High-Density SNP Maps in Rose to Understand the Meiotic Behavior and Determine the Synteny with Fragaria

Tetraploid rose is thought to have been derived from hybridisation between up to 10 different species. This would imply it should be considered as an allopolyploid. Nevertheless, its inheritance pattern is usually considered to be that of an autopolyploid, but this has not been studied in detail. It may also fall under the term “segmental allopolyploid” to describe an in-between situation

We used a tetraploid cut rose population, genotyped using the 68K WagRhSNP Axiom array, to construct an ultra-high density linkage map using methods previously developed for autotetraploids. We mapped many markers per bin as the dense map is also intended to assist in assembly of the rose genome. Using the predicted bivalent configurations in this population, we uncovered differences in pairing behaviour between linkage groups, leading us to correct our recombination frequency estimates to take account of this behaviour. This resulted in the re-mapping of 25,695 SNP markers across the seven rose chromosomes, tailored to the pairing behaviour of each chromosome. We confirmed our findings by examining repulsion-phase linkage estimates, which also carry information about preferential pairing.

A comparison of these rose maps with the Fragaria vesca genome sequence provided a detailed picture of their synteny, which is largely colinear but also contains a few rearrangements. Our results suggest that pairing affinities may vary along chromosome arms, which may help broaden our current understanding of segmental allopolyploidy.