Tools for Genetic Studies in Experimental Populations of Polyploids

Research output: Contribution to journalArticleAcademicpeer-review

18 Citations (Scopus)

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.
Original languageEnglish
Article number513
JournalFrontiers in Plant Science
Volume9
DOIs
Publication statusPublished - 18 Apr 2018

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polyploidy
inheritance (genetics)
chromosome mapping
alleles
chromosomes
genome assembly
disomics
allopolyploidy
physical chromosome mapping
organisms
plant breeding
quantitative traits
marker-assisted selection
genotyping
linkage (genetics)
quantitative trait loci
haplotypes
diploidy
genomics
genome

Cite this

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title = "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 domesticatedplant 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 alsohelp elucidate the mode of inheritance (disomic, polysomic or a mixture of bothas 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.",
author = "P.M. Bourke and R.E. Voorrips and R.G.F. Visser and C.A. Maliepaard",
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Tools for Genetic Studies in Experimental Populations of Polyploids. / Bourke, P.M.; Voorrips, R.E.; Visser, R.G.F.; Maliepaard, C.A.

In: Frontiers in Plant Science, Vol. 9, 513, 18.04.2018.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Tools for Genetic Studies in Experimental Populations of Polyploids

AU - Bourke, P.M.

AU - Voorrips, R.E.

AU - Visser, R.G.F.

AU - Maliepaard, C.A.

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N2 - 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 domesticatedplant 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 alsohelp elucidate the mode of inheritance (disomic, polysomic or a mixture of bothas 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.

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JO - Frontiers in Plant Science

JF - Frontiers in Plant Science

SN - 1664-462X

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