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Santos S, Oliveira M, Amorim A, van Asch B. A forensic perspective on the genetic identification of grapevine (Vitis vinifera L.) varieties using STR markers. Electrophoresis 2014; 35:3201-7. [PMID: 25146979 DOI: 10.1002/elps.201400107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 08/10/2014] [Accepted: 08/12/2014] [Indexed: 11/07/2022]
Abstract
The grapevine (Vitis vinifera subsp. vinifera) is one of the most important agricultural crops worldwide. A long interest in the historical origins of ancient and cultivated current grapevines, as well as the need to establish phylogenetic relationships and parentage, solve homonymies and synonymies, fingerprint cultivars and clones, and assess the authenticity of plants and wines has encouraged the development of genetic identification methods. STR analysis is currently the most commonly used method for these purposes. A large dataset of grapevines genotypes for many cultivars worldwide has been produced in the last decade using a common set of recommended dinucleotide nuclear STRs. This type of marker has been replaced by long core-repeat loci in standardized state-of-the-art human forensic genotyping. The first steps toward harmonized grapevine genotyping have already been taken to bring the genetic identification methods closer to human forensic STR standards by previous authors. In this context, we bring forward a set of basic suggestions that reinforce the need to (i) guarantee trueness-to-type of the sample; (ii) use the long core-repeat markers; (iii) verify the specificity and amplification consistency of PCR primers; (iv) sequence frequent alleles and use these standardized allele ladders; (v) consider mutation rates when evaluating results of STR-based parentage and pedigree analysis; (vi) genotype large and representative samples in order to obtain allele frequency databases; (vii) standardize genotype data by establishing allele nomenclature based on repeat number to facilitate information exchange and data compilation.
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Affiliation(s)
- Sara Santos
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal; Faculdade de Ciências da Universidade do Porto, Porto, Portugal
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Genotyping of Vitis vinifera L. within the Slovak national collection of genetic resources. Open Life Sci 2014. [DOI: 10.2478/s11535-014-0314-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractMicrosatellites were used as a very effective tool for genetic diversity analysis and characterization of 51 grapevine (Vitis vinifera L.) accessions from the national collection of genetic resources. Genetic diversity was relatively high, 8.91 alleles were detected per analysed microsatellite locus in average, and fifty-one accessions were distinguished into 45 groups. Distribution of recent Slovak cultivars across the dendrogram accented both their genetic diversity and the effectiveness of the national breeding program in maintaining genetic diversity and generating new genetic variants. Each cultivar was different from the others and twelve of them contained 77.6% of the total genetic diversity of the whole analysed set. Microsatellite patterns were also able to confirm parentage in selected Slovak cultivars. An unusual phenomenon of triallelism was also detected in one of the analysed accessions. The present study has initiated molecular characterization within the national grapevine genetic resource collection and their comparison with well-established international cultivars.
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Wu B, Zhong GY, Yue JQ, Yang RT, Li C, Li YJ, Zhong Y, Wang X, Jiang B, Zeng JW, Zhang L, Yan ST, Bei XJ, Zhou DG. Identification of pummelo cultivars by using a panel of 25 selected SNPs and 12 DNA segments. PLoS One 2014; 9:e94506. [PMID: 24732455 PMCID: PMC3986212 DOI: 10.1371/journal.pone.0094506] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 03/17/2014] [Indexed: 11/18/2022] Open
Abstract
Pummelo cultivars are usually difficult to identify morphologically, especially when fruits are unavailable. The problem was addressed in this study with the use of two methods: high resolution melting analysis of SNPs and sequencing of DNA segments. In the first method, a set of 25 SNPs with high polymorphic information content were selected from SNPs predicted by analyzing ESTs and sequenced DNA segments. High resolution melting analysis was then used to genotype 260 accessions including 55 from Myanmar, and 178 different genotypes were thus identified. A total of 99 cultivars were assigned to 86 different genotypes since the known somatic mutants were identical to their original genotypes at the analyzed SNP loci. The Myanmar samples were genotypically different from each other and from all other samples, indicating they were derived from sexual propagation. Statistical analysis showed that the set of SNPs was powerful enough for identifying at least 1000 pummelo genotypes, though the discrimination power varied in different pummelo groups and populations. In the second method, 12 genomic DNA segments of 24 representative pummelo accessions were sequenced. Analysis of the sequences revealed the existence of a high haplotype polymorphism in pummelo, and statistical analysis showed that the segments could be used as genetic barcodes that should be informative enough to allow reliable identification of 1200 pummelo cultivars. The high level of haplotype diversity and an apparent population structure shown by DNA segments and by SNP genotypes, respectively, were discussed in relation to the origin and domestication of the pummelo species.
