Abstract
Dense genetic maps create a base for QTL analysis of important traits and future implementation of marker-assisted breeding. In tetraploid rose, the existing linkage maps include <300 markers to cover 28 linkage groups (4 homologous sets of 7 chromosomes). Here we used the 68k WagRhSNP Axiom single-nucleotide polymorphism (SNP) array for rose, in combination with SNP dosage calling at the tetraploid level, to genotype offspring from the garden rose cultivar ‘Red New Dawn’. The offspring proved to be not from a single bi-parental cross. In rose breeding, crosses with unintended parents occur regularly. We developed a strategy to separate progeny into putative populations, even while one of the parents was unknown, using principle component analysis on pairwise genetic distances based on sets of selected SNP markers that were homozygous, and therefore uninformative for one parent. One of the inferred populations was consistent with self-fertilization of ‘Red New Dawn’. Subsequently, linkage maps were generated for a bi-parental and a self-pollinated population with ‘Red New Dawn’ as the common maternal parent. The densest map, for the selfed parent, had 1929 SNP markers on 25 linkage groups, covering 1765.5 cM at an average marker distance of 0.9 cM. Synteny with the strawberry (Fragaria vesca) genome was extensive. Rose ICM1 corresponded to F. vesca pseudochromosome 7 (Fv7), ICM4 to Fv4, ICM5 to Fv3, ICM6 to Fv2 and ICM7 to Fv5. Rose ICM2 corresponded to parts of F. vesca pseudochromosomes 1 and 6, whereas ICM3 is syntenic to the remainder of Fv6.
Highlights
Garden roses are tetraploid woody perennials from the genus Rosa
We developed a strategy to separate progeny into putative populations, even while one of the parents was unknown, using principle component analysis on pairwise genetic distances based on sets of selected single-nucleotide polymorphism (SNP) markers that were homozygous, and uninformative for one parent
We generated two principle component analysis (PCO) plots for all offspring using pairwise similarities based on selected SNP markers, namely, those for which Red New Dawn (RND) (Figure 1a) or Morden Centennial’ (MC) (Figure 1b) were monomorphic
Summary
Garden roses are tetraploid woody perennials from the genus Rosa (family Rosaceae, subfamily Rosidae). The frequent hybridization with and introgression from wild species into cultivated roses[4,5,6] have led to a complex taxonomy.[7,8] The result of these introgression events may be that some chromosomal regions may be more diverse than others among garden rose cultivars,[9,10] and possibly genetically differentiated from those in cut rose. In the case of tetrasomic (random), pairing the chromosomes can form quadrivalents in meiosis, after which (parts of) sister chromatids may find themselves in the same gamete during the second meiotic division. Double reduction is contingent on the occurrence of quadrivalents and on the occurrence of a crossover between the centromere and the observed locus;[14] the frequency increases towards the distal ends of chromosomes
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