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Open AccessArticle

Single Nucleotide Polymorphisms as Practical Molecular Tools to Support European Chestnut Agrobiodiversity Management

1
C.R.E.A. Council for Agricultural Research and Economics—Research Centre for Olive, Fruits and Citrus Crops, Via Torrino 2, 81100 Caserta, Italy
2
Biomeets Consulting, ITNIG—Carrer d’Àlaba, 6108005 Barcelona, Spain
3
National Research Council (CNR), Institute of Biosciences and BioResources (IBBR), Via Università 133, 80055 Portici (NA), Italy
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2020, 21(13), 4805; https://doi.org/10.3390/ijms21134805
Received: 15 June 2020 / Revised: 2 July 2020 / Accepted: 6 July 2020 / Published: 7 July 2020
(This article belongs to the Collection Genetics and Molecular Breeding in Plants)
European chestnut orchards are multifunctional agroforestry systems with a key role in environmental management. Their biodiversity is at risk of erosion and farmers do not have enough tools to protect and valorize traditional ecotypes. In particular, cost effective and reliable molecular markers for cultivar identification are lacking. The aim of this research was to develop a new molecular tool for varietal identification in European chestnuts. A set of cultivars was preliminarily characterized to evaluate the range of genetic diversity using random amplified polymorphic DNA (RAPD) markers. The genetic distances indicated a sufficiently wide variability range among tested genotypes and confirmed they were suitable for our goal. A single nucleotide polymorphism (SNP) mining within 64 expressed sequence tags (EST), covering all the linkage groups, was performed by high-resolution melting (HRM) and validated by target resequencing. Fifty-six SNPs were retrieved by monitoring the variability present on the whole set of considered cultivars in loci uniformly distributed on the genome. A subset of 37 SNPs was finally transformed into kompetitive allele-specific PCR (KASP) markers that were successfully evaluated for varietal discrimination. Three assays (C1083, G0115 and A5096) were identified as necessary and sufficient for distinguishing among the tested cultivars. The developed tools can be effectively exploited by stakeholders for improving the management of the European chestnut genetic resources. View Full-Text
Keywords: Castanea sativa; cultivar; molecular markers; DNA polymorphism; RAPD; EST; HRM; SNP; KASP Castanea sativa; cultivar; molecular markers; DNA polymorphism; RAPD; EST; HRM; SNP; KASP
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MDPI and ACS Style

Nunziata, A.; Ruggieri, V.; Petriccione, M.; De Masi, L. Single Nucleotide Polymorphisms as Practical Molecular Tools to Support European Chestnut Agrobiodiversity Management. Int. J. Mol. Sci. 2020, 21, 4805.

AMA Style

Nunziata A, Ruggieri V, Petriccione M, De Masi L. Single Nucleotide Polymorphisms as Practical Molecular Tools to Support European Chestnut Agrobiodiversity Management. International Journal of Molecular Sciences. 2020; 21(13):4805.

Chicago/Turabian Style

Nunziata, Angelina; Ruggieri, Valentino; Petriccione, Milena; De Masi, Luigi. 2020. "Single Nucleotide Polymorphisms as Practical Molecular Tools to Support European Chestnut Agrobiodiversity Management" Int. J. Mol. Sci. 21, no. 13: 4805.

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