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Affiliation(s)
- Bo Wu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Guang-yan Zhong
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- * E-mail:
| | - Jian-qiang Yue
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Science, Dehong, Yunnan, China
| | - Run-ting Yang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Chong Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Yue-jia Li
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yun Zhong
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xuan Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Bo Jiang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ji-wu Zeng
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Li Zhang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shu-tang Yan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Xue-jun Bei
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Dong-guo Zhou
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Science, Dehong, Yunnan, China
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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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Singh N, Choudhury DR, Singh AK, Kumar S, Srinivasan K, Tyagi RK, Singh NK, Singh R. Comparison of SSR and SNP markers in estimation of genetic diversity and population structure of Indian rice varieties. PLoS One 2013; 8:e84136. [PMID: 24367635 PMCID: PMC3868579 DOI: 10.1371/journal.pone.0084136] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 11/12/2013] [Indexed: 12/02/2022] Open
Abstract
Simple sequence repeat (SSR) and Single Nucleotide Polymorphic (SNP), the two most robust markers for identifying rice varieties were compared for assessment of genetic diversity and population structure. Total 375 varieties of rice from various regions of India archived at the Indian National GeneBank, NBPGR, New Delhi, were analyzed using thirty six genetic markers, each of hypervariable SSR (HvSSR) and SNP which were distributed across 12 rice chromosomes. A total of 80 alleles were amplified with the SSR markers with an average of 2.22 alleles per locus whereas, 72 alleles were amplified with SNP markers. Polymorphic information content (PIC) values for HvSSR ranged from 0.04 to 0.5 with an average of 0.25. In the case of SNP markers, PIC values ranged from 0.03 to 0.37 with an average of 0.23. Genetic relatedness among the varieties was studied; utilizing an unrooted tree all the genotypes were grouped into three major clusters with both SSR and SNP markers. Analysis of molecular variance (AMOVA) indicated that maximum diversity was partitioned between and within individual level but not between populations. Principal coordinate analysis (PCoA) with SSR markers showed that genotypes were uniformly distributed across the two axes with 13.33% of cumulative variation whereas, in case of SNP markers varieties were grouped into three broad groups across two axes with 45.20% of cumulative variation. Population structure were tested using K values from 1 to 20, but there was no clear population structure, therefore Ln(PD) derived Δk was plotted against the K to determine the number of populations. In case of SSR maximum Δk was at K=5 whereas, in case of SNP maximum Δk was found at K=15, suggesting that resolution of population was higher with SNP markers, but SSR were more efficient for diversity analysis.
