Genetic structure and molecular diversity of Brazilian grapevine germplasm: Management and use in breeding programs

Abstract

The management of germplasm banks is complex, especially when many accessions are involved. Microsatellite markers are an efficient tool for assessing the genetic diversity of germplasm collections, optimizing their use in breeding programs. This study genetically characterizes a large collection of 410 grapevine accessions maintained at the Agronomic Institute of Campinas (IAC) (Brazil). The accessions were genotyped with 17 highly polymorphic microsatellite markers. Genetic data were analyzed to determine the genetic structure of the germplasm, quantify its allelic diversity, suggest the composition of a core collection, and discover cases of synonymy, duplication, and misnaming. A total of 304 alleles were obtained, and 334 unique genotypes were identified. The molecular profiles of 145 accessions were confirmed according to the literature and databases, and the molecular profiles of more than 100 genotypes were reported for the first time. The analysis of the genetic structure revealed different levels of stratification. The primary division was between accessions related to Vitis vinifera and V. labrusca, followed by their separation from wild grapevine. A core collection of 120 genotypes captured 100% of all detected alleles. The accessions selected for the core collection may be used in future phenotyping efforts, in genome association studies, and for conservation purposes. Genetic divergence among accessions has practical applications in grape breeding programs, as the choice of relatively divergent parents will maximize the frequency of progeny with superior characteristics. Together, our results can enhance the management of grapevine germplasm and guide the efficient exploitation of genetic diversity to facilitate the development of new grape cultivars for fresh fruits, wine, and rootstock.

Genetic Diversity of Armenian Grapevine (Vitis vinifera L.) Germplasm: Molecular Characterization and Parentage Analysis

“…Nuclear simple sequence repeats (nSSRs) or microsatellites are the most appropriate and efficient markers which are co-dominant, highly polymorphic, and easily transferable across related Vitis species. They are widely used primarily for the differentiation and identification of cultivars, parentage analysis, and genetic mapping [ 24 , 25 , 26 , 27 , 28 , 29 , 30 ].…”

Genetic diversity, population structure and parentage analysis of Brazilian grapevine hybrids after half a century of genetic breeding

“…PCR was performed using forward primers labeled with fluorescent dyes (6-FAM, PET, VIC, or NED), and amplification was conducted as described by De Oliveira et al (2020). Capillary electrophoresis was conducted in an ABI 3500 (Applied Biosystems, Foster City, CA, USA).…”

Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops

“…Both national and international databases with SSR marker information have been developed for the identification of cultivars (e.g., Pl@ntGrape, le catalogue des vignes cultivées en France Vitis , ; Swiss Vitis microsatellite database [ 88 ]; International Variety Catalog (VIVC), ). An internationally developed set of nine SSR loci is used as a standard for large-scale screening of Vitis genetic resource collections [ 1 , 89 , 90 ]. The SSR methodology developed for cultivated grapes ( V. vinifera L.) is applied also to other Vitis species [ 91 ], such as V. riparia Michx, V. rupestris Scheele, and V. berlandieri Planch., which are used as rootstocks and donors of important traits.…”