Partial preferential chromosome pairing is genotype dependent in tetraploid rose

Abstract

SUMMARYIt has long been recognised that polyploid species do not always neatly fall into the categories of autoor allopolyploid, leading to the term 'segmental allopolyploid' to describe everything in between. The meiotic behaviour of such intermediate species is not fully understood, nor is there consensus as to how to model their inheritance patterns. In this study we used a tetraploid cut rose (Rosa hybrida) population, genotyped using the 68K WagRhSNP array, to construct an ultra-high-density linkage map of all homologous chromosomes using methods previously developed for autotetraploids. Using the predicted bivalent configurations in this population we quantified differences in pairing behaviour among and along homologous chromosomes, leading us to correct our estimates of recombination frequency to account for this behaviour. This resulted in the re-mapping of 25 695 SNP markers across all homologues of the seven rose chromosomes, tailored to the pairing behaviour of each chromosome in each parent. We confirmed the inferred differences in pairing behaviour among chromosomes by examining repulsionphase linkage estimates, which also carry information about preferential pairing and recombination. Currently, the closest sequenced relative to rose is Fragaria vesca. Aligning the integrated ultra-dense rose map with the strawberry genome sequence provided a detailed picture of the synteny, confirming overall co-linearity but also revealing new genomic rearrangements. Our results suggest that pairing affinities may vary along chromosome arms, which broadens our current understanding of segmental allopolyploidy.

Genetic mapping in polyploids

“…In order to estimate presence of parental haplotypes in the offspring, we calculated IBD probabilities as described by (Bourke, 2014). A schematic overview of the method is shown in Figure 2.…”

“…QTL analysis was performed on block-corrected mean phenotypic values using an IBD probability model, as described before for tetraploids (Bourke, 2014). An additive model modified from (Kempthorne, 1957) as suggested by (Hackett et al, 2013;Hackett et al, 2014) was modified to the hexaploid level: = + 2 2 + 3 3 + 4 4 + 5 5 + 6 6 + 8 8 + 9 9 + 10 10 + 11 11 + 12 12 where αi and Xi are the main effects and indicator variables for allele i, respectively.…”

“…We used a relatively simple approach to estimate IBD probabilities for absence or presence of parental haplotypes in our segregating population (Bourke, 2014). The method only uses information of dosage scores if they are fully informative.…”

“…(Hackett et al, 2013;Bourke, 2014)). We can consider the IBD probability of inheritance of a particular homologue to be the inheritance probability of the so-called alternative allele ( ), with the corresponding probability of inheritance of the reference allele = 1 − .…”

“…Such haplotypes can be identified based on the configuration of neighbouring alleles. Methods for reconstruction of haplotype inheritance by estimating probabilities of identity-by-descent (IBD) in tetraploid bi-parental populations have been developed (Hackett et al, 2013;Bourke, 2014;Zheng et al, 2016). Although all methods are theoretically extendible to hexaploids, the method developed by (Bourke, 2014) is ploidy-level independent and is therefore directly applicable to hexaploids.…”