Development of an efficient molecular-marker assisted selection strategy for berry color in grapevine

Marker-assisted selection (MAS) represents one of the most effective strategies to reduce costs and time in plant breeding programs. MAS benefits from the identification of markers in strong linkage disequilibrium (LD) with causative genes and from the development of fast, scalable, and reproducible screening techniques. In grape, berry color is a valuable trait, highly related to the sensory characteristics of fresh grape and wine quality. The present work aims to develop a MAS strategy to select skin color by High-Resolution Melting (HRM), a 'close-tube' method capable of detecting polymorphisms within PCR-amplified DNA fragments. To identify molecular markers associated with the berry skin color phenotypic trait, the total genome of 3 white-berry and 3 red-berry accessions were sequenced using Illumina technology and aligned to the reference genome PN40024 v4. The sequencing results revealed the presence of three highly polymorphic regions on chromosome 2 between 15 Kbp and 17 Kbp for red berry genotypes. HRM analyses were carried out on a total of 95 genotypes, 70 of which comprised a berry color segregating population: ['Italia' (white berry) x cv 'Crimson Seedless' (red berry)] and 25 genotypes belonging to a commercial grapevine germplasm collection consisting of 11 red and 14 white berry accessions. The HRM profiles of the three regions tested strongly correlated with the phenotypic trait of color. The results of this work represent an effective, fast, and reliable genotyping strategy that enables the discrimination of genotypes based on the presence or absence of berry pigmentation.