Integrating haplotype-specific linkage maps in tetraploid species using SNP markers.

Peter M Bourke,Richard G F Visser,Johannes Jansen,Twan Kranenburg,Roeland E Voorrips,Chris Maliepaard

doi:10.1007/s00122-016-2768-1

Peter M Bourke, Richard G F Visser + Show 4 more

Open Access

https://doi.org/10.1007/s00122-016-2768-1

Copy DOI

Abstract

Key message Linkage mapping can help unravel the complexities of polyploid genomes. Here, we integrate haplotype-specific linkage maps in autotetraploid potato and explore the possibilities for mapping in other polyploid species. High-density linkage mapping in autopolyploid species has become possible in recent years given the increasing number of molecular markers now available through modern genotyping platforms. Such maps along with larger experimental populations are needed before we can obtain sufficient accuracy to make marker-trait association studies useful in practice. Here, we describe a method to create genetic linkage maps for an autotetraploid species with large numbers of markers and apply it to an F1 population of tetraploid potato (Solanum tuberosum L.) of 235 individuals genotyped using a 20K SNP array. SNP intensity values were converted to allele dosages after which we calculated pairwise maximum likelihood estimates of recombination frequencies between all marker segregation types under the assumption of random bivalent pairing. These estimates were used in the clustering of markers into linkage groups and their subsequent ordering into 96 homologue maps. The homologue maps were integrated per chromosome, resulting in a total map length of 1061 cM from 6910 markers covering all 12 potato chromosomes. We examined the questions of marker phasing and binning and propose optimal strategies for both. We also investigated the effect of quadrivalent formation and preferential pairing on recombination frequency estimation and marker phasing, which is of great relevance not only for potato but also for genetic studies in other tetraploid species for which the meiotic pairing behaviour is less well understood.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-016-2768-1) contains supplementary material, which is available to authorized users.

Highlights

Polyploid species, where the basic diploid number of chromosome copies is exceeded, are increasingly becoming the subject of studies that aim to determine the links between genetic polymorphisms and phenotypic traits
We investigated the effect of quadrivalent formation and preferential pairing on recombination frequency estimation and marker phasing, which is of great relevance for potato and for genetic studies in other tetraploid species for which the meiotic pairing behaviour is less well understood
We describe a method to perform linkage mapping in an autotetraploid species under the assumption of random bivalent pairing, and apply it to a genotyped mapping population of tetraploid potato

Summary

Introduction

Polyploid species, where the basic diploid number of chromosome copies is exceeded, are increasingly becoming the subject of studies that aim to determine the links between genetic polymorphisms and phenotypic traits. Researchers have needed to create maps of these species through linkage studies or sequencing efforts (or both). Affordable, high-throughput genotyping technologies together with greater computing power and the software needed to assemble these maps are enhancing our ability to perform such studies. There have been a relatively large number of published tetraploid linkage maps in economically important allotetraploid species, such as cotton (Gossypium hirsutum L.) and durum wheat (Triticum durum L.). Autotetraploid maps are far fewer, with the exception of alfalfa (Medicago sativa L.) (Brouwer and Osborn 1999; Robins et al 2008), potato (Solanum tuberosum L.) (Hackett et al 2013; Meyer et al 1998), and rose (Rosa hybrida) (KoningBoucoiran et al 2012; Rajapakse et al 2001).

Methods

Results

Discussion

Conclusion