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Gavrilenko T, Chukhina I, Antonova O, Krylova E, Shipilina L, Oskina N, Kostina L. Comparative Analysis of the Genetic Diversity of Chilean Cultivated Potato Based on a Molecular Study of Authentic Herbarium Specimens and Present-Day Gene Bank Accessions. PLANTS (BASEL, SWITZERLAND) 2022; 12:174. [PMID: 36616303 PMCID: PMC9823414 DOI: 10.3390/plants12010174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
At the end of the 1920s, Vavilov organized several potato-collecting missions in South and Central America. Vavilov and his colleagues, Juzepczuk and Bukasov, participated in these expeditions and worked on gathered material, designated two centers of potato varietal riches and diversity-the Peru-Bolivia high-mountain center and the southern coast of Chile. The WIR Herbarium holds authentic specimens of many taxa described by Russian taxonomists. Here, a set of 20 plastid DNA-specific markers was applied for 49 authentic herbarium specimens of Solanum tuberosum L. from the WIR Herbarium to analyze the genetic diversity of the landrace population collected by Juzepczuk in 1928 in southern-central Chile. Two plastid DNA types, T and A, and two chlorotypes were identified in herbarium specimens, with a clear predominance (96%) of chlorotype cpT_III. In addition, we analyzed 46 living Chilean accessions from the VIR field potato gene bank that were collected after the appearance of Phytophthora infestans in Chile. These living accessions were differentiated into four chlorotypes. Finding a D-type cytoplasm in living Chilean accessions that possess two new chlorotypes indicates a replacement of native cultivars and introgression from the wild Mexican species S. demissum that was actively used in breeding as a source of race-specific resistance to late blight.
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Hosaka K, Sanetomo R. Development of a rapid identification method for potato cytoplasm and its use for evaluating Japanese collections. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1237-51. [PMID: 22696007 DOI: 10.1007/s00122-012-1909-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 05/25/2012] [Indexed: 05/11/2023]
Abstract
The cytoplasm of potatoes, characterized by the presence of T-type chloroplast DNA and β-type mitochondrial DNA, is sensitive to nuclear chromosomal genes that contribute to various types of male sterility. Past breeding efforts with various potato varieties have resulted in several different cytoplasms other than T/β. Varieties with Solanum stoloniferum-derived cytoplasm (W/γ) show complete male sterility, while those with S. demissum-derived cytoplasm (W/α) produce abundant, but non-functional pollen. Thus, identification of cytoplasmic types is important for designing efficient mating combinations. To date, only T-type chloroplast DNA can be accurately identified by a PCR marker. Here, we report a rapid identification technique by multiplex PCR, followed by restriction digestion with BamHI in one reaction tube, and propose a new nomenclature for potato cytoplasm types (T, D, P, A, M, and W). Using this new technique, our collections of 748 genotypes, including 84 Japanese named varieties, 378 breeding lines and 26 landraces, and 260 foreign varieties and breeding lines, were grouped into cytoplasm types: T (73.9 %), D (17.4 %), P (4.5 %), A (1.5 %), M (0.3 %), and W (2.4 %). The utility of this marker system for breeding is discussed.
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Affiliation(s)
- Kazuyoshi Hosaka
- NARO Hokkaido Agricultural Research Center, Shinsei, Memuro, Hokkaido, 082-0081, Japan.
