QTL mapping of juice color in a Vitis interspecific hybrid ‘Chambourcin’-based population

Abstract

Berry juice color plays a critical role in determining grape and wine quality, influencing consumer preferences and market appeal. Whilemost prior research has concentrated on berry skin pigmentation, studies examining juice color remain limited. This work explores the genetic basis of juice color in an F1 population of 273 genotypes derived from the Vitis interspecific hybrid ‘Chambourcin’ and V. vinifera‘Cabernet Sauvignon.’ To evaluate juice color, a nine-category visual scoring system was developed based on OIV 225 and complemented by quantitative, image-based measurements of CIELAB parameters (L*, a*, b*), Hue, and Chroma. Additionally, a high-density linkage map was constructed with 421 simple sequence repeats (SSR) and 2,011 RNase H2-dependent amplicon sequencing (rhAmpSeq)-derived haplotype markers that clustered into 19 linkage groups (LGs). Across four harvest years, a stable quantitative trait locus (QTL) for juice color was identified on LG 2 within a 4.8 cM interval. Two rhAmpSeq-derived markers within this QTL region (rh_chr2_14239122 andrh_chr2_14464718) flank three MYBAgenes associated with anthocyanin biosynthesis.

Haplotypes at these two markers were used to screen 1,512 genotypes from the USDA–ARS cold-hardy Vitis Collection in Geneva, NY, resulting in the identification of 72 accessions carrying at least one of the target haplotype combinations.

Among these, 70 (97.2 %) were classified as Noir-skinned based on data from the Vitis International Variety Catalogue (VIVC). This high level of concordance was achieved despite the potential influence of the Gret1 retrotransposon and the possibility of recombination eventsin the region, both of which can affect berry juice color. Collectively, these findings facilitate marker-assisted selection and enhanceinsight into the genetic regulation of anthocyanin-related traits.

Acknowledgements

This study is supported by the Specialty Crop Research Initiative Competitive Grant, Award No. 2022-51181-38240, and Capacity Building Grants for Non-Land Grant College of Agriculture, Award No. 2023-70001-40990, from the USDA National Institute of Food and Agriculture. This study is also supported by the Missouri Specialty Crop Block Grant Program, Award No. 23SCBPMO1196, from the USDAAgricultural Marketing Service.