Tools for Genetic Studies in Experimental Populations of Polyploids

Abstract

Polyploid organisms carry more than two copies of each chromosome, a condition rarely tolerated in animals but which occurs relatively frequently in the plant kingdom. One of the principal challenges faced by polyploid organisms is to evolve stable meiotic mechanisms to faithfully transmit genetic information to the next generation upon which the study of inheritance is based. In this review we look at the tools available to the research community to better understand polyploid inheritance, many of which have only recently been developed. Most of these tools are intended for experimental populations (rather than natural populations), facilitating genomics-assisted crop improvement and plant breeding. This is hardly surprising given that a large proportion of domesticated plant species are polyploid. We focus on three main areas: (1) polyploid genotyping; (2) genetic and physical mapping; and (3) quantitative trait analysis and genomic selection. We also briefly review some miscellaneous topics such as the mode of inheritance and the availability of polyploid simulation software. The current polyploid analytic toolbox includes software for assigning marker genotypes (and in particular, estimating the dosage of marker alleles in the heterozygous condition), establishing chromosome-scale linkage phase among marker alleles, constructing (short-range) haplotypes, generating linkage maps, performing genome-wide association studies (GWAS) and quantitative trait locus (QTL) analyses, and simulating polyploid populations. These tools can also help elucidate the mode of inheritance (disomic, polysomic or a mixture of both as in segmental allopolyploids) or reveal whether double reduction and multivalent chromosomal pairing occur. An increasing number of polyploids (or associated diploids) are being sequenced, leading to publicly available reference genome assemblies. Much work remains in order to keep pace with developments in genomic technologies. However, such technologies also offer the promise of understanding polyploid genomes at a level which hitherto has remained elusive.

Keywords: allopolyploid; autopolyploid; polyploid genetics; polyploid software tools; segmental allopolyploid.

FIGURE 1

In a tetraploid, five distinct dosages are possible at a bi-allelic marker positions, ranging from 0 copies of the alternative allele through to 4 copies. Here, the alternative allele is colored red, with the reference allele colored blue.

FIGURE 2

Generation of multi-SNP haplotypes. (A) In this example, three possible haplotypes exist spanning polymorphic positions SNP 1, 2, and 3. (B) Single-SNP genotyping cannot distinguish between the “A” allele originating from different haplotypes, combining them into a single allele as illustrated in the second SNP call. (C) In a haplotyping approach, overlapping reads are used to re-assemble and phase single SNP genotypes. Here, the known ploidy level of the species (4×) is used to impute the dosage of the two haplotypes identified in this individual, given a 1:1 ratio between the assembled haplotype read-depths.

FIGURE 3

Simplex markers (carrying a single copy of the segregating marker allele) inherit similarly across all ploidy levels and pairing behaviors, allowing diploid mapping software to be used. Here, the (simplex) SNP allele is colored red.

FIGURE 4

Theoretical rate of decrease in heterozygosity in polyploid species from repeated rounds of inbreeding/selfing, using expressions derived by Haldane (1930). For autotetraploids (red line), 95% homozygosity (horizontal dotted line) is achieved after on average 19 generations of selfing, while for a hexaploid (blue line) 95% homozygosity is reached after approximately 32 generations. By contrast, a diploid reaches 95% homozygosity after approximately 5 generations of selfing (black dashed line).