Fig. 4

GWAS of flesh color around the stone. a Manhattan plot of flesh color around the stone on chromosome 3 (top) and LD plot of the 200-kb region surrounding the most significant signal. The dotted black line indicates the highest signal for this trait. Color for each box in LD plot represents LD relationship, showing increasing LD from white to red color. The number in each box represents the LD value multiplied by 100. b Two different alleles of PpMYB10.1. WT allele stands for the reference allele, while the ALT allele is the alternate allele that has a 487-bp deletion (DEL) in its promoter. c Allelotypes of the deletion in the promoter of PpMYB10.1 observed in 295 peach accessions and their relationship with flesh color around the stone. The white color represents no red color around the stone, while the red-pink color stands for red color around the stone. d Relative expression of PpMYB10.1 during fruit development determined by qRT-PCR. “TJ” is a red-fleshed cultivar and “HK” is a white-fleshed cultivar. The fruit ripens at 95 days after full bloom (DAFB). e Promoter activity analysis by dual-luciferase assay. 0/0 stands for the reference promoter sequence, while 1/1 represents the promoter with a 487-bp deletion