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Sanetomo R, Hosaka K. A maternally inherited DNA marker, descended from Solanum demissum (2n = 6x = 72) to S. tuberosum (2n = 4x = 48). BREEDING SCIENCE 2011; 61:426-34. [PMID: 23136481 PMCID: PMC3406774 DOI: 10.1270/jsbbs.61.426] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 09/02/2011] [Indexed: 05/25/2023]
Abstract
A Mexican hexaploid wild potato species, Solanum demissum (dms), was only used as a female in previous breeding programs. The resulting clones with dms cytoplasm produced abundant, but non-functional pollen. A 170 bp DNA fragment, named Band 1, was originally detected in the F(1) hybrid between dms and S. tuberosum. In this study, the sequenced region was extended to 1,032 bp; nevertheless, it did not show any homology to known sequences. This extended region harboring Band 1 was, without introns, all transcribed to mRNA and was maternally inherited from dms to S. tuberosum through backcrosses. Three dms accessions, 168 accessions of 38 cultivated and closely related wild species, and 158 varieties and breeding lines were surveyed, which demonstrated that Band 1 was specific to dms and varieties and breeding lines with dms cytoplasm. Thus, Band 1 is a useful marker to distinguish dms cytoplasm, which enables us to design efficient mating combinations in breeding programs.
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Affiliation(s)
- Rena Sanetomo
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Hyogo 657-8501, Japan
- National Agricultural Research Center for Hokkaido Region, Shinsei, Memuro, Hokkaido 082-0081, Japan
| | - Kazuyoshi Hosaka
- National Agricultural Research Center for Hokkaido Region, Shinsei, Memuro, Hokkaido 082-0081, Japan
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Hosaka K, Sanetomo R. Comparative differentiation in mitochondrial and chloroplast DNA among cultivated potatoes and closely related wild species. Genes Genet Syst 2010; 84:371-8. [PMID: 20154424 DOI: 10.1266/ggs.84.371] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A total of 476 accessions of seven cultivated and 32 wild potato species previously characterized by nuclear DNA (nDNA) and chloroplast DNA (ctDNA) marker analyses were employed to the mitochondrial DNA (mtDNA) marker analysis. Fourteen simple sequence repeat (SSR) markers with mononucleotide repeat regions were developed from the potato mtDNA, although their variability was extremely low. Six mtDNA markers including three developed SSR markers disclosed 40 banding patterns that discriminated 63 different mtDNAs. For the same set of samples, 72 ctDNA banding patterns discriminated 129 different ctDNAs. Consequently, 164 haplotypes were distinguished. The correlation between ctDNA and mtDNA differentiation was positive (r = 0.226), but poor when compared with that between ctDNA and nDNA (r = 0.415), which likely lowered the utility of mtDNA polymorphisms in evaluating relationships among these species. Nevertheless, a finding of a unique mtDNA type in all T-type ctDNA holders (S. tuberosum and S. tarijense) strongly supports S. tarijense functioned as a maternal ancestor of potato.
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Affiliation(s)
- Kazuyoshi Hosaka
- Food Resources Education and Research Center, Kobe University, 1348 Uzurano, Kasai, Hyogo 675-2103, Japan.
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Ames M, Spooner DM. DNA from herbarium specimens settles a controversy about origins of the European potato. AMERICAN JOURNAL OF BOTANY 2008; 95:252-7. [PMID: 21632349 DOI: 10.3732/ajb.95.2.252] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Landrace potato cultivars are native to two areas in South America: the high Andes from eastern Venezuela to northern Argentina and the lowlands of south-central Chile. Potato first appeared outside of South America in Europe in 1567 and rapidly diffused worldwide. Two competing hypotheses suggested the origin of the "European" potato from the Andes or from lowland Chile, but the Andean origin has been widely accepted over the last 60 years. All modern potato cultivars predominantly have Chilean germplasm, explained as originating from breeding with Chilean landraces subsequent to the late blight epidemics beginning in 1845 in the UK. The Andean origin has been questioned recently through examination of landraces in India and the Canary Islands, but this evidence is inferential. Through a plastid DNA deletion marker from historical herbarium specimens, we report that the Andean potato predominated in the 1700s, but the Chilean potato was introduced into Europe as early as 1811 and became predominant long before the late blight epidemics in the UK. Our results provide the first direct evidence of these events and change the history of introduction of the European potato. They shed new light on the value of past breeding efforts to recreate the European potato from Andean forms and highlight the value of herbarium specimens in investigating origins of crop plants.
