Genetic variation and association analyses identify genes linked to fruit set-related traits in grapevine

Grapevine is one of the most valuable fruit crops in the world. Adverse environmental conditions reduce fruit quality and crop yield, so understanding the genetic and molecular mechanisms determining crop yield components is essential to optimize grape production. The analysis of a diverse collection of grapevine cultivars allowed us to evaluate the relationship between fruit set-related components of yield, including the incidence of reproductive disorders such as coulure and millerandage. The collection displayed a great phenotypic variation that we surveyed in a genetics association study using 15, 309 single nucleotide polymorphisms (SNPs) detected in the sequence of 289 candidate genes scattered across the 19 grapevine linkage groups. After correcting statistical models for population structure and linkage disequilibrium effects, 164 SNPs from 34 of these genes were found to associate with fruit set-related traits, supporting a complex polygenic determinism. Many of them were found in the sequence of different putative MADS-box transcription factors, a gene family related with plant reproductive development control. In addition, we observed an additive effect of some of the associated SNPs on the phenotype, suggesting that advantageous alleles from different loci could be pyramided to generate superior cultivars with optimized fruit production

Genetic diversity and parentage of Tunisian wild and cultivated grapevines (Vitis vinifera L.) as revealed by single nucleotide polymorphism (SNP) markers

Based on 261 single nucleotide polymorphism (SNP) markers, we analyzed 57 grapevine genotypes, consisting of 29 wild grapevines (Vitis vinifera subsp. sylvestris) prospected from the northwest part of Tunisia and 28 cultivated accessions (V. vinifera subsp. vinifera) maintained in the repository of the Arid Land Institute of Medenine (Tunisia). Pair-wise multilocus comparison with the ICVV SNP database allowed the identification of 13 cultivated genotypes, including ten synonymous groups with known Mediterranean or international varieties, three cases of color sports, and two misnomers. Genotypic analysis showed a high level of genetic diversity for both wild and cultivated groups. Multivariate and structure analyses clearly differentiated wild from cultivated grapevines and showed high average posterior probabilities of assignment to their group of origin. The clustering results largely supported the perceived classification and reflect that most of the present Tunisian cultivated varieties do not derive directly from the local wild populations but could correspond to materials introduced from different locations during historical times. Parentage analysis allowed the determination of the genetic origin of four Tunisian cultivars, "Garai", "Jerbi" (from Kerkennah), "Mahdoui", and "Reine de Vignes faux", and showed that "Heptakilo" and "Planta Fina", two old and widely distributed varieties in the Mediterranean basin, had an important role in the origin of Tunisian grapevines. The present study demonstrates the efficacy of SNP makers for germplasm characterization and genetic studies in grapevine. © 2014 Springer-Verlag Berlin Heidelberg

Pedigree analysis of the Spanish grapevine cultivar 'Heben'

The use of Single Nucleotide Polymorphism (SNP) markers allows genetic identification and parentage analysis of grapevine cultivars. Ancient cultivars like 'Heben' were widely cultivated in the Iberian Peninsula along its history and likely contributed to the origin of varieties which are still cultivated today. The goal of our study was to search for possible first-degree relationships between the female variety 'Heben' and other Iberian and Mediterranean cultivars. For this purpose, we used a set of 261 SNP markers which allowed identifying 23 trios and 37 parent-offspring relationships supported by high overall likelihood ratios (LOD scores). The results shed light on the relationships among several cultivars from Spain and Portugal, and demonstrated that 'Heben' is a major founder of current varieties in the Iberian Peninsula viticulture, and contributed to spread the chlorotype A in this region

Grapevine cultivar 'Alfrocheiro' or 'Brunal' plays a primary role in the relationship among Iberian grapevines

The grapevine cultivar known in Portugal as 'Alfrocheiro', and in Spain as 'Bastardo Negro', 'Brunal' or 'Baboso Negro', plays a central role in the genetic network of the Iberian Peninsula grapevine cultivars. Three sets of different molecular markers, SNPs, nS-SRs and cpSSRs, revealed more than twenty parentoffspring links with this cultivar. 'Alfrocheiro' chlorotype is definitely Western European but their parents are still unknown. The distribution of the cultivar, their offspring as well as the two main co-parents direct to a geographic origin around the Portuguese and Spanish border. This cultivar and their progenies represent about 15 % of the total grapevine acreage in Portugal, stressing the importance of 'Alfrocheiro' in the Portuguese wine character