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Giulia T, Vallauri G, Pavese V, Valentini N, Ruffa P, Botta R, Torello Marinoni D. Identification of the hazelnut cultivar in raw kernels and in semi-processed and processed products. Eur Food Res Technol 2022. [DOI: 10.1007/s00217-022-04058-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractThe request for an efficient traceability system able to identify hazelnut cultivars along the entire processing chain is becoming a critical point for avoiding fraudulent practices and safeguarding the interests of growers, food processors and consumers. In this study, DNA was extracted from different hazelnut matrices, including plant material (leaf, kernel and kernel episperm), and processed foods (paste, grain, flour and different types of snacks containing hazelnuts). The efficiency of Simple Sequence Repeat (SSR) markers was tested to identify the hazelnut cultivar ‘Tonda Gentile’ in all the supply chain. The analysis at 10 SSR loci was able to verify the presence/absence of the alleles of a declared cultivar contained in these matrices. The SSR analysis of DNA from raw episperm offers the possibility of identifying the mother cultivar and is suggested as an effective way to discover frauds since DNA analysis can be performed on individual kernels. For food matrices containing hazelnuts, the presence of the mother cultivar’s DNA can be assessed based on the identification of its alleles in the sample, although the presence of multiple alleles from the pollenizers makes the interpretation of results more difficult.
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Applicability of DNA traceability along the entire wine production chain in the real case of a large Italian cooperative winery. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.107929] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Stagnati L, Soffritti G, Martino M, Bortolini C, Lanubile A, Busconi M, Marocco A. Cocoa beans and liquor fingerprinting: A real case involving SSR profiling of CCN51 and “Nacional” varieties. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107392] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Endo T, Fujii H, Yoshioka T, Omura M, Shimada T. TaqMan-MGB SNP genotyping assay to identify 48 citrus cultivars distributed in the Japanese market. BREEDING SCIENCE 2020; 70:363-372. [PMID: 32714059 PMCID: PMC7372028 DOI: 10.1270/jsbbs.19142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 02/18/2020] [Indexed: 06/11/2023]
Abstract
A citrus cultivar identification system using CAPS marker has been developed on nursery trees, but this needs to be extended to include various product types, such as imported fruits and processed products. Here, we developed a new cultivar identification system using TaqMan-MGB SNP genotyping assay. Eight probe and primer sets were designed to amplify PCR fragments <100 bp to enable the genotyping of fresh and processed fruits in which predicted that insufficient quantities of DNA and residual impurities in the DNA extracts. The TaqMan-MGB SNP genotyping assay was stable and reproducible, and were confirmed to apply various sample sources, including leaves, fresh fruit, juice, canned fruit, and dry fruit. They could provide at least a single differentiating SNP to discriminate any paired combination among 48 citrus cultivars. Minimal marker subsets to identify the target cultivar were listed for each of 18 registered cultivars with valid patent. The allelic SNP genotypes of 48 citrus cultivars, which cover more than 98% of all citrus fruit shipment produced in Japan, is valuable for the referencing information in the DNA-based identification for fresh and processed fruits. This identification system will help protect registered cultivars and facilitate food fraud inspections.
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Affiliation(s)
- Tomoko Endo
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka 424-0292, Japan
| | - Hiroshi Fujii
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka 424-0292, Japan
| | - Terutaka Yoshioka
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka 424-0292, Japan
| | - Mitsuo Omura
- Faculty of Agriculture, Shizuoka University, Suruga, Shizuoka 422-8529, Japan
| | - Takehiko Shimada
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka 424-0292, Japan
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Thareja G, Mathew S, Mathew LS, Mohamoud YA, Suhre K, Malek JA. Genotyping-by-sequencing identifies date palm clone preference in agronomics of the State of Qatar. PLoS One 2018; 13:e0207299. [PMID: 30517143 PMCID: PMC6281209 DOI: 10.1371/journal.pone.0207299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 10/29/2018] [Indexed: 11/30/2022] Open
Abstract
Understanding the genetic diversity in a crop population is key to its targeted breeding for desired traits, such as higher yields, better fruit quality and resistance to disease and changing climates. Date fruits represent a major crop in the Middle East and are key to achieving future food independence in arid countries like Qatar. We previously determined the genome of the date palm Phoenix dactylifera and showed that date palm trees world-wide divide into two distinct subpopulations of Eastern and Western origins. Here we applied a resource of SNPs from 179 commercially available date fruits to assess the genetic diversity of date palm trees grown in the State of Qatar. We found that palm trees in Qatar are mainly of Eastern origin, and that their genetic diversity doesn’t associate with regions of the State. Together with targeted genetic assays, our resource can be used in the future for date palm cultivar identification, to aid selecting suitable cultivars for targeted breeding, to improve a country’s date palm genetic diversity, and to certify the origin of date fruits and trees.