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Affiliation(s)
- Mercedes Ames
- USDA, Agricultural Research Service, Vegetable Crops Research Unit, Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin 53706 USA
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Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification. Proc Natl Acad Sci U S A 2007; 104:19398-403. [PMID: 18042704 DOI: 10.1073/pnas.0709796104] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Contrasting taxonomic treatments of potato landraces have continued over the last century, with the recognition of anywhere from 1 to 21 distinct Linnean species, or of Cultivar Groups within the single species Solanum tuberosum. We provide one of the largest molecular marker studies of any crop landraces to date, to include an extensive study of 742 landraces of all cultivated species (or Cultivar Groups) and 8 closely related wild species progenitors, with 50 nuclear simple sequence repeat (SSR) (also known as microsatellite) primer pairs and a plastid DNA deletion marker that distinguishes most lowland Chilean from upland Andean landraces. Neighbor-joining results highlight a tendency to separate three groups: (i) putative diploids, (ii) putative tetraploids, and (iii) the hybrid cultivated species S. ajanhuiri (diploid), S. juzepczukii (triploid), and S. curtilobum (pentaploid). However, there are many exceptions to grouping by ploidy. Strong statistical support occurs only for S. ajanhuiri, S. juzepczukii, and S. curtilobum. In combination with recent morphological analyses and an examination of the identification history of these collections, we support the reclassification of the cultivated potatoes into four species: (i) S. tuberosum, with two Cultivar Groups (Andigenum Group of upland Andean genotypes containing diploids, triploids, and tetraploids, and the Chilotanum Group of lowland tetraploid Chilean landraces); (ii) S. ajanhuiri (diploid); (iii) S. juzepczukii (triploid); and (iv) S. curtilobum (pentaploid). For other classifications, consistent and stable identifications are impossible, and their classification as species is artificial and only maintains the confusion of users of the gene banks and literature.
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Chung HJ, Jung JD, Park HW, Kim JH, Cha HW, Min SR, Jeong WJ, Liu JR. The complete chloroplast genome sequences of Solanum tuberosum and comparative analysis with Solanaceae species identified the presence of a 241-bp deletion in cultivated potato chloroplast DNA sequence. PLANT CELL REPORTS 2006; 25:1369-79. [PMID: 16835751 DOI: 10.1007/s00299-006-0196-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2006] [Revised: 05/29/2006] [Accepted: 06/09/2006] [Indexed: 05/07/2023]
Abstract
The complete nucleotide sequence of the chloroplast genome of potato Solanum tuberosum L. cv. Desiree was determined. The circular double-stranded DNA, which consists of 155,312 bp, contains a pair of inverted repeat regions (IRa, IRb) of 25,595 bp each. The inverted repeat regions are separated by small and large single copy regions of 18,373 and 85,749 bp, respectively. The genome contains 79 proteins, 30 tRNAs, 4 rRNAs, and unidentified genes. A comparison of chloroplast genomes of seven Solanaceae species revealed that the gene content and their relative positions of S. tuberosum are similar to the other six Solanaceae species. However, undefined open reading frames (ORFs) in LSC region were highly diverged in Solanaceae species except N. sylvestris. Detailed comparison was identified by numerous indels in the intergenic regions that were mostly located in the LSC region. Among them, a single large 241-bp deletion, was not associated with direct repeats and found in only S. tuberosum, clearly discriminates a cultivated potato from wild potato species Solanum bulbocastanum. The extent of sequence divergence may provide the basis for evaluating genetic diversity within the Solanaceae species, and will be useful to examine the evolutionary processes in potato landraces.
