The Double-Reduction Landscape in Tetraploid Potato as Revealed by a High-Density Linkage Map

Abstract

The creation of genetic linkage maps in polyploid species has been a long-standing problem for which various approaches have been proposed. In the case of autopolyploids, a commonly used simplification is that random bivalents form during meiosis. This leads to relatively straightforward estimation of recombination frequencies using maximum likelihood, from which a genetic map can be derived. However, autopolyploids such as tetraploid potato (Solanum tuberosum L.) may exhibit additional features, such as double reduction, not normally encountered in diploid or allopolyploid species. In this study, we produced a high-density linkage map of tetraploid potato and used it to identify regions of double reduction in a biparental mapping population. The frequency of multivalents required to produce this degree of double reduction was determined through simulation. We also determined the effect that multivalents or preferential pairing between homologous chromosomes has on linkage mapping. Low levels of multivalents or preferential pairing do not adversely affect map construction when highly informative marker types and phases are used. We reveal the double-reduction landscape in tetraploid potato, clearly showing that this phenomenon increases with distance from the centromeres.

Keywords: double reduction; linkage mapping; multivalents; potato; tetraploid.

Figure 1

Homolog linkage maps of potato chromosome 1 for parent 2.

Figure 2

Comparison of genetic-to-physical distance with homolog maps of potato chromosome 1. Approximate centromere bounds are shown as dashed lines, corresponding to the inflection points in the curve (averaged over P₁ and P₂). Homolog maps were aligned prior to graphing by redefining the 0-cM positions, if necessary.

Figure 3

Average recombination rate across homologous chromosome arms. Rates calculated per homolog arm (north or south of the centromere) by linear regression of marker positions on the physical vs. genetic distance plots. Points are colored by chromosome, with upward-pointing triangles denoting north (p) arms and downward denoting south (q) arms. P₁ data are shown by filled triangles, P₂ data by empty triangles.

Figure 4

Average rate of DR vs. distance from the centromeres. Shaded areas represent 95% confidence regions around the simulated mean rate of DR arising from fraction quadrivalents 0.2 and 0.3. The SD of the simulated mean rate of DR increases toward the telomeres, coinciding with greater fluctuations in the true rate of DR in these regions.

Figure 5

True vs. estimated r (using ML) for coupling-phase simplex markers with fraction quadrivalents 0.2. The green line (y = x) shows the line of perfect correspondence between true and estimated values.

Figure 6

(A) Proportion of incorrectly phased markers pairs under different levels of quadrivalent formation. (B) Effect of quadrivalents on accuracy of r ML estimates for coupling- and repulsion-phase simplex marker pairs

Figure 7

(A) Proportion of incorrectly phased marker pairs with different levels of preferential pairing. (B) Effect of preferential pairing on accuracy of r ML estimates for coupling- and repulsion-phase simplex marker pairs