Phylogenetic relationship and genetic background of blueberry (Vaccinium spp.) based on retrotransposon-based SSAP molecular markers

Abstract

A total length of 98 070 bp long terminal repeat retrotransposon (LTR-RT) sequences were found after preliminary prediction and subsequent screening, accounting for 3.96% of the whole blueberry genome. Thirty-three members belonged to Ty1/Copia retrotransposon family and 60 members of Ty3/Gypsy retrotransposon family were identified according to their sequence similarity to previously reported retrotransposons, accounting for 1.57% and 2.39% of the whole genome, respectively. Nineteen sequences from Ty1/Copia family and thirty-three Ty3/Gypsy sequences were used for primer design. Sixty-six pairs of primers were synthesized randomly, in which forty-two pairs of primers were screened to validate the availability and transferability of LTR-RT on 48 blueberry cultivars. We found that 4, 236 bands were amplified using 42 pairs of primers, of which 4184 were polymorphic bands. Bands at each locus ranged from 34 to 219, with an average of 101. To elucidate genetic relationship of 48 blueberry cultivars, principle coordinate analysis (PCoA) was carried out based on SSAP genotyping data. The results showed that the first two coordinates could explain 14.11% of the total variation among all cultivars, of which the first and second coordinate accounted for 8.13% and 5.98% of total variation, respectively. The first three axes accounted for 18.84% of the total variation. In order to estimate genetic background and phylogenetic relationship of these cultivars, phylogenetic tree was constructed based on neighbor-joining algorithm. The results showed that 48 cultivars could be clustered into five groups, indicating that genetic background of 48 blueberry cultivars used in this study was relatively simple. The genetic composition of highbush blueberry cultivars was similar, which consisted of a single genepool. Genetic background of rabbiteye blueberry cultivars presented multiple source of genepools, which was probably related to the involvement of several species in the artificial selection. ‘Bluegem’ resembles genetic composition with highbush blueberries, suggesting that several cultivars possibly involved in its breeding process. The original lineage from V. virgatum was supposed to be replaced gradually with repeated hybridization during cross fertilization. The cross breeding among cultivars genetically distant from one other would enrich the genetic diversity of blueberry cultivars. All these results provided valuable references for the selection of parental cultivars in blueberry breeding.