Quantifying the Power and Precision of QTL Analysis in Autopolyploids Under Bivalent and Multivalent Genetic Models

Peter M. Bourke*, Christine A. Hackett, Roeland E. Voorrips, Richard G.F. Visser, Chris Maliepaard

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

New genotyping technologies, offering the possibility of high genetic resolution at low cost, have helped fuel a surge in interest in the genetic analysis of polyploid species. Nevertheless, autopolyploid species present extra challenges not encountered in diploids and allopolyploids, such as polysomic inheritance or double reduction. Here we investigate the power and precision of quantitative trait locus (QTL) analysis in outcrossing autopolyploids, comparing the results of a model that assumes random bivalent chromosomal pairing during meiosis to one that also allows for multivalents and double reduction. Through a series of simulation studies we found that marginal gains in QTL detection power are achieved using the double reduction model when multivalent pairing occurs. However, when exploring the effect of variable genotypic information across parental homologs, we found that both QTL detection power and precision require high and uniform genotypic information contents. This effect far outweighed considerations regarding bivalent or multivalent pairing (and double reduction) during meiosis. We propose that autopolyploid QTL studies be accompanied by both marker coverage information and per-homolog genotypic information coefficients (GIC). Application of these methods to an autotetraploid potato (Solanum tuberosum L.) mapping population confirmed our ability to locate and dissect QTL in highly heterozygous outcrossing autotetraploid populations.

Original languageEnglish
Pages (from-to)2107-2122
Number of pages16
JournalG3 (Bethesda, Md.)
Volume9
Issue number7
DOIs
Publication statusPublished - 9 Jul 2019

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Quantitative Trait Loci
Genetic Models
Meiosis
Solanum tuberosum
Polyploidy
Diploidy
Population
Technology
Costs and Cost Analysis

Keywords

  • autopolyploid
  • Bayesian Information Criterion (BIC)
  • double reduction
  • genotypic information coefficient (GIC)
  • Quantitative Trait Locus (QTL) analysis

Cite this

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title = "Quantifying the Power and Precision of QTL Analysis in Autopolyploids Under Bivalent and Multivalent Genetic Models",
abstract = "New genotyping technologies, offering the possibility of high genetic resolution at low cost, have helped fuel a surge in interest in the genetic analysis of polyploid species. Nevertheless, autopolyploid species present extra challenges not encountered in diploids and allopolyploids, such as polysomic inheritance or double reduction. Here we investigate the power and precision of quantitative trait locus (QTL) analysis in outcrossing autopolyploids, comparing the results of a model that assumes random bivalent chromosomal pairing during meiosis to one that also allows for multivalents and double reduction. Through a series of simulation studies we found that marginal gains in QTL detection power are achieved using the double reduction model when multivalent pairing occurs. However, when exploring the effect of variable genotypic information across parental homologs, we found that both QTL detection power and precision require high and uniform genotypic information contents. This effect far outweighed considerations regarding bivalent or multivalent pairing (and double reduction) during meiosis. We propose that autopolyploid QTL studies be accompanied by both marker coverage information and per-homolog genotypic information coefficients (GIC). Application of these methods to an autotetraploid potato (Solanum tuberosum L.) mapping population confirmed our ability to locate and dissect QTL in highly heterozygous outcrossing autotetraploid populations.",
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Quantifying the Power and Precision of QTL Analysis in Autopolyploids Under Bivalent and Multivalent Genetic Models. / Bourke, Peter M.; Hackett, Christine A.; Voorrips, Roeland E.; Visser, Richard G.F.; Maliepaard, Chris.

In: G3 (Bethesda, Md.), Vol. 9, No. 7, 09.07.2019, p. 2107-2122.

Research output: Contribution to journalArticleAcademicpeer-review

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