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Affiliation(s)
- Hwa-Jee Chung
- Plant Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Korea
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Spooner DM, Nuñez J, Rodríguez F, Naik PS, Ghislain M. Nuclear and chloroplast DNA reassessment of the origin of Indian potato varieties and its implications for the origin of the early European potato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 110:1020-1026. [PMID: 15754208 DOI: 10.1007/s00122-004-1917-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2004] [Accepted: 12/20/2004] [Indexed: 05/24/2023]
Abstract
The modern cultivated potato was first recorded in Europe in 1562, but its area(s) of exportation has long been in dispute. Two competing hypotheses have proposed an "Andean" area (somewhere from upland Venezuela to northern Argentina) or a lowland south central "Chilean" area. Potato landraces from these two areas can be distinguished, although sometimes with difficulty, by (1) cytoplasmic sterility factors, (2) morphological traits, (3) daylength adaptation, (4) microsatellite markers, and (5) co-evolved chloroplast (cp) and mitochondria (mt) DNA. The Chilean introduction hypothesis originally was proposed because of similarities among Chilean landraces and modern "European" cultivars with respect to traits 2 and 3. Alternatively, the Andean introduction hypothesis suggests that (1) traits 2 and 3 of European potato evolved rapidly, in parallel, from Andean landraces to a Chilean type through selection following import to Europe, and (2) the worldwide late blight epidemics beginning in 1845 in the United Kingdom displaced most existing European cultivars and the potato was subsequently improved by importations of Chilean landraces. We reassess these two competing hypotheses with nuclear microsatellite and cpDNA analyses of (1) 32 Indian cultivars, some of which are thought to preserve putatively remnant populations of Andean landraces, (2) 12 Andean landraces, and (3) five Chilean landraces. Our microsatellite results cluster all Indian cultivars, including putatively remnant Andean landrace populations, with the Chilean landraces, and none with the "old Andigenum" landraces. Some of these Indian landraces, however, lack the cpDNA typical of Chilean landraces and advanced cultivars, indicating they likely are hybrids of Andean landraces with Chilean clones or more advanced cultivars. These results lead us to reexamine the hypothesis that early introductions of potato to Europe were solely from the Andes.
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Affiliation(s)
- D M Spooner
- USDA-ARS, Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706-1590, USA.
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Scotti N, Monti L, Cardi T. Organelle DNA variation in parental Solanum spp. genotypes and nuclear-cytoplasmic interactions in Solanum tuberosum (+) S. commersonii somatic hybrid-backcross progeny. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2003; 108:87-94. [PMID: 12955209 DOI: 10.1007/s00122-003-1406-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2003] [Accepted: 05/12/2003] [Indexed: 05/24/2023]
Abstract
Nuclear-cytoplasmic interactions can influence fertility and agronomic performance of interspecific hybrids in potato as well as other species. With the aim of assessing the potential value of a novel recombinant cytoplasm derived by interspecific somatic hybridization, backcross progeny were produced by crossing a somatic hybrid between Solanum tuberosum (tbr) and the wild incongruous species S. commersonii (cmm) with various potato clones. BC1 clones were evaluated for male fertility and other agronomic traits. Male fertility clearly depended on the cross direction and the cytoplasm source. Genotypes with cytoplasms sensitive to nuclear genes derived from Solanum commersonii and inducing male sterility showed identical mtDNA composition, as based on mtDNA analyses with various PCR-based and RFLP markers. On the other hand, genotypes with cytoplasms not inducing male sterility in the presence of the cmm nuclear genes showed a different mtDNA organisation. Analysis of cpDNA confirmed similarity of cytoplasmic composition in CMS-inducing genotypes and clear differences with the others. Genotypes with recombinant cytoplasm induced by somatic hybridization generally showed similar agronomic performances in reciprocal hybrids with tbr cytoplasm, suggesting that the novel cytoplasm can be used in potato breeding.
