Discordant Chloroplast and Nuclear Divergence Among Eight Rubus crataegifolius (Rosaceae) Cultivars

Background: Cultivar identification and the reconstruction of breeding relationships require markers that reflect both parents, yet plastome sequencing is often applied to these problems on its own. Methods: We tested how far chloroplast data alone can go in Rubus crataegifolius Bunge, using one plant of each of eight cultivars from Korean breeding programs. Complete chloroplast genomes (155,664–155,770 bp) were assembled for all eight and compared with nuclear resequencing data from the same plants. Results: The 526 plastome variants were concentrated in non-coding regions, and Ka/Ks ratios well below one indicated strong purifying selection on plastid genes. The eight cultivars carried only five distinct plastome haplotypes: three shared one identical sequence and two another. Mapping to a Rubus idaeus reference recovered 4,872,213 cultivar-polymorphic nuclear SNPs, which separated every cultivar pair, including all four with identical plastomes, and the result was unchanged after stringent filtering of heterozygous calls. Cultivars sharing an identical plastome spanned 27% of the entire range of nuclear distances, and the two measures were only weakly correlated. Conclusions: Plastome sequencing therefore describes maternal lineage rather than cultivar identity among these cultivars; genome-wide nuclear SNPs discriminate them, and the five-SNP panel derived from them is a candidate tool that requires validation on independent plants.