Two noir juice color-associated markers identified from a 'Chambourcin'-based population demonstrate broad applicability across Vitis germplasm.

Berry juice color is one of the key factors influencing grape and wine quality, consumer preference, and marketability. While most previous studies on berry color have focused on the skin, research on juice color remains limited. This study validated the utility of RNase H2-dependent amplicon sequencing (rhAmpSeq)-derived microhaplotype marker system for investigating the genetic basis of berry juice color in a hybrid population derived from the Vitis interspecific hybrid 'Chambourcin' and V. vinifera 'Cabernet Sauvignon'. A new nine-category visual scoring system, based on OIV 225, was developed to assess juice color. To achieve comprehensive precision and quantitative analysis, CIELAB parameters (L*, a*, b*), Hue, and Chroma were extracted from image-based measurements. Using berries harvested over four different years, a stable quantitative trait locus (QTL) associated with juice color was identified on linkage group (LG) 2 spanning a 4.8 cM interval. Two rhAmpSeq markers within the QTL peak region (rh_chr2_14239122 and rh_chr2_14464718) flank three MYBA genes involved in anthocyanin synthesis. This locus coincides with the region controlling berry skin color, highlighting the effectiveness of the rhAmpSeq platform for genetic analysis of color-related traits. Haplotypes associated with the pigmentation alleles at these two markers were used to identify Noir varieties in a diversity panel with 97.2% accuracy. This was accomplished by assessing a germplasm collection representing 1,512 genotypes, including various Vitis species, from the USDA-ARS cold-hardy Vitis Collection in Geneva, NY, USA. These findings not only demonstrate the excellent cross-species transferability of rhAmpSeq-derived markers but also provide a valuable resource for marker-assisted selection in grape breeding programs, enabling the development of cultivars with specific juice color traits and advancing understanding of the genetic regulation of anthocyanin-related characteristics.