Large-fragment deletion encompasses the R2R3 MYB transcription factor, PavMYB10.1, causes yellow fruits in sweet cherry (Prunus avium L.)

Abstract

Due to different accumulation and distribution patterns of anthocyanin, the fruits of sweet cherry (Prunus avium L.) display considerable color variation, ranging from yellow, blush to dark red. Yellow-skinned sweet cherries are characterized by the absence of anthocyanin in the fruits, providing a good candidate for research on yellow coloration in sweet cherry fruits. In this study, we identified the underlying genetic mechanism by integrating BSA-seq, RNA-seq, whole-genome sequencing and marker-trait association analyses. A ∼90 kb deletion on chromosome 3 containing PavMYB10.1 TF was found to be an nonfunctional allele, PavMYB10.1Del, responsible for yellow fruit skin. Other two functional alleles of PavMYB10.1, PavMYB10.1a and PavMYB10.1b, result in red or blush skin color. Furthermore, evaluation of variant-trait association in F1 populations and a set of advanced breeding selections revealed strong co-segregation of the fruit skin color phenotypes and the EFC marker which combined by primers specific to PavMYB10.1a/b and PavMYB10.1Del separately. These results provide novel insights into yellow fruit skin coloration in sweet cherry and represent a useful tool for the pre-selection of fruit color in molecular-assisted breeding programs.