Genetic diversity and signature of divergence in the genome of grapevine clones of Southern Italy varieties

Clizia Villano; Silvia Procino; Giuseppe Blaiotta; Domenico Carputo; Nunzio D'Agostino; Ermanno Di Serio; Valentina Fanelli; Pierfederico La Notte; Monica Marilena Miazzi; Cinzia Montemurro; Francesca Taranto; Riccardo Aversano

doi:10.3389/fpls.2023.1201287

Genetic diversity and signature of divergence in the genome of grapevine clones of Southern Italy varieties

Front Plant Sci. 2023 Sep 13:14:1201287. doi: 10.3389/fpls.2023.1201287. eCollection 2023.

Authors

Affiliations

¹ Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
² Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy.
³ Institute of Biosciences and Bioresources (CNR-IBBR), Bari, Italy.
⁴ Support Unit Bari, Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Bari, Italy.
⁵ SINAGRI S.r.l., Spin Off of the University of Bari Aldo Moro, Bari, Italy.

Abstract

Sexual reproduction has contributed to a significant degree of variability in cultivated grapevine populations. However, the additional influence of spontaneous somatic mutations has played a pivotal role in shaping the diverse landscape of grapevine agrobiodiversity. These naturally occurring selections, termed 'clones,' represent a vast reservoir of potentially valuable traits and alleles that hold promise for enhancing grape quality and bolstering plant resilience against environmental and biotic challenges. Despite their potential, many of these clones remain largely untapped.In light of this context, this study aims to delve into the population structure, genetic diversity, and distinctive genetic loci within a collection of 138 clones derived from six Campanian and Apulian grapevine varieties, known for their desirable attributes in viticulture and winemaking. Employing two reduced representation sequencing methods, we extracted Single-Nucleotide Polymorphism (SNP) markers. Population structure analysis and fixation index (FST) calculations were conducted both between populations and at individual loci. Notably, varieties originating from the same geographical region exhibited pronounced genetic similarity.The resulting SNP dataset facilitated the identification of approximately two hundred loci featuring divergent markers (FST ≥ 0.80) within annotated exons. Several of these loci exhibited associations with essential traits like phenotypic adaptability and environmental responsiveness, offering compelling opportunities for grapevine breeding initiatives. By shedding light on the genetic variability inherent in these treasured traditional grapevines, our study contributes to the broader understanding of their potential. Importantly, it underscores the urgency of preserving and characterizing these valuable genetic resources to safeguard their intra-varietal diversity and foster future advancements in grapevine cultivation.

Keywords: Vitis vinifera; divergent loci; double digest restriction associated DNA; genotyping by sequencing; intra-varietal diversity; molecular markers.

Grants and funding

This research was supported by the INDIGENA (CUP G12C21000190003), RINNOVALA (CUP J92C20001030009), and DICOVALE (CUP B24I19000450009) projects, all funded by the Campania Region, under the Rural Development Program 2014/2020, Measure 16.1, Action 2. The research was also supported by the Apulia Region within the PSR Puglia 2014-2020 REGEVIP project, (CUP B17H22003530009); Misura 10-Pagamenti agro-climatico-ambientali; Sottomisura 10.2-Sostegno per la conservazione, l’uso e lo sviluppo sostenibili delle risorse genetiche in agricoltura; Operazione 10.2.1-Progetti per la conservazione e valorizzazione. This study was also carried out within the Agritech National Research Center and received funding from the European Union Next- GenerationEU (PIANO NAZIONALE DI RIPRESA E RESILIENZA 6 (PNRR) – MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 – D.D. 1032 17/06/2022, CN00000022).