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Affiliation(s)
- Gaurav Thareja
- Bioinformatics Core, Weill Cornell Medicine–Qatar, Doha, Qatar
| | - Sweety Mathew
- Bioinformatics Core, Weill Cornell Medicine–Qatar, Doha, Qatar
| | - Lisa S. Mathew
- Genomics Core, Weill Cornell Medicine–Qatar, Doha, Qatar
| | | | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine–Qatar, Doha, Qatar
- * E-mail: (KS); (JAM)
| | - Joel A. Malek
- Genomics Core, Weill Cornell Medicine–Qatar, Doha, Qatar
- * E-mail: (KS); (JAM)
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Lian DS, Zeng HS. Capillary Electrophoresis Based on Nucleic Acid Detection as Used in Food Analysis. Compr Rev Food Sci Food Saf 2017; 16:1281-1295. [DOI: 10.1111/1541-4337.12297] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/14/2017] [Accepted: 07/19/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Dong-Sheng Lian
- Guangzhou Women and Children's Medical Center of Guangzhou Medical University; NO. 9 at Jinsui Rd., Tianhe District Guangzhou Guangdong China
| | - Hua-Song Zeng
- Guangzhou Women and Children's Medical Center of Guangzhou Medical University; NO. 9 at Jinsui Rd., Tianhe District Guangzhou Guangdong China
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Baldina S, Picarella ME, Troise AD, Pucci A, Ruggieri V, Ferracane R, Barone A, Fogliano V, Mazzucato A. Metabolite Profiling of Italian Tomato Landraces with Different Fruit Types. FRONTIERS IN PLANT SCIENCE 2016; 7:664. [PMID: 27242865 PMCID: PMC4872001 DOI: 10.3389/fpls.2016.00664] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/29/2016] [Indexed: 05/18/2023]
Abstract
Increased interest toward traditional tomato varieties is fueled by the need to rescue desirable organoleptic traits and to improve the quality of fresh and processed tomatoes in the market. In addition, the phenotypic and genetic variation preserved in tomato landraces represents a means to understand the genetic basis of traits related to health and organoleptic aspects and improve them in modern varieties. To establish a framework for this approach, we studied the content of several metabolites in a panel of Italian tomato landraces categorized into three broad fruit type classes (flattened/ribbed, pear/oxheart, round/elongate). Three modern hybrids, corresponding to the three fruit shape typologies, were included as reference. Red ripe fruits were morphologically characterized and biochemically analyzed for their content in glycoalkaloids, phenols, amino acids, and Amadori products. The round/elongate types showed a higher content in glycoalkaloids, whereas flattened types had higher levels of phenolic compounds. Flattened tomatoes were also rich in total amino acids and in particular in glutamic acid. Multivariate analysis of amino acid content clearly separated the three classes of fruit types. Making allowance of the very low number of genotypes, phenotype-marker relationships were analyzed after retrieving single nucleotide polymorphisms (SNPs) among the landraces available in the literature. Sixty-six markers were significantly associated with the studied traits. The positions of several of these SNPs showed correspondence with already described genomic regions and QTLs supporting the reliability of the association. Overall the data indicated that significant changes in quality-related metabolites occur depending on the genetic background in traditional tomato germplasm, frequently according to specific fruit shape categories. Such a variability is suitable to harness association mapping for metabolic quality traits using this germplasm as an experimental population, paving the way for investigating their genetic/molecular basis, and facilitating breeding for quality-related compounds in tomato fruits.
