title: Partial preferential chromosome pairing is genotype dependent in tetraploid rose.
abstract: It has long been recognised that polyploid species do not always neatly fall into the categories of auto- or 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 repulsion-phase 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.
authors.affiliation: Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
authors.forename: Peter M
authors.identifier: http://orcid.org/0000-0002-0665-6508
authors.initials: PM
authors.lastname: Bourke
authors.affiliation: Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
authors.forename: Paul
authors.initials: P
authors.lastname: Arens
authors.affiliation: Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
authors.forename: Roeland E
authors.initials: RE
authors.lastname: Voorrips
authors.affiliation: Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
authors.forename: G Danny
authors.initials: GD
authors.lastname: Esselink
authors.affiliation: Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
authors.forename: Carole F S
authors.initials: CF
authors.lastname: Koning-Boucoiran
authors.affiliation: Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
authors.forename: Wendy P C
authors.initials: WP
authors.lastname: Van't Westende
authors.affiliation: Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
authors.forename: Tiago
authors.initials: T
authors.lastname: Santos Leonardo
authors.affiliation: Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
authors.forename: Patrick
authors.initials: P
authors.lastname: Wissink
authors.affiliation: Biometris, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
authors.forename: Chaozhi
authors.initials: C
authors.lastname: Zheng
authors.affiliation: Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.|Horticulture and Product Physiology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
authors.forename: Geert
authors.initials: G
authors.lastname: van Geest
authors.affiliation: Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
authors.forename: Richard G F
authors.initials: RG
authors.lastname: Visser
authors.affiliation: Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
authors.forename: Frans A
authors.initials: FA
authors.lastname: Krens
authors.affiliation: Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
authors.forename: Marinus J M
authors.initials: MJ
authors.lastname: Smulders
authors.affiliation: Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
authors.forename: Chris
authors.initials: C
authors.lastname: Maliepaard
mesh_terms: D002874:Chromosome Mapping; D023902:Chromosome Pairing / Q000235:genetics / Q000502:physiology; D008040:Genetic Linkage; D005838:Genotype; D008540:Meiosis / Q000235:genetics; D011123:Polyploidy; D027826:Rosa / Q000235:genetics*; D057891:Tetraploidy
keywords: 
  Rosa hybrida
  ; high-density integrated map; meiotic chromosomal pairing behaviour; polyploid genetic linkage map; segmental allopolyploid