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.

Insights Into the Genetic Basis of Blueberry Fruit-Related Traits Using Diploid and Polyploid Models in a GWAS Context

“…We expect that the improvement of genome contiguity might impact the reads alignment quality, providing a more accurate SNP calling and a more precise location of the markers associated with traits. Dosage calling has also been recognized to be a major challenge in genomic studies of polyploid species (Bourke et al, 2018), and it is an area that when fully developed could contribute significantly to association studies in autopolyploids. Population structure is another issue that could be affecting the current results.…”

Development of a cost‐effective single nucleotide polymorphism genotyping array for management of greater yam germplasm collections

“…Regarding the recent explosion of genotyping related to next-generation sequencing, bioinformatics tools have been developed to accurately determine dosages (e.g., GBS2ploidy; Gompert & Mock, 2017). However, this requires deep sequencing and usually an assumption of ploidy levels present in the dataset (Bourke, Voorrips, Visser, & Maliepaard, 2018).…”

High-resolution Linkage Map with Allele Dosage Allows the Identification of an Apomixis Region and Complex Traits in Guinea Grass (Megathyrsus maximus)

“…Most linkage maps in grasses include only single-dose markers with segregation ratios of 1:1 and 3:1; thus, the heterozygous classes were grouped with one of the homozygous classes, resulting in a loss of information (Bourke et al, 2018b). The use of linkage maps with simplex SNPs for most linkage groups and a high density of higher-dosage markers provides greater confidence in the modeling of allelic effects of QTLs (Hackett et al, 2014).…”