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Affiliation(s)
- Svetlana Baldina
- Department of Agricultural and Forestry Sciences, University of TusciaViterbo, Italy
| | - Maurizio E. Picarella
- Department of Agricultural and Forestry Sciences, University of TusciaViterbo, Italy
| | - Antonio D. Troise
- Food Quality Design Group, Wageningen UniversityWageningen, Netherlands
- Department of Agricultural Sciences, University of Naples “Federico II”Napoli, Italy
| | - Anna Pucci
- Department of Agricultural and Forestry Sciences, University of TusciaViterbo, Italy
| | - Valentino Ruggieri
- Department of Agricultural Sciences, University of Naples “Federico II”Napoli, Italy
| | - Rosalia Ferracane
- Department of Agricultural Sciences, University of Naples “Federico II”Napoli, Italy
| | - Amalia Barone
- Department of Agricultural Sciences, University of Naples “Federico II”Napoli, Italy
| | - Vincenzo Fogliano
- Food Quality Design Group, Wageningen UniversityWageningen, Netherlands
| | - Andrea Mazzucato
- Department of Agricultural and Forestry Sciences, University of TusciaViterbo, Italy
- *Correspondence: Andrea Mazzucato
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Scarano D, Rao R, Masi P, Corrado G. SSR fingerprint reveals mislabeling in commercial processed tomato products. Food Control 2015. [DOI: 10.1016/j.foodcont.2014.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Shrestha S, Deleuran LC, Olesen MH, Gislum R. Use of multispectral imaging in varietal identification of tomato. SENSORS 2015; 15:4496-512. [PMID: 25690549 PMCID: PMC4367422 DOI: 10.3390/s150204496] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 02/08/2015] [Accepted: 02/09/2015] [Indexed: 11/16/2022]
Abstract
Multispectral imaging is an emerging non-destructive technology. In this work its potential for varietal discrimination and identification of tomato cultivars of Nepal was investigated. Two sample sets were used for the study, one with two parents and their crosses and other with eleven cultivars to study parents and offspring relationship and varietal identification respectively. Normalized canonical discriminant analysis (nCDA) and principal component analysis (PCA) were used to analyze and compare the results for parents and offspring study. Both the results showed clear discrimination of parents and offspring. nCDA was also used for pairwise discrimination of the eleven cultivars, which correctly discriminated upto 100% and only few pairs below 85%. Partial least square discriminant analysis (PLS-DA) was further used to classify all the cultivars. The model displayed an overall classification accuracy of 82%, which was further improved to 96% and 86% with stepwise PLS-DA models on high (seven) and poor (four) sensitivity cultivars, respectively. The stepwise PLS-DA models had satisfactory classification errors for cross-validation and prediction 7% and 7%, respectively. The results obtained provide an opportunity of using multispectral imaging technology as a primary tool in a scientific community for identification/discrimination of plant varieties in regard to genetic purity and plant variety protection/registration.
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Affiliation(s)
- Santosh Shrestha
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse 4200, Denmark.
| | - Lise Christina Deleuran
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse 4200, Denmark.
| | - Merete Halkjær Olesen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse 4200, Denmark.
| | - René Gislum
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse 4200, Denmark.
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Corrado G, Piffanelli P, Caramante M, Coppola M, Rao R. SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato. BMC Genomics 2013; 14:835. [PMID: 24279304 PMCID: PMC4046682 DOI: 10.1186/1471-2164-14-835] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 11/20/2013] [Indexed: 11/10/2022] Open
Abstract
Background The tomato (Solanum lycopersium L.) is the most widely grown vegetable in the world. It was domesticated in Latin America and Italy and Spain are considered secondary centers of diversification. This food crop has experienced severe genetic bottlenecks and modern breeding activities have been characterized by trait introgression from wild species and divergence in different market classes. Results With the aim to examine patterns of polymorphism, characterize population structure and identify putative loci under positive selection, we genotyped 214 tomato accessions (which include cultivated landraces, commercial varieties and wild relatives) using a custom-made Illumina SNP-panel. Most of the 175 successfully scored SNP loci were found to be polymorphic. Population structure analysis and estimates of genetic differentiation indicated that landraces constitute distinct sub-populations. Furthermore, contemporary varieties could be separated in groups (processing, fresh and cherry) that are consistent with the recent breeding aimed at market-class specialization. In addition, at the 95% confidence level, we identified 30, 34 and 37 loci under positive selection between landraces and each of the groups of commercial variety (cherry, processing and fresh market, respectively). Their number and genomic locations imply the presence of some extended regions with high genetic variation between landraces and contemporary varieties. Conclusions Our work provides knowledge concerning the level and distribution of genetic variation within cultivated tomato landraces and increases our understanding of the genetic subdivision of contemporary varieties. The data indicate that adaptation and selection have led to a genomic signature in cultivated landraces and that the subpopulation structure of contemporary varieties is shaped by directed breeding and largely of recent origin. The genomic characterization presented here is an essential step towards a future exploitation of the available tomato genetic resources in research and breeding programs. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-14-835) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Giandomenico Corrado
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, via Università 100, 80055 Portici, NA, Italy.
