Genetic Diversity and Structure in a Spanish Grape Germplasm Collection Assessed by SSR Markers

Abstract

Background and Aims. Vitis vinifera L. is a major global horticulture crop which holds historical connections contributing to the development of human culture. The main objective of the study was to explore the genetic diversity and structure of grapes curated at the germplasm bank of Aragón and link them to cultivar utilization, putative geographic origin, and historical events. Methods and Results. The genetic diversity of the 411 accessions of the Grapevine Germplasm Bank was assessed using 26 SSR markers. SSR markers VVIP31, VMC4F3-1, VVIV67, and VVS2 distinguished the 156 nonredundant genotypes found in the collection. The profiles were compared to the El Encin database, and 105 were identified as known cultivars, of which 93 were Spanish, 12 were from other European origins, and 51 others were not known. The 51 profiles, as they were all collected in Spain, were designated as Spanish unknown for further analysis. To establish a comparative study for principal coordinate analysis (PCoA) and structure, we kept 113 identified genotypes from this collection but added 61 representative genotypes with diverse European and oriental origins. Bayesian analysis and PCoA showed four distinct groups of grape cultivars: (1) traditional Spanish wine grape from Aragón or cultivated along the Ebro River, (2) Spanish wine grape, (3) Spanish and oriental table grape, and (4) Italian, Portuguese, French, and German-Slovenian wine grape varieties. Conclusions. The 51 unknown Spanish genotypes were not registered yet in any European commercial list and are of special interest. These genotypes could be ancient cultivars adapted to local climatic and environmental conditions and probably resilient to face the new conditions derived from climate change.

Analysis of Wine-Producing Vitis vinifera L. Biotypes, Autochthonous to Crete (Greece), Employing Ampelographic and Microsatellite Markers

“…The estimated average value of genetic diversity (expected heterozygosity, He) for tested genotypes was 0.7991 and was lower than this found in northern Greece cultivars by [ 2 ] and from three Anatolian locations [ 54 ]. Moreover, He was higher than [ 24 ], who studied 1378 wild and cultivated grapevines collected around the Mediterranean basin and from Central Asia; higher than [ 12 ] who studied 15 Georgian aboriginal cultivars and 42 individuals of wild grapevine from different regions of Georgia and adjacent Turkey, higher than [ 17 ] who studied 411 accessions of Spanish Vitis germplasm, higher than [ 55 ] where 196 grapevine samples from five countries of the Western Balkan region assessed with SSR markers and also higher than [ 30 ] who studied 222 cultivated ( Vitis vinifera ) and 22 wild ( V. vinifera ssp. sylvestris) grape accessions.…”

“…In Greece, traditionally ampelographic descriptors, which are based on the comparison of their morphology were used [ 4 , 5 ] until the discovery of DNA-based markers such as Random Amplified Length Polymorphism (RAPD [ 6 ]), Inter Simple Sequence Repeats (ISSR, [ 7 ]) and Simple Sequence Repeats (SSR, [ 8 , 9 , 10 ]). SSR markers have become the preferred markers for the standardization and analysis of genetic variation with regard to grapevine genetic resources, as numerous studies prove [ 2 , 3 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 ]. Studies use SSR in order to distinguish grape cultivars, for example, in Cyprus molecular genotyping analysis using 11 SSR markers allowed the accurate identification and discrimination of a set of autochthonous cultivars, clarifying their relationship with Greek, Bulgarian, and western European Vitis genetic material [ 13 ].…”

“…Sardinian grapevine cultivars were genotyped with SSR markers towards accurate identification of indigenous cultivars, resolving issues of synonyms/homonyms and false name assigning [ 16 ]. Other studies completing this scope can be also mentioned such as [ 17 ] where 411 accessions of the Grapevine Germplasm Bank were assessed using 26 SSR markers in Spain. SSRs remain the markers of choice in recent years, e.g., in 2022, in Argentina discrimination of cultivars was accomplished with SSR markers [ 18 ].…”