Challenges of Genotyping Polyploid Species

Mason, Annaliese S.

doi:10.1007/978-1-4939-1966-6_12

Cited by 20 publications

(15 citation statements)

References 23 publications

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“…All individuals were genotyped with amplified fragment length polymorphisms (AFLPs) following Parisod and Christin (). Despite limitations inherent to their dominant nature, AFLP loci are widely distributed across the genome and support appropriate genotyping that is hardly outperformed by current high‐throughput approaches in polyploids (Mason, ). In short, genomic DNA was digested with Eco RI and Mse I before ligation of adaptors to perform preselective and selective amplifications.…”

Section: Methodsmentioning

confidence: 99%

“…As polyploid populations strongly violate Hardy–Weinberg expectations, most standard methods in population genetics cannot be applied (Ronfort, Jenczewski, Bataillon, & Rousset, ). Furthermore, inferential frameworks accounting for the evolutionary genetics of polyploids must rely on accurate datasets assessing dosage of the multiple alleles at each locus, which still is technically challenging with high‐throughput genotyping (Mason, ). Accordingly, approaches deprived from population genetics pre‐requisites should currently be privileged among the applicable methods to evaluate local adaptation from genetic data.…”

Section: Methodsmentioning

confidence: 99%

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Multiscale landscape genomic models to detect signatures of selection in the alpine plant Biscutella laevigata

Leempoel

Parisod

Geiser

et al. 2018

Ecology and Evolution

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Plant species are known to adapt locally to their environment, particularly in mountainous areas where conditions can vary drastically over short distances. The climate of such landscapes being largely influenced by topography, using fine‐scale models to evaluate environmental heterogeneity may help detecting adaptation to micro‐habitats. Here, we applied a multiscale landscape genomic approