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

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. AbstractHigh-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.

Partial preferential chromosome pairing is genotype dependent in tetraploid rose

“…We followed the mapping procedure as described for potato in Bourke et al . (), although it was not possible to associate homologue (simplex × nulliplex, or S × N) clusters into chromosomal groups on the basis of repulsion‐phase linkages due to more noise in the data. Instead, coupling linkages with duplex × nulliplex (D × N) markers were used to provide these associations.…”

“…Recently, methods for creating integrated genetic maps in autotetraploid species using single nucleotide polymorphism (SNP) marker data have been developed (Hackett et al ., ; Bourke et al ., ). These methods offer the possibility of identifying repulsion‐linkages that can help reveal pairing behaviour.…”

“…The 68K WagRhSNP array (Koning‐Boucoiran et al ., ; Schulz et al ., ; Vukosavljev et al ., ) was used to create an ultra‐high‐density tetraploid linkage map, enabling the quantification of preferential pairing, quadrivalent formation and double reduction during parental meiosis. In a previous study using simulated data it was hypothesised that preferential pairing could effectively be ignored in polyploid linkage mapping (up to a 70% deviation from random pairing) (Bourke et al ., ). In this study we had the opportunity to test this prediction by correcting each linkage map for the observed pairing behaviour and comparing them with those created under a random model.…”

polymapR – linkage analysis and genetic map construction from F1 populations of outcrossing polyploids

“…It has been demonstrated that double reduction introduces some bias in recombination frequency estimates under a random bivalent model. This can be safely ignored if the rate of quadrivalent pairing is low (Bourke et al, 2015;Bourke et al, 2016).…”

Mapfuser: an integrative toolbox for consensus map construction and Marey maps

“…For several applications it is useful to integrate multiple genetic maps, for example to compare QTLs across populations, 22 to anchor genome assemblies, or to integrate haplotype specific linkage maps in autopolyploids (Bourke et al, 2016). 23…”