Quantitative trait loci-based genomics-assisted prediction for the degree of apple fruit cover color

Apple fruit cover color is an important appearance trait determining fruit quality, high degree of fruit cover color or completely red fruit skin is also the ultimate breeding goal. MdMYB1 has repeatedly been reported as a major gene controlling apple fruit cover color. There are also multiple minor-effect genes affecting degree of fruit cover color (DFC). This study was to identify genome-wide quantitative trait loci (QTLs) and to develop genomics-assisted prediction for apple DFC. The DFC phenotype data of 9,422 hybrids from five full-sib families of Malus asiatica 'Zisai Pearl', M. domestica 'Red Fuji', 'Golden Delicious', and 'Jonathan' were collected in 2014-2017. The phenotype varied considerably among hybrids with the same MdMYB1 genotype. Ten QTLs for DFC were identified using MapQTL and bulked segregant analysis via sequencing. From these QTLs, ten candidate genes were predicted, including MdMYB1 from a year-stable QTL on chromosome 9 of 'Zisai Pearl' and 'Red Fuji'. Then, kompetitive allele-specific polymerase chain reaction (KASP) markers were designed on these candidate genes and 821 randomly selected hybrids were genotyped. The genotype effects of the markers were estimated. MdMYB1-1 (represented by marker H162) exhibited a partial dominant allelic effect on MdMYB1-2 and showed non-allelic epistasis on markers H1245 and G6. Finally, a non-additive QTL-based genomics assisted prediction model was established for DFC. The Pearson's correlation coefficient between the genomic predicted value and the observed phenotype value was 0.5690. These results can be beneficial for apple genomics-assisted breeding and may provide insights for understanding the mechanism of fruit coloration.