High Resolution Melting DNA analysis for the traceability of plants and juices of blond and pigmented sweet orange
The economic relevance of sweet orange [Citrus sinensis (L.) Osbeck] raised the interest for the set-up of robust and scalable methods to assess the origin of plants and derived products. Molecular markers, such as singlenucleotide polymorphisms (SNPs), represent a robust tool for the univocal ide...
| Main Authors: | , , , , , , , |
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| Format: | Artículo |
| Language: | Inglés |
| Published: |
ELSEVIER
2025
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| Subjects: | |
| Online Access: | https://hdl.handle.net/20.500.11939/9077 https://www.sciencedirect.com/science/article/pii/S2666154325001267?via%3Dihub |
| _version_ | 1855492619685068800 |
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| author | Seminara, Sebastiano Bennici, Stefania Scollo, Francesco Di Guardo, Mario Aleza, Pablo La Malfa, Stefano Gentile, Alessandra Gaetano, Stefano |
| author_browse | Aleza, Pablo Bennici, Stefania Di Guardo, Mario Gaetano, Stefano Gentile, Alessandra La Malfa, Stefano Scollo, Francesco Seminara, Sebastiano |
| author_facet | Seminara, Sebastiano Bennici, Stefania Scollo, Francesco Di Guardo, Mario Aleza, Pablo La Malfa, Stefano Gentile, Alessandra Gaetano, Stefano |
| author_sort | Seminara, Sebastiano |
| collection | ReDivia |
| description | The economic relevance of sweet orange [Citrus sinensis (L.) Osbeck] raised the interest for the set-up of robust
and scalable methods to assess the origin of plants and derived products. Molecular markers, such as singlenucleotide
polymorphisms (SNPs), represent a robust tool for the univocal identification of the genetic origin
of a specific cultivar (or group of accessions) with relevant application for traceability.
In this work, the whole-genome sequencing of 29 accessions representing the four varietal groups of sweet
orange (i.e.: Common, Navel, Acidless and Pigmented) allowed the in silico detection of unique SNPs to
discriminate each group (group-specific SNPs) and ten pigmented orange accessions (genotype-specific SNPs).
A subset of the SNPs detected in silico was then validated through a high-resolution melting assay (HRM) on
additional 81 genotypes held in three ex-situ collections in Italy and Spain and on several matrices: leaves, handsqueezed
and commercial fresh-squeezed juices, processed orange juices, and beverages. The HRM assay allowed
the identification of 13 group-specific and 30 genotype-specific SNPs showing consistent results across the whole
germplasm and the different food matrices tested. The HRM assay proved its efficacy also for the identification of
juice blending with other sweet orange varieties (with a detection limit of 5 %). The identified unique SNPs
represent a valuable tool to trace the varietal correspondence of plants and fruit-derived products. Their
implementation with a scalable and robust HRM assay could be readily employed by growers and the food
processing industry to ensure traceability along the chain. |
| format | Artículo |
| id | ReDivia9077 |
| institution | Instituto Valenciano de Investigaciones Agrarias (IVIA) |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | ELSEVIER |
| publisherStr | ELSEVIER |
| record_format | dspace |
| spelling | ReDivia90772025-07-07T10:38:36Z High Resolution Melting DNA analysis for the traceability of plants and juices of blond and pigmented sweet orange Seminara, Sebastiano Bennici, Stefania Scollo, Francesco Di Guardo, Mario Aleza, Pablo La Malfa, Stefano Gentile, Alessandra Gaetano, Stefano Single nucleotide polymorphism (SNP) HRM Mislabelling Whole genome sequencing Juice blending true-to-type analysis F30 Plant genetics and breeding Citrus sinensis The economic relevance of sweet orange [Citrus sinensis (L.) Osbeck] raised the interest for the set-up of robust and scalable methods to assess the origin of plants and derived products. Molecular markers, such as singlenucleotide polymorphisms (SNPs), represent a robust tool for the univocal identification of the genetic origin of a specific cultivar (or