Development of seven SNP molecular markers based on the key genes related to red colour of fruit skin in Japanese apricot ( Prunus mume )

Fruit color is an important factor that affects its quality. The red-skinned cultivars of Japanese apricot ( Prunus mume Sieb. et Zucc.) have high medicinal economic benefits and are mainly used for deep-processed products because of their eye-catching red pigmentation. In contrast, molecular markers related to the red color trait in Japanese apricot fruit haven’t been reported. This study identified twenty-eight SNPs markers based on genome resequencing data. The average number of alleles per SNP marker site in red and green-skinned groups of Japanese apricot cultivars was 1.9643, with heterozygosity ranging from 0.02 to 0.75, and an average Shannon index of 0.517 and 0.4420, respectively, indicating high dispersion and diversity. The total germplasm was divided into two (K = 2) clusters, including 10 and 34. Most red-skinned Japanese apricot cultivars were classified as cluster I, showing the significant genetic difference between the two cultivar groups ( Fst = 0.54). According to PIC values, a total of seven SNPs markers showed high polymorphism ( PIC > 0.5), including PmSNP_1 ( 4-CL ), PmSNP_4 ( WD40 ), PmSNP_5 ( MYB29 ), PmSNP_18 ( UFGT6 ) and PmSNP_27 ( UFGT3 ) that were highly correlated with red color trait. Among them, PmUFGT3 exhibited the highest polymorphism, which is significant for future research on developing and utilizing germplasm resources related to red fruit skin.