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.

Original languageEnglish
Pages (from-to)330-343
JournalThe Plant Journal
Volume90
Issue number2
DOIs
Publication statusPublished - 2017

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Chromosome Pairing
chromosome pairing
Tetraploidy
tetraploidy
Rosa
Chromosomes
Genotype
chromosomes
allopolyploidy
genotype
Fragaria
Genetic Recombination
Fragaria vesca
autopolyploidy
Synteny
Inheritance Patterns
Polyploidy
polyploidy
Population
strawberries

Keywords

  • high-density integrated map
  • meiotic chromosomal pairing behaviour
  • polyploid genetic linkage map
  • Rosa hybrida
  • segmental allopolyploid

Cite this

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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.",
keywords = "high-density integrated map, meiotic chromosomal pairing behaviour, polyploid genetic linkage map, Rosa hybrida, segmental allopolyploid",
author = "Bourke, {Peter M.} and Paul Arens and Voorrips, {Roeland E.} and Danny Esselink and Koning-Boucoiran, {Carole F.S.} and {van 't Westende}, Wendy and {Santos Leonardo}, Tiago and Patrick Wissink and Chaozhi Zheng and {van Geest}, Geert and Visser, {Richard G.F.} and Krens, {Frans A.} and Rene Smulders and Chris Maliepaard",
note = "KV 1605-020 / TU-16006",
year = "2017",
doi = "10.1111/tpj.13496",
language = "English",
volume = "90",
pages = "330--343",
journal = "The Plant Journal",
issn = "0960-7412",
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T1 - Partial preferential chromosome pairing is genotype dependent in tetraploid rose

AU - Bourke, Peter M.

AU - Arens, Paul

AU - Voorrips, Roeland E.

AU - Esselink, Danny

AU - Koning-Boucoiran, Carole F.S.

AU - van 't Westende, Wendy

AU - Santos Leonardo, Tiago

AU - Wissink, Patrick

AU - Zheng, Chaozhi

AU - van Geest, Geert

AU - Visser, Richard G.F.

AU - Krens, Frans A.

AU - Smulders, Rene

AU - Maliepaard, Chris

N1 - KV 1605-020 / TU-16006

PY - 2017

Y1 - 2017

N2 - 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.

AB - 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.

KW - high-density integrated map

KW - meiotic chromosomal pairing behaviour

KW - polyploid genetic linkage map

KW - Rosa hybrida

KW - segmental allopolyploid

U2 - 10.1111/tpj.13496

DO - 10.1111/tpj.13496

M3 - Article

VL - 90

SP - 330

EP - 343

JO - The Plant Journal

JF - The Plant Journal

SN - 0960-7412

IS - 2

ER -