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Genetic relationships between fruiting and flowering mei (Prunus mume) cultivars using SNP markers

Summary Genetic relationships among 68 mei cultivars (Prunus mume Sieb. et Zucc.), including 36 flowering mei and 32 fruiting mei cultivars, were assessed using single nucleotide polymorphism (SNP) markers. Sequence alignments of nine groups of genomic sequences, consisting of a total length of 2,916 bp amplified from 68 DNA samples using nine pairs of PCR primers, yielded 92 SNPs with a distribution frequency of one SNP per 32 bp. Among these SNPs, 51 (55.4%) were transitions, 34 (37%) were transversions, 4 (4.4%) were InDels, and 3 (3.3%) were multiple changes. Among the 92 SNP loci in these 68 mei cultivars, five different forms existed between different cultivars: 13 (14.1%) were shown to be two kinds of homozygotes in different cultivars; 22 (23.9%) were recognised as heterozygotes in some cultivars and as two kinds of homozygotes in other cultivars; and 50 (54.3%) were heterozygotes and only one kind of homozygote in other cultivars. Cluster analysis of the 68 mei cultivars was carried out using the 92 SNPs, and a consensus cladogram was constructed. All 68 mei cultivars could be classified into 13 groups, instead of two groups consisting of only flowering mei or fruiting mei, respectively. This suggested that flowering and fruiting mei trees are genetically similar and might be more different in their floral and fruit characteristics which have been the main parameters used to screen new fruit cultivars or elite trees.