Microsatellite marker development and population structure analysis in japanese apricot (Prunus mume sieb. et zucc.)

Abstract

Japanese apricot (Prunus mume Sieb. et Zucc.) is one of the major fruit tree crops in Japan. However, a paucity of molecular tools has limited studies on the species’ genetic diversity and clone identification. Therefore, we newly designed 201 microsatellite markers using the P. mume reference genome and selected 20 highly polymorphic markers. The markers showed higher polymorphism detectability than those previously developed using peach and apricot genomes. They were used successfully for fingerprinting most of the Prunus cultivars examined (124 P. mume accessions and one accession each of P. armeniaca, P. salicina, P. persica, and P. dulcis), and the resulting genotype data were used to examine the genetic differentiation of six Japanese apricot cultivar groups, including those producing normal fruit, small-fruit, and ornamental flowers, as well as Taiwanese cultivars, putative hybrids of P. armeniaca and P. mume, and putative hybrids of P. salicina and P. mume. Phylogenetic cluster analysis showed three clades with high support values; one clade comprised the putative P. armeniaca × P. mume hybrids, and the two others included Taiwanese and ornamental cultivars. The rest of the accessions were grouped into two wide clusters, but not clearly divided into the respective cultivar groups. These complex relationships were supported by the principal coordinate and STRUCTURE analyses. Since Japanese apricot is thought to have originated in China, many factors such as human preference, geographical separation, introgression, and local breeding, may have been involved to form the present complex genetic structure in Japanese apricot.