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Affiliation(s)
- Nivedita Singh
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, New Delhi, Delhi, India
| | - Debjani Roy Choudhury
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, New Delhi, Delhi, India
| | - Amit Kumar Singh
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, New Delhi, Delhi, India
| | - Sundeep Kumar
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, New Delhi, Delhi, India
| | - Kalyani Srinivasan
- Germplasm Conservation Division, National Bureau of Plant Genetic Resources, New Delhi, Delhi, India
| | - R. K. Tyagi
- Germplasm Conservation Division, National Bureau of Plant Genetic Resources, New Delhi, Delhi, India
| | - N. K. Singh
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, New Delhi, Delhi, India
- * E-mail:
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Nicolè S, Barcaccia G, Erickson DL, Kress JW, Lucchin M. The coding region of the UFGT gene is a source of diagnostic SNP markers that allow single-locus DNA genotyping for the assessment of cultivar identity and ancestry in grapevine (Vitis vinifera L.). BMC Res Notes 2013; 6:502. [PMID: 24298902 PMCID: PMC4222114 DOI: 10.1186/1756-0500-6-502] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 11/23/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Vitis vinifera L. is one of society's most important agricultural crops with a broad genetic variability. The difficulty in recognizing grapevine genotypes based on ampelographic traits and secondary metabolites prompted the development of molecular markers suitable for achieving variety genetic identification. FINDINGS Here, we propose a comparison between a multi-locus barcoding approach based on six chloroplast markers and a single-copy nuclear gene sequencing method using five coding regions combined with a character-based system with the aim of reconstructing cultivar-specific haplotypes and genotypes to be exploited for the molecular characterization of 157 V. vinifera accessions. The analysis of the chloroplast target regions proved the inadequacy of the DNA barcoding approach at the subspecies level, and hence further DNA genotyping analyses were targeted on the sequences of five nuclear single-copy genes amplified across all of the accessions. The sequencing of the coding region of the UFGT nuclear gene (UDP-glucose: flavonoid 3-0-glucosyltransferase, the key enzyme for the accumulation of anthocyanins in berry skins) enabled the discovery of discriminant SNPs (1/34 bp) and the reconstruction of 130 V. vinifera distinct genotypes. Most of the genotypes proved to be cultivar-specific, and only few genotypes were shared by more, although strictly related, cultivars. CONCLUSION On the whole, this technique was successful for inferring SNP-based genotypes of grapevine accessions suitable for assessing the genetic identity and ancestry of international cultivars and also useful for corroborating some hypotheses regarding the origin of local varieties, suggesting several issues of misidentification (synonymy/homonymy).
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Affiliation(s)
- Silvia Nicolè
- Laboratory of Plant Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis - Viale Università 16, 35020 Padova, Legnaro, Italy
| | - Gianni Barcaccia
- Laboratory of Plant Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis - Viale Università 16, 35020 Padova, Legnaro, Italy
| | - David L Erickson
- Department of Botany and Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012 USA
| | - John W Kress
- Department of Botany and Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012 USA
| | - Margherita Lucchin
- Laboratory of Plant Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis - Viale Università 16, 35020 Padova, Legnaro, Italy
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57
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Riahi L, Ayari B, Zoghlami N, Dereeper A, Laucou V, Mliki A, This P. High efficiency and informativeness of a set of SNP molecular markers in Tunisian local grapevines discrimination. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.08.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Bolger ME, Weisshaar B, Scholz U, Stein N, Usadel B, Mayer KFX. Plant genome sequencing - applications for crop improvement. Curr Opin Biotechnol 2013; 26:31-7. [PMID: 24679255 DOI: 10.1016/j.copbio.2013.08.019] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 08/24/2013] [Accepted: 08/26/2013] [Indexed: 10/26/2022]
Abstract
It is over 10 years since the genome sequence of the first crop was published. Since then, the number of crop genomes sequenced each year has increased steadily. The amazing pace at which genome sequences are becoming available is largely due to the improvement in sequencing technologies both in terms of cost and speed. Modern sequencing technologies allow the sequencing of multiple cultivars of smaller crop genomes at a reasonable cost. Though many of the published genomes are considered incomplete, they nevertheless have proved a valuable tool to understand important crop traits such as fruit ripening, grain traits and flowering time adaptation.
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Affiliation(s)
- Marie E Bolger
- RWTH Aachen University, IBMG Institute for Botany and Molecular Genetics, Aachen, Germany
| | - Bernd Weisshaar
- CeBiTec, Department of Biology, Bielefeld University, Bielefeld, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland (OT) Gatersleben, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland (OT) Gatersleben, Germany
| | - Björn Usadel
- RWTH Aachen University, IBMG Institute for Botany and Molecular Genetics, Aachen, Germany; IBG-2: Plant Sciences, Institute for Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany.
