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

•Genetic analysis indicated that the fruit skin color of sweet cherry was controlled by a single locus, and the yellow fruit skin color was recessive to blush and red.•Using a mapping-by-sequencing approach, a ∼90 kb deletion on chromosome 3 containing PavMYB10.1 TF was found to be an nonfunctional allele, PavMYB10.1Del, responsible for responsible for anthocyanin deficiency in yellow-skinned varieties.•Two functional alleles of PavMYB10.1, PavMYB10.1a and PavMYB10.1b, causally lead to red or blush fruit skin color in sweet cherry.•Marker-trait association analysis revealed strong co-segregation of the fruit skin color phenotype and EFC markers in F1 populations and a set of advanced breeding selections.