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Sardaro MLS, Marmiroli M, Maestri E, Marmiroli N. Genetic characterization of Italian tomato varieties and their traceability in tomato food products-Sardaro-2012-Food Science & Nutrition-Wiley Online Library. Food Sci Nutr 2013; 1:54-62. [PMID: 24804014 PMCID: PMC3951568 DOI: 10.1002/fsn3.8] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/29/2012] [Accepted: 10/29/2012] [Indexed: 12/12/2022] Open
Abstract
Genetic diversity underlies the improvement of crops by plant breeding. Landraces of tomato (Solanum lycopersicum L.) can contain valuable alleles not common in modern germplasms. The aim was to measure genetic diversity present in 47 most common tomato varieties grown in Italy, 35 were varieties used for processing and 12 were landraces considered “salad varieties”. Furthermore, we demonstrated the possibility that the variety traceability can be extended through the entire production chain. Diversity was measured using 11 microsatellite markers and 94 genotypes. Among the markers used, a total of 48 alleles were detected. A dendrogram based on total microsatellite polymorphism grouped 47 varieties into three major clusters at 0.75 similarity coefficient, differentiating the modern varieties from tomatoes landraces. The DNA markers developed confirmed the possibility to support the genotype identification all along the tomato production chain. The number of alleles and genotypes identified in the present work is the largest considering papers on food traceability.
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Affiliation(s)
- Maria Luisa Savo Sardaro
- Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy
| | - Marta Marmiroli
- Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy
| | - Elena Maestri
- Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy
| | - Nelson Marmiroli
- Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy
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Manoj-Kumar A, Reddy KN, Manjulatha M, Blanco L. Polysaccharide-free nucleic acids and proteins of Abelmoschus esculentus for versatile molecular studies. Mol Biol 2012. [DOI: 10.1134/s0026893312030065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Korir NK, Han J, Shangguan L, Wang C, Kayesh E, Zhang Y, Fang J. Plant variety and cultivar identification: advances and prospects. Crit Rev Biotechnol 2012; 33:111-25. [PMID: 22698516 DOI: 10.3109/07388551.2012.675314] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Plant variety and cultivar identification is one of the most important aspects in agricultural systems. The large number of varieties or landraces among crop plants has made it difficult to identify and characterize varieties solely on the basis of morphological characters because they are non stable and originate due to environmental and climatic conditions, and therefore phenotypic plasticity is an outcome of adaptation. To mitigate this, scientists have developed and employed molecular markers, statistical tests and software to identify and characterize the required plant cultivars or varieties for cultivation, breeding programs as well as for cultivar-right-protection. The establishment of genome and transcriptome sequencing projects for many crops has led to generation of a huge wealth of sequence information that could find much use in identification of plants and their varieties. We review the current status of plant variety and cultivar identification, where an attempt has been made to describe the different strategies available for plant identification. We have found that despite the availability of methods and suitable markers for a wide range of crops, there is dearth of simple ways of making both morphological descriptors and molecular markers easy, referable and practical to use although there are ongoing attempts at making this possible. Certain limitations present a number of challenges for the development and utilization of modern scientific methods in variety or cultivar identification in many important crops.
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Affiliation(s)
- Nicholas Kibet Korir
- College of Horticulture, Nanjing Agricultural University, Weigang, Nanjing, China
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Tedeschi T, Calabretta A, Bencivenni M, Manicardi A, Corrado G, Caramante M, Corradini R, Rao R, Sforza S, Marchelli R. A PNA microarray for tomato genotyping. MOLECULAR BIOSYSTEMS 2011; 7:1902-7. [PMID: 21465054 DOI: 10.1039/c1mb05048f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The design and development of a PNA microarray designed for the simultaneous identification of several SNPs characteristic of seven different tomato varieties is described. Highly selective arginine-based monomer containing PNAs (Arg-PNAs) have been used in order to obtain very selective probes. Seven modified PNA probes were synthesised and their binding properties in solution were studied. PNA-microarrays based on these probes were prepared and applied to SNP discrimination in model experiments using oligonucleotide mixtures simulating the different sequences of the seven tomato varieties. The strength and the limitations of such a system for SNP recognition are thoroughly discussed.
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Affiliation(s)
- Tullia Tedeschi
- Dipartimento di Chimica Organica e Industriale, University of Parma, Parco Area delle Scienze 17a, I-43124, Parma, Italy
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