Editorial: Polyploid Population Genetics and Evolution—From Theory to Practice (original) (raw)

Insights into population genetics and evolution of polyploids and their ancestors

Molecular Ecology Resources, 2018

We have developed the first comprehensive simulator for polyploid genomes (PolySim), and demonstrated its value by performing large-scale simulations to examine the effect of different population parameters on the evolution of polyploids. PolySim is unlimited in terms of ploidy, population size, or number of simulated loci. Our process considered the evolution of polyploids from diploid ancestors, polysomic inheritance, inbreeding, recombination rate change in polyploids and gene flow from lower to higher ploidies. We compared the number of segregating SNPs, minor allele frequency, heterozygosity, R 2 and average kinship relatedness between different simulated scenarios, and to real data from polyploid species. As expected, allotetraploid populations showed no difference from their ancestral diploids when population size remained constant and there was no gene flow or multivalent pairing between subgenomes. Autotetraploid populations showed significant differences from their ancestors for most parameters and diverged from their ancestral populations faster than allotetraploids. Autotetraploids can have significantly higher heterozygosity, relatedness and extended linkage disequilibrium compared with allotetraploids. Interestingly, autotetraploids were more sensitive to increasing selfing rate and decreasing population size. Multivalent formation can homogenise allotetraploid subgenomes, but this homogenisation requires a higher multivalent rate than previously proposed. Our results can be considered as the first building block to understand polyploid population evolutionary dynamics. PolySim can be used to simulate a wide variety of polyploid organisms that mimic empirical populations which, in combination with quantitative genetics tools, can be used to investigate the power of genome-wide association, genomic selection, or breeding program designs in these species.

The Analysis of Polyploid Genetic Data

Journal of Heredity, 2018

Though polyploidy is an important aspect of the evolutionary genetics of both plants and animals, the development of population genetic theory of polyploids has seriously lagged behind that of diploids. This is unfortunate since the analysis of polyploid genetic data-and the interpretation of the results-requires even more scrutiny than with diploid data. This is because of several polyploidy-specific complications in segregation and genotyping such as tetrasomy, double reduction, and missing dosage information. Here, we review the theoretical and statistical aspects of the population genetics of polyploids. We discuss several widely used types of inferences, including genetic diversity, Hardy-Weinberg equilibrium, population differentiation, genetic distance, and detecting population structure. For each, we point out how the statistical approach, expected result, and interpretation differ between different ploidy levels. We also discuss for each type of inference what biases may arise from the polyploid-specific complications and how these biases can be overcome. From our overview, it is clear that the statistical toolbox that is available for the analysis of genetic data is flexible and still expanding. Modern sequencing techniques will soon be able to overcome some of the current limitations to the analysis of polyploid data, though the techniques are lagging behind those available for diploids. Furthermore, the availability of more data may aggravate the biases that can arise, and increase the risk of false inferences. Therefore, simulations such as we used throughout this review are an important tool to verify the results of analyses of polyploid genetic data.

Advances in the study of polyploidy since Plant speciation

New Phytologist, 2003

Enormous strides have been made in the study of polyploidy over the last 20 yr. Here, we highlight some of these discoveries and note where our understanding of polyploid evolution has changed. Genetic and genomic studies have dramatically altered the polyploidy paradigm. The estimated frequency of polyploidy has increased, and it is now recognized that multiple origins are the rule for most polyploids. Likewise, autopolyploidy is much more common than traditionally maintained. Rapid genomic rearrangements, genomic downsizing, movement of genetic elements across genomes, and the movement of foreign genetic materials into the polyploid genome illustrate the complex dynamics of polyploid genomes. Following polyploidization, both genetic and epigenetic mechanisms may play an important role in altering gene expression. Ecological studies reveal that plant polyploidy can have profound effects on interactions with animal herbivores and pollinators and that polyploidy may trigger changes in the reproductive biology of a species. Despite the recent advances in our understanding of polyploid evolution, many exciting aspects remain under-investigated. Some of these include the consequences of genetic and genomic changes in natural polyploid populations, the physiological and ecological effects of polyploidy, and whether recurrent polyploidy prompts evolution to repeat itself.

Dating the origins of polyploidy events

New Phytologist, 2010

Polyploidy is a widespread speciation mechanism, particularly in plants. Estimating the time of origin of polyploid species is important for understanding issues such as gene loss and changes in regulation and expression among homoeologous copies that coexist in a single genome owing to polyploidy.

Tools for Genetic Studies in Experimental Populations of Polyploids

Frontiers in Plant Science, 2018

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.

What we still don't know about polyploidy

TAXON, 2010

During the past decade there has been a tremendous resurgence of interest in polyploidy that has in large part been stimulated by the development of increasingly powerful genetic and genomic tools. The result has been numerous new insights into the genomic and genetic consequences of polyploidy. The plethora of new discoveries has dramatically reshaped traditional views and concomitantly revealed that polyploidy is a highly dynamic and ubiquitous process. These recent advances in our understanding of polyploidy have stimulated numerous reviews, most focused on the various genetic, epigenetic, and genomic consequences of polyploid evolution. Whereas genetic and genomic attributes of polyploidization have received considerable attention, other crucial areas of polyploid evolution have received much less (e.g., ecology, pollination biology, physiology). The focus of this paper is not to review again recent discoveries, but to emphasize what we do not yet know about polyploidy, which despite all that has been learned about genome doubling is still an enormous amount. Our list is not meant to be comprehensive, but includes a range of topics that we have placed in several general categories, including mode of formation, ecological and physiological consequences, and genomic rules. Questions include: What is (are) the most frequent mechanism(s) of polyploidization? What factors promote/facilitate polyploidization? What factors favor autopolyploid vs. allopolyploid formation? Do multiple origins result in lineages with differing evolutionary trajectories and/or cryptic species? Our major goals are to stimulate discussion and promote further research.

A look at polyploidy and plant breeding

Journal of Plant Science and Phytopathology

Polyploidization is a process that generates genetic variability and therefore one of the engines of biological evolution. Since polyploidization produces important changes in the phenotype, mainly an increase in the size of the organs (i.e.: flowers and fruits), it is also a very important and powerful tool for plant improvement. Despite its intense use in breeding programs for various species, very little is known so far about the nature of this phenomenon. This work presents a brief review of the results obtained by the use of this tool in plant breeding and also raises some reflections on its mechanism of action.