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Sweet Cherry Diversity and Relationships in Modern and Local Varieties Based on SNP Markers

The sweet cherry is an important fruit species that is widespread globally. In addition to the well-known traditional and modern varieties, a myriad of landraces is present in Europe, as well as in southern Italy. This study aims to evaluate the population structure, genetic relationships, and cases...

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Autores principales: Palasciano, Marino, Zuluaga, Diana L., Cerbino, Domenico, Blanco, Emanuela, Aufiero, Gaetano, D’Agostino, Nunzio, Sonnante, Gabriella
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9824393/
https://www.ncbi.nlm.nih.gov/pubmed/36616264
http://dx.doi.org/10.3390/plants12010136
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author Palasciano, Marino
Zuluaga, Diana L.
Cerbino, Domenico
Blanco, Emanuela
Aufiero, Gaetano
D’Agostino, Nunzio
Sonnante, Gabriella
author_facet Palasciano, Marino
Zuluaga, Diana L.
Cerbino, Domenico
Blanco, Emanuela
Aufiero, Gaetano
D’Agostino, Nunzio
Sonnante, Gabriella
author_sort Palasciano, Marino
collection PubMed
description The sweet cherry is an important fruit species that is widespread globally. In addition to the well-known traditional and modern varieties, a myriad of landraces is present in Europe, as well as in southern Italy. This study aims to evaluate the population structure, genetic relationships, and cases of duplicate samples in a collection of 143 accessions using GBS-derived SNP markers. The genetic material under investigation includes modern commercial varieties, ancient European and American varieties, landraces, and individuals retrieved from small orchards. Some of the known varieties were genetically analyzed here for the first time. In addition, several genotypes were collected from the Basilicata region (southern Italy), an area largely unexplored for sweet cherry genetic resources. The relationships among genotypes were assessed using four different methods: allele frequency and ancestry estimation, principal component analysis, Neighbor-Joining tree, and identity-by-state estimation. The analyses returned quite congruent results and highlighted the presence of four main genetic groups, namely: (i) American varieties, (ii) the ‘Germersdorfer-Ferrovia’ cluster, (iii) the ‘Burlat’ group, and (iv) the group of Italian landraces. The main drivers of clustering were ancestry, geographical distribution, and some important traits such as self-compatibility. The sweet cherries from Basilicata, herewith examined for the first time, were mostly distributed within the group of Italian landraces, being particularly linked to the autochthonous varieties of the Campania region. However, some genotypes were outside this group, thus suggesting the introduction of genetic material from other Italian regions or from European countries. The considerable amount of American and European modern varieties analyzed are genetically very closely related, suggesting a reduced genetic basis. In addition, we highlighted the discriminating ability of SNP markers to distinguish between an original variety and its mutant. Overall, our results may be useful in defining conservation strategies for sweet cherry germplasm and developing future breeding programs to enlarge the genetic basis of commercial varieties.
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spelling pubmed-98243932023-01-08 Sweet Cherry Diversity and Relationships in Modern and Local Varieties Based on SNP Markers Palasciano, Marino Zuluaga, Diana L. Cerbino, Domenico Blanco, Emanuela Aufiero, Gaetano D’Agostino, Nunzio Sonnante, Gabriella Plants (Basel) Article The sweet cherry is an important fruit species that is widespread globally. In addition to the well-known traditional and modern varieties, a myriad of landraces is present in Europe, as well as in southern Italy. This study aims to evaluate the population structure, genetic relationships, and cases of duplicate samples in a collection of 143 accessions using GBS-derived SNP markers. The genetic material under investigation includes modern commercial varieties, ancient European and American varieties, landraces, and individuals retrieved from small orchards. Some of the known varieties were genetically analyzed here for the first time. In addition, several genotypes were collected from the Basilicata region (southern Italy), an area largely unexplored for sweet cherry genetic resources. The relationships among genotypes were assessed using four different methods: allele frequency and ancestry estimation, principal component analysis, Neighbor-Joining tree, and identity-by-state estimation. The analyses returned quite congruent results and highlighted the presence of four main genetic groups, namely: (i) American varieties, (ii) the ‘Germersdorfer-Ferrovia’ cluster, (iii) the ‘Burlat’ group, and (iv) the group of Italian landraces. The main drivers of clustering were ancestry, geographical distribution, and some important traits such as self-compatibility. The sweet cherries from Basilicata, herewith examined for the first time, were mostly distributed within the group of Italian landraces, being particularly linked to the autochthonous varieties of the Campania region. However, some genotypes were outside this group, thus suggesting the introduction of genetic material from other Italian regions or from European countries. The considerable amount of American and European modern varieties analyzed are genetically very closely related, suggesting a reduced genetic basis. In addition, we highlighted the discriminating ability of SNP markers to distinguish between an original variety and its mutant. Overall, our results may be useful in defining conservation strategies for sweet cherry germplasm and developing future breeding programs to enlarge the genetic basis of commercial varieties. MDPI 2022-12-27 /pmc/articles/PMC9824393/ /pubmed/36616264 http://dx.doi.org/10.3390/plants12010136 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Palasciano, Marino
Zuluaga, Diana L.
Cerbino, Domenico
Blanco, Emanuela
Aufiero, Gaetano
D’Agostino, Nunzio
Sonnante, Gabriella
Sweet Cherry Diversity and Relationships in Modern and Local Varieties Based on SNP Markers
title Sweet Cherry Diversity and Relationships in Modern and Local Varieties Based on SNP Markers
title_full Sweet Cherry Diversity and Relationships in Modern and Local Varieties Based on SNP Markers
title_fullStr Sweet Cherry Diversity and Relationships in Modern and Local Varieties Based on SNP Markers
title_full_unstemmed Sweet Cherry Diversity and Relationships in Modern and Local Varieties Based on SNP Markers
title_short Sweet Cherry Diversity and Relationships in Modern and Local Varieties Based on SNP Markers
title_sort sweet cherry diversity and relationships in modern and local varieties based on snp markers
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9824393/
https://www.ncbi.nlm.nih.gov/pubmed/36616264
http://dx.doi.org/10.3390/plants12010136
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