austria
| | - Pedro Escobar García
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Andreas Gattringer
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Michaela Sonnleitner
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Karl Hülber
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria.,Vienna Institute for Nature Conservation & Analyses, Giessergasse 6/7, Vienna, A-1090, Austria
| | - Peter Schönswetter
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, Innsbruck, A-6020, Austria
| | - Gerald M Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
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Vukosavljev M, Arens P, Voorrips RE, van ‘t Westende WPC, Esselink GD, Bourke PM, Cox P, van de Weg WE, Visser RGF, Maliepaard C, Smulders MJM. High-density SNP-based genetic maps for the parents of an outcrossed and a selfed tetraploid garden rose cross, inferred from admixed progeny using the 68k rose SNP array. HORTICULTURE RESEARCH 2016; 3:16052. [PMID: 27818777 PMCID: PMC5080978 DOI: 10.1038/hortres.2016.52] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 09/26/2016] [Accepted: 09/30/2016] [Indexed: 05/21/2023]
Abstract
Dense genetic maps create a base for QTL analysis of important traits and future implementation of marker-assisted breeding. In tetraploid rose, the existing linkage maps include <300 markers to cover 28 linkage groups (4 homologous sets of 7 chromosomes). Here we used the 68k WagRhSNP Axiom single-nucleotide polymorphism (SNP) array for rose, in combination with SNP dosage calling at the tetraploid level, to genotype offspring from the garden rose cultivar 'Red New Dawn'. The offspring proved to be not from a single bi-parental cross. In rose breeding, crosses with unintended parents occur regularly. We developed a strategy to separate progeny into putative populations, even while one of the parents was unknown, using principle component analysis on pairwise genetic distances based on sets of selected SNP markers that were homozygous, and therefore uninformative for one parent. One of the inferred populations was consistent with self-fertilization of 'Red New Dawn'. Subsequently, linkage maps were generated for a bi-parental and a self-pollinated population with 'Red New Dawn' as the common maternal parent. The densest map, for the selfed parent, had 1929 SNP markers on 25 linkage groups, covering 1765.5 cM at an average marker distance of 0.9 cM. Synteny with the strawberry (Fragaria vesca) genome was extensive. Rose ICM1 corresponded to F. vesca pseudochromosome 7 (Fv7), ICM4 to Fv4, ICM5 to Fv3, ICM6 to Fv2 and ICM7 to Fv5. Rose ICM2 corresponded to parts of F. vesca pseudochromosomes 1 and 6, whereas ICM3 is syntenic to the remainder of Fv6.
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Affiliation(s)
- Mirjana Vukosavljev
- Wageningen UR Plant Breeding, Wageningen University & Research, NL-6700 AJ Wageningen, The Netherlands
| | - Paul Arens
- Wageningen UR Plant Breeding, Wageningen University & Research, NL-6700 AJ Wageningen, The Netherlands
| | - Roeland E Voorrips
- Wageningen UR Plant Breeding, Wageningen University & Research, NL-6700 AJ Wageningen, The Netherlands
| | - Wendy PC van ‘t Westende
- Wageningen UR Plant Breeding, Wageningen University & Research, NL-6700 AJ Wageningen, The Netherlands
| | - GD Esselink
- Wageningen UR Plant Breeding, Wageningen University & Research, NL-6700 AJ Wageningen, The Netherlands
| | - Peter M Bourke
- Wageningen UR Plant Breeding, Wageningen University & Research, NL-6700 AJ Wageningen, The Netherlands
| | - Peter Cox
- Roath BV, Eindhoven, The Netherlands
| | - W Eric van de Weg
- Wageningen UR Plant Breeding, Wageningen University & Research, NL-6700 AJ Wageningen, The Netherlands
| | - Richard GF Visser
- Wageningen UR Plant Breeding, Wageningen University & Research, NL-6700 AJ Wageningen, The Netherlands
| | - Chris Maliepaard
- Wageningen UR Plant Breeding, Wageningen University & Research, NL-6700 AJ Wageningen, The Netherlands
| | - Marinus JM Smulders
- Wageningen UR Plant Breeding, Wageningen University & Research, NL-6700 AJ Wageningen, The Netherlands
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Phylogeny of Rosa sections Chinenses and Synstylae (Rosaceae) based on chloroplast and nuclear markers. Mol Phylogenet Evol 2015; 87:50-64. [PMID: 25812912 DOI: 10.1016/j.ympev.2015.03.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 03/04/2015] [Accepted: 03/14/2015] [Indexed: 11/23/2022]
Abstract
Rosa sections Chinenses and Synstylae contain approximately 39 wild species mainly distributed in East Asia and are closely related according to previous studies. But the specific relationships within these two sections were still obscure due to limited sampling, low genetic variation of molecular markers, and complex evolutionary histories. In this study, we used four chloroplast (ndhC-trnV, ndhF-rpl32, ndhJ-trnF and psbJ-petA) and two nuclear (ribosomal ITS and GAPDH) markers with an extensive geographic and taxonomic sampling to explore their evolutionary history. Our phylogenetic analyses suggested that Rosa sections Chinenses and Synstylae defined in traditional taxonomic system are not monophyletic and close to sections Caninae and Gallicanae. Additionally, our results showed incongruence between chloroplast and nuclear markers, and the patterns of incongruence might be due to ancient hybridization (genetic introgression). One putative hybrid species and three samples identified as interspecific hybrids are further discussed in terms of topological incongruence, biological characters and distribution patterns.