| | - Klaus F X Mayer
- MIPS, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany
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Emanuelli F, Lorenzi S, Grzeskowiak L, Catalano V, Stefanini M, Troggio M, Myles S, Martinez-Zapater JM, Zyprian E, Moreira FM, Grando MS. Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape. BMC PLANT BIOLOGY 2013; 13:39. [PMID: 23497049 PMCID: PMC3610244 DOI: 10.1186/1471-2229-13-39] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 02/27/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND The economic importance of grapevine has driven significant efforts in genomics to accelerate the exploitation of Vitis resources for development of new cultivars. However, although a large number of clonally propagated accessions are maintained in grape germplasm collections worldwide, their use for crop improvement is limited by the scarcity of information on genetic diversity, population structure and proper phenotypic assessment. The identification of representative and manageable subset of accessions would facilitate access to the diversity available in large collections. A genome-wide germplasm characterization using molecular markers can offer reliable tools for adjusting the quality and representativeness of such core samples. RESULTS We investigated patterns of molecular diversity at 22 common microsatellite loci and 384 single nucleotide polymorphisms (SNPs) in 2273 accessions of domesticated grapevine V. vinifera ssp. sativa, its wild relative V. vinifera ssp. sylvestris, interspecific hybrid cultivars and rootstocks. Despite the large number of putative duplicates and extensive clonal relationships among the accessions, we observed high level of genetic variation. In the total germplasm collection the average genetic diversity, as quantified by the expected heterozygosity, was higher for SSR loci (0.81) than for SNPs (0.34). The analysis of the genetic structure in the grape germplasm collection revealed several levels of stratification. The primary division was between accessions of V. vinifera and non-vinifera, followed by the distinction between wild and domesticated grapevine. Intra-specific subgroups were detected within cultivated grapevine representing different eco-geographic groups. The comparison of a phenological core collection and genetic core collections showed that the latter retained more genetic diversity, while maintaining a similar phenotypic variability. CONCLUSIONS The comprehensive molecular characterization of our grape germplasm collection contributes to the knowledge about levels and distribution of genetic diversity in the existing resources of Vitis and provides insights into genetic subdivision within the European germplasm. Genotypic and phenotypic information compared in this study may efficiently guide further exploration of this diversity for facilitating its practical use.
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Affiliation(s)
- Francesco Emanuelli
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
| | - Silvia Lorenzi
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
| | - Lukasz Grzeskowiak
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
| | - Valentina Catalano
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
| | - Marco Stefanini
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
| | - Michela Troggio
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
| | - Sean Myles
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, B2N 5E3, Canada
| | - José M Martinez-Zapater
- Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), C/ Madre de dios 51, Logroño, 26006, Spain
| | - Eva Zyprian
- JKI Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, 76833, Germany
| | - Flavia M Moreira
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
- Instituto Federal de Santa Catarina, Rua José Lino Kretzer 608 - Praia Comprida, São José, Santa Catarina, 88130-310, Brasil
| | - M Stella Grando
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
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Lacombe T, Boursiquot JM, Laucou V, Di Vecchi-Staraz M, Péros JP, This P. Large-scale parentage analysis in an extended set of grapevine cultivars (Vitis vinifera L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:401-14. [PMID: 23015217 DOI: 10.1007/s00122-012-1988-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 09/15/2012] [Indexed: 05/06/2023]
Abstract
Inheritance of nuclear microsatellite markers (nSSR) has been proved to be a powerful tool to verify or uncover the parentage of grapevine cultivars. The aim of the present study was to undertake an extended parentage analysis using a large sample of Vitis vinifera cultivars held in the INRA "Domaine de Vassal" Grape Germplasm Repository (France). A dataset of 2,344 unique genotypes (i.e. cultivars without synonyms, clones or mutants) identified using 20 nSSR was analysed with FAMOZ software. Parentages showing a logarithm of odds score higher than 18 were validated in relation to the historical data available. The analysis first revealed the full parentage of 828 cultivars resulting in: (1) 315 original full parentages uncovered for traditional cultivars, (2) 100 full parentages confirming results established with molecular markers in prior papers and 32 full parentages that invalidated prior results, (3) 255 full parentages confirming pedigrees as disclosed by the breeders and (4) 126 full parentages that invalidated breeders' data. Second, incomplete parentages were determined in 1,087 cultivars due to the absence of complementary parents in our cultivar sample. Last, a group of 276 genotypes showed no direct relationship with any other cultivar in the collection. Compiling these results from the largest set of parentage data published so far both enlarges and clarifies our knowledge of the genetic constitution of cultivated V. vinifera germplasm. It also allows the identification of the main genitors involved in varietal assortment evolution and grapevine breeding.
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Affiliation(s)
- Thierry Lacombe
- UMR AGAP, Equipe Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes, INRA, 2 Place Viala, 34060 Montpellier, France.
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