Development of molecular markers for fruit skin color in Japanese plum (Prunus salicina Lindl.)

Abstract

Japanese plum is a diploid fruit tree species, member of the Rosaceae family, generated by hybridization of Prunus salicina with diverse Prunus species. Cultivars show great variability for fruit skin and flesh color, which are both major objectives in plum breeding. Subsequently, molecular markers for early selection of these traits in breeding programs are highly desirable. Despite candidate genes for fruit color have been identified in several Rosaceae species, no markers have been described for Japanese plum yet. In Rosaceae family, MYB10 transcription factor has been described as the main gene determining anthocyanin pigment accumulation, which is responsible for red, purple and black coloration. In order to design a useful marker for marker-assisted selection (MAS), we have explored the variability of the MYB10 gene group in Japanese plum and its association with fruit color. Primers designed in peach (Prunus persica) conserved MYB10 domains were used to genotype a collection of P. salicina cultivars and several progenies. Allele cloning identified 12 MYB10 amplicons. Homology and segregation analysis in progenies allowed assigning some of them to five loci, homologous to the three MYB10 genes located in peach LG3, suggesting the duplication of the MYB10.1 peach gene. Whole genome-resequencing with Illumina technology of two varieties with contrasting phenotypes allowed full gene cloning and detection of polymorphisms. Our data identified one dominant allele associated with anthocyanin accumulation in the skin and two other recessive alleles associate with yellow/green skin phenotypes. Current work is focusing in the design of a marker specifically targeting the associated alleles. This marker will be validated in a wider germplasm collection of commercial varieties and segregating progenies. Future assembly of long-range reads of a red variety will give more insight into the complexity of the region, and will serve for other P.salicina genomic studies.