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Fougère-Danezan M, Joly S, Bruneau A, Gao XF, Zhang LB. Phylogeny and biogeography of wild roses with specific attention to polyploids. ANNALS OF BOTANY 2015; 115:275-91. [PMID: 25550144 PMCID: PMC4551085 DOI: 10.1093/aob/mcu245] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 09/15/2014] [Accepted: 10/27/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS The genus Rosa (150-200 species) is widely distributed throughout temperate and sub-tropical habitats from the northern hemisphere to tropical Asia, with only one tropical African species. In order to better understand the evolution of roses, this study examines infrageneric relationships with respect to conventional taxonomy, considers the extent of allopolyploidization and infers macroevolutionary processes that have led to the current distribution of the genus. METHODS Phylogenetic relationships among 101 species of the genus Rosa were reconstructed using sequences from the plastid psbA-trnH spacer, trnL intron, trnL-F spacer, trnS-G spacer and trnG intron, as well as from nuclear glyceraldehyde 3-phosphate dehydrogenase (GAPDH), which was used to identify putative allopolyploids and infer their possible origins. Chloroplast phylogeny was used to estimate divergence times and reconstruct ancestral areas. KEY RESULTS Most subgenera and sections defined by traditional taxonomy are not monophyletic. However, several clades are partly consistent with currently recognized sections. Allopolyploidy seems to have played an important role in stabilizing intersectional hybrids. Biogeographic analyses suggest that Asia played a central role as a genetic reservoir in the evolution of the genus Rosa. CONCLUSIONS The ancestral area reconstruction suggests that despite an early presence on the American continent, most extant American species are the results of a later re-colonization from Asia, probably through the Bering Land Bridge. The results suggest more recent exchanges between Asia and western North America than with eastern North America. The current distribution of roses from the Synstylae lineage in Europe is probably the result of a migration from Asia approx. 30 million years ago, after the closure of the Turgai strait. Directions for a new sectional classification of the genus Rosa are proposed, and the analyses provide an evolutionary framework for future studies on this notoriously difficult genus.
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Affiliation(s)
- Marie Fougère-Danezan
- Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu, Sichuan 610041, China, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China, Institut de Recherche en Biologie Végétale (Département de Sciences biologiques), Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada, Montreal Botanical Garden, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada and Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299, USA Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu, Sichuan 610041, China, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China, Institut de Recherche en Biologie Végétale (Département de Sciences biologiques), Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada, Montreal Botanical Garden, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada and Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299, USA
| | - Simon Joly
- Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu, Sichuan 610041, China, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China, Institut de Recherche en Biologie Végétale (Département de Sciences biologiques), Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada, Montreal Botanical Garden, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada and Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299, USA Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu, Sichuan 610041, China, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China, Institut de Recherche en Biologie Végétale (Département de Sciences biologiques), Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada, Montreal Botanical Garden, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada and Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299, USA
| | - Anne Bruneau
- Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu, Sichuan 610041, China, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China, Institut de Recherche en Biologie Végétale (Département de Sciences biologiques), Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada, Montreal Botanical Garden, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada and Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299, USA
| | - Xin-Fen Gao
- Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu, Sichuan 610041, China, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China, Institut de Recherche en Biologie Végétale (Département de Sciences biologiques), Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada, Montreal Botanical Garden, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada and Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299, USA
| | - Li-Bing Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu, Sichuan 610041, China, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China, Institut de Recherche en Biologie Végétale (Département de Sciences biologiques), Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada, Montreal Botanical Garden, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada and Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299, USA Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu, Sichuan 610041, China, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China, Institut de Recherche en Biologie Végétale (Département de Sciences biologiques), Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada, Montreal Botanical Garden, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada and Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299, USA