group of accessions) with relevant application for traceability. In this work, the whole-genome sequencing of 29 accessions representing the four varietal groups of sweet orange (i.e.: Common, Navel, Acidless and Pigmented) allowed the in silico detection of unique SNPs to discriminate each group (group-specific SNPs) and ten pigmented orange accessions (genotype-specific SNPs). A subset of the SNPs detected in silico was then validated through a high-resolution melting assay (HRM) on additional 81 genotypes held in three ex-situ collections in Italy and Spain and on several matrices: leaves, handsqueezed and commercial fresh-squeezed juices, processed orange juices, and beverages. The HRM assay allowed the identification of 13 group-specific and 30 genotype-specific SNPs showing consistent results across the whole germplasm and the different food matrices tested. The HRM assay proved its efficacy also for the identification of juice blending with other sweet orange varieties (with a detection limit of 5 %). The identified unique SNPs represent a valuable tool to trace the varietal correspondence of plants and fruit-derived products. Their implementation with a scalable and robust HRM assay could be readily employed by growers and the food processing industry to ensure traceability along the chain. 2025-07-07T10:38:35Z 2025-07-07T10:38:35Z 2025 article publishedVersion Seminara, S., Bennici, S., Scollo, F., Di Guardo, M., Aleza, P., La Malfa, S., ... & Distefano, G. (2025). High Resolution Melting DNA analysis for the traceability of plants and juices of blond and pigmented sweet orange. Journal of Agriculture and Food Research, 21, 101755. 2666-1543 https://hdl.handle.net/20.500.11939/9077 10.1016/j.jafr.2025.101755 https://www.sciencedirect.com/science/article/pii/S2666154325001267?via%3Dihub en This work was funded by the Ministero dell’Istruzione dell’Universit`a e della Ricerca—DD.MM. n. 1061/2021 e 1062/2021 nell’ambito dell’Azione IV.4—‘Dottorati e contratti di ricerca su tema tiche dell’innovazione’ del nuovo Asse IV del PON Ricerca e Innovazione 2014–2020 ‘Istruzione e ricerca per il recupero REACT-EU’ (CUP E69J21011300006 and E61B21004310007), University of Catania and AAT Oranfresh spa and the project ‘Valutazione di genotipi di agrumi per l’individuazione di fonti di resistenza a stress biotici e abiotici’ (Linea 3 del Piano della Ricerca di Ateneo 2020, University of Catania). Attribution-NonCommercial-NoDerivatives 4.0 Internacional http://creativecommons.org/licenses/by-nc-nd/4.0/ openAccess ELSEVIER electronico |
| spellingShingle | Single nucleotide polymorphism (SNP) HRM Mislabelling Whole genome sequencing Juice blending true-to-type analysis F30 Plant genetics and breeding Citrus sinensis Seminara, Sebastiano Bennici, Stefania Scollo, Francesco Di Guardo, Mario Aleza, Pablo La Malfa, Stefano Gentile, Alessandra Gaetano, Stefano High Resolution Melting DNA analysis for the traceability of plants and juices of blond and pigmented sweet orange |
| title | High Resolution Melting DNA analysis for the traceability of plants and juices of blond and pigmented sweet orange |
| title_full | High Resolution Melting DNA analysis for the traceability of plants and juices of blond and pigmented sweet orange |
| title_fullStr | High Resolution Melting DNA analysis for the traceability of plants and juices of blond and pigmented sweet orange |
| title_full_unstemmed | High Resolution Melting DNA analysis for the traceability of plants and juices of blond and pigmented sweet orange |
| title_short | High Resolution Melting DNA analysis for the traceability of plants and juices of blond and pigmented sweet orange |
| title_sort | high resolution melting dna analysis for the traceability of plants and juices of blond and pigmented sweet orange |
| topic | Single nucleotide polymorphism (SNP) HRM Mislabelling Whole genome sequencing Juice blending true-to-type analysis F30 Plant genetics and breeding Citrus sinensis |
| url | https://hdl.handle.net/20.500.11939/9077 https://www.sciencedirect.com/science/article/pii/S2666154325001267?via%3Dihub |
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