Allelic composition of MdMYB1 drives red skin color intensity in apple (Malus x domestica Borkh.) and its application to breeding

Since apple fruit skin reddens poorly under warmer climates, new apple cultivars are desired that are adapted to global warming in terms of bearing well-reddened fruit. We developed a simple sequence repeat marker, Mdo.chr9.4, which is suitable for red skin color selection. It amplified four alleles (Mdo.chr9.4-R-0, Mdo.chr9.4-Y-3, Mdo.chr9.4-Y-9, and Mdo.chr9.4-Y-15) distinguished by length. Mdo. chr9.4-R-0 associated with MdMYB1-1 which confers red fruit skin. The presence of Mdo. chr9.4-R-0 was consistent with empirical skin color in all 160 tested accessions. Mdo. chr9.4 was identified as the only significant marker that contributed to red skin color intensity by a genome wide association study (GWAS), and it accounted for 52.0% of phenotypic variation, confirming that MdMYB1 was the major and principal determinant of fruit skin color in apples. Individuals with a homozygous state of Mdo.chr9.4-R-0 (dose 2) were significantly redder than those showing a heterozygote state (dose 1) in both the accession set and full-sib families, indicating a partially dominant effect of MdMYB1-1. Therefore, the selection of dose 2 individuals would target individuals with intensive red skin. We applied Mdo.chr9.4 to several application populations using a time and cost-efficient genotyping system developed in the present study. This system, along with Mdo.chr9.4, provide advanced marker-assisted breeding for intensive red skin color apples adapted to a global warming climate.