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Crhak Khaitova L, Werlemark G, Kovarikova A, Nybom H, Kovarik A. High penetrance of a pan-canina type rDNA family in intersection Rosa hybrids suggests strong selection of bivalent chromosomes in the section Caninae. Cytogenet Genome Res 2014; 143:104-13. [PMID: 24685720 DOI: 10.1159/000360437] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
All dogroses (Rosa sect. Caninae) are characterized by the peculiar canina meiosis in which genetic material is unevenly distributed between female and male gametes. The pan-canina rDNA family (termed beta) appears to be conserved in all dogroses analyzed so far. Here, we have studied rDNAs in experimental hybrids obtained from open pollination of F1 plants derived from 2 independent intersectional crosses between the pentaploid dogrose species (2n = 5x = 35) Rosa rubiginosa as female parent (producing 4x egg cells due to the unique asymmetrical canina meiosis) and the tetraploid (2n = 4x = 28) garden rose R. hybrida 'André Brichet' as male parent (producing 2x pollen after normal meiosis). We analyzed the structure of rDNA units by molecular methods [CAPS and extensive sequencing of internal transcribed spacers (ITS)] and determined the number of loci on chromosomes by FISH. FISH showed that R. rubiginosa and 'André Brichet' harbored 5 and 4 highly heteromorphic rDNA loci, respectively. In the second generation of hybrid lines, we observed a reduced number of loci (4 and 5 instead of the expected 6). In R. rubiginosa and 'André Brichet', 2-3 major ITS types were found which is consistent with a weak homogenization pressure maintaining high diversity of ITS types in this genus. In contrast to expectation (the null hypothesis of Mendelian inheritance of ITS families), we observed reduced ITS diversity in some individuals of the second generation which might derive from self-fertilization or from a backcross to R. rubiginosa. In these individuals, the pan-canina beta family appeared to be markedly enriched, while the paternal families were lost or diminished in copies. Although the mechanism of biased meiotic transmission of certain rDNA types is currently unknown, we speculate that the bivalent-forming chromosomes carrying the beta rDNA family exhibit extraordinary pairing efficiency and/or are subjected to strong selection in Caninae polyploids.
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Affiliation(s)
- Lucie Crhak Khaitova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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Nybom H, Weising K, Rotter B. DNA fingerprinting in botany: past, present, future. INVESTIGATIVE GENETICS 2014; 5:1. [PMID: 24386986 PMCID: PMC3880010 DOI: 10.1186/2041-2223-5-1] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 12/02/2013] [Indexed: 12/20/2022]
Abstract
Almost three decades ago Alec Jeffreys published his seminal Nature papers on the use of minisatellite probes for DNA fingerprinting of humans (Jeffreys and colleagues Nature 1985, 314:67-73 and Nature 1985, 316:76-79). The new technology was soon adopted for many other organisms including plants, and when Hilde Nybom, Kurt Weising and Alec Jeffreys first met at the very First International Conference on DNA Fingerprinting in Berne, Switzerland, in 1990, everybody was enthusiastic about the novel method that allowed us for the first time to discriminate between humans, animals, plants and fungi on the individual level using DNA markers. A newsletter coined "Fingerprint News" was launched, T-shirts were sold, and the proceedings of the Berne conference filled a first book on "DNA fingerprinting: approaches and applications". Four more conferences were about to follow, one on each continent, and Alec Jeffreys of course was invited to all of them. Since these early days, methodologies have undergone a rapid evolution and diversification. A multitude of techniques have been developed, optimized, and eventually abandoned when novel and more efficient and/or more reliable methods appeared. Despite some overlap between the lifetimes of the different technologies, three phases can be defined that coincide with major technological advances. Whereas the first phase of DNA fingerprinting ("the past") was dominated by restriction fragment analysis in conjunction with Southern blot hybridization, the advent of the PCR in the late 1980s gave way to the development of PCR-based single- or multi-locus profiling techniques in the second phase. Given that many routine applications of plant DNA fingerprinting still rely on PCR-based markers, we here refer to these methods as "DNA fingerprinting in the present", and include numerous examples in the present review. The beginning of the third phase actually dates back to 2005, when several novel, highly parallel DNA sequencing strategies were developed that increased the throughput over current Sanger sequencing technology 1000-fold and more. High-speed DNA sequencing was soon also exploited for DNA fingerprinting in plants, either in terms of facilitated marker development, or directly in the sense of "genotyping-by-sequencing". Whereas these novel approaches are applied at an ever increasing rate also in non-model species, they are still far from routine, and we therefore treat them here as "DNA fingerprinting in the future".
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Affiliation(s)
- Hilde Nybom
- Department of Plant Breeding–Balsgård, Swedish University for Agricultural Sciences, Fjälkestadsvägen 459, Kristianstad 29194, Sweden
| | - Kurt Weising
- Plant Molecular Systematics, Institute of Biology, University of Kassel, Kassel 34109, Germany
| | - Björn Rotter
- GenXPro GmbH, Altenhöferallee 3, Frankfurt 60438, Germany
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