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Open AccessArticle

Marginal Grapevine Germplasm from Apulia (Southern Italy) Represents an Unexplored Source of Genetic Diversity

1
Department of Soil, Plant and Food Sciences (DISSPA), University of Bari, Via Amendola 165, 70126 Bari, Italy
2
Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, Italy
3
Research, Experimentation and Education Centre in Agriculture “Basile Caramia” (CRSFA), Via Cisternino 281, 70010 Locorotondo, Italy
4
Department of Agricultural and Environmental Sciences, University of Bari Aldo Moro, Via Amendola 165, 70126 Bari, Italy
5
SINAGRI S.r.l.—Spin Off of the University of Bari Aldo Moro, 70126 Bari, Italy
6
Institute of Plant Virology—Support Unit Grugliasco, National Research Council of Italy (CNR), Via L. da Vinci 44, 10095 Grugliasco, Italy
7
Institute for Sustainable Plant Protection–Support Unit Bari, National Research Council of Italy (CNR), Via Amendola 122/D, 70126 Bari, Italy
8
Institute of Biosciences and Bioresources (CNR-IBBR), National Research Council of Italy, Research Division Portici, 80055 Portici, Italy
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Agronomy 2020, 10(4), 563; https://doi.org/10.3390/agronomy10040563
Received: 6 March 2020 / Revised: 9 April 2020 / Accepted: 11 April 2020 / Published: 14 April 2020
(This article belongs to the Special Issue Bioinformatics Applied to Genetic Improvement of Crop Species)
The investigation on the genetic diversity of grapevine germplasm is crucial for a more efficient use of grapevine genetic resources in light of changing environmental conditions. Here, we used simple sequence repeats (SSRs) coupled with single nucleotide polymorphism (SNP) markers to disclose grapevine genetic diversity of a collection of Apulian minor/neglected genotypes. Their relationships with national or international cultivars were also examined. Genetic diversity was investigated using 10 SSR markers and 1,178 SNPs generated by genotyping by sequencing (GBS). Based on the SSR data, the 128 genotypes were classified into six main genetic clusters. Twenty-four putative cases of synonymy and 2 of misnamings were detected. Ten “unknown” autochthonous genotypes did not show high similarity to Apulian, national, or international varieties. We took advantage of available GBS-derived SNP data points for only forty genotypes to better investigate the genetic distance among them, identify private SNP alleles, and divergent loci putatively under selection. Based on SNP alleles, two interesting gene pools of minor/neglected Apulian samples were identified. Genetic divergence was investigated by FST and allowed the detection of loci capable of differentiating the gene pools. Overall, this work emphasizes the need for recovering the untapped genetic variability that characterizes minor/neglected grapevine Apulian genotypes and the requirement to preserve and use more efficiently grapevine genetic resources in breeding programs. View Full-Text
Keywords: grapevine; SSR; genotyping by sequencing; SNP; genetic diversity; private alleles; divergent loci grapevine; SSR; genotyping by sequencing; SNP; genetic diversity; private alleles; divergent loci
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Miazzi, M.M.; D’Agostino, N.; di Rienzo, V.; Venerito, P.; Savino, V.N.; Fucilli, V.; Ruffa, P.; Roseti, V.; Pirolo, C.; La Notte, P.; Montemurro, C.; Taranto, F. Marginal Grapevine Germplasm from Apulia (Southern Italy) Represents an Unexplored Source of Genetic Diversity. Agronomy 2020, 10, 563.

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