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Affiliation(s)
- N Scotti
- CNR-IGV, Institute of Plant Genetics, Research Division Portici, via Università 133, 80055, Portici, Italy
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Zanke C, Borisjuk N, Ruoss B, Schilde-Rentschler L, Ninnemann H, Hemleben V. A specific oligonucleotide of the 5S rDNA spacer and species-specific elements identify symmetric somatic hybrids between Solanum tuberosum and S. pinnatisectum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 90:720-726. [PMID: 24174033 DOI: 10.1007/bf00222139] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/1994] [Accepted: 07/28/1994] [Indexed: 06/02/2023]
Abstract
The nucleotide sequences of the 5S rRNA genes (5S rDNA) of two Solanum tuberosum breeding lines (R1 and B15) and of the Mexican wild species S. pinnatisectum were determined and compared with each other and to the 5S rDNA of other Solanaceae species (Lycopersicon esculentum, Nicotiana rustica and Petunia hybrida). The 5S rDNA repeats of the Solanum species are 324-329 bp in length, and they exhibit 91-95% sequence identity. Sequence variability is mainly located in a short region of the spacer separating the 5S rRNA coding regions. A synthetic 28-mer oligonucleotide constructed according to this region can be used as a specific hybridization probe to distinguish symmetric somatic hybrids between S. tubersosum breeding line B15 and S. pinnatisectum produced by protoplast fusion. Interestingly, the two Solanum breeding lines R1 and B15 differ also in this spacer region.
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Affiliation(s)
- C Zanke
- Lehrstuhl für Allgemeine Genetik, Biologisches Institut, Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
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Hosaka K. Successive domestication and evolution of the Andean potatoes as revealed by chloroplast DNA restriction endonuclease analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 90:356-363. [PMID: 24173925 DOI: 10.1007/bf00221977] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/1994] [Accepted: 07/06/1994] [Indexed: 06/02/2023]
Abstract
Five chloroplast DNA (ctDNA) types (W, T, C, S, and A) have previously been identified in the Andean tetraploid cultivated potatoes (Solanum tuberosum ssp. andigena) and three types (C, S, and A) in diploid cultivated potatoes (S. stenotomum). In this study, ctDNA types were determined for an additional 35 accessions of S. stenotomum and 97 accessions of putative ancestral wild species (15 of S. brevicaule, 26 of S. bukasovii, 4 of S. candolleanum, 25 of S. canasense, 17 of S. leptophyes, and 10 of S. multidissectum). The first five ctDNA types were also identified in S. stenotomum. The wild species were also polymorphic for ctDNA types except for S. brevicaule, which had only W-type ctDNA. T-type ctDNA was not found in any of the wild species and could have originated from W-type ctDNA after S. stenotomum arose. The other types of ctDNA evolved in wild species. The geographical distribution of each ctDNA type indicated that A-type ctDNA arose in central Peru and T-type ctDNA in the Bolivia-Argentine boundary. It is implied that potatoes were successively domesticated and that, in parallel, several wild species were differentiated from time to time and place to place from the 'ancestral species' complex. Subsequent sexual polyploidization formed a wide ctDNA diversity among the Andean tetraploid potatoes, and selection from them formed the limited ctDNA diversity found in Chilean tetraploid potatoes (ssp. tuberosum).
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Affiliation(s)
- K Hosaka
- Experimental Farm, Kobe University, 1348 Uzurano, Kasai, 675-21, Hyogo, Japan
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Borisjuk N, Hemleben V. Nucleotide sequence of the potato rDNA intergenic spacer. PLANT MOLECULAR BIOLOGY 1993; 21:381-4. [PMID: 8425062 DOI: 10.1007/bf00019953] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The large intergenic spacer (IGS) of potato rDNA was sequenced and compared to the IGS sequence of tomato. Both spacers exhibit similar length and architecture. Absence of repeated elements down-stream of the putative transcription initiation site (TIS) in potato is compensated by the larger number of subrepeats upstream of the TIS. Especially high level of similarity (86% and 86.5%, respectively) is found in the AT-rich domain containing the TIS and the region approx. 800 bp upstream of the 18S rRNA gene.
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Affiliation(s)
- N Borisjuk
- Biologisches Institut der Universität Tübingen, Lehrstuhl für Allgemeine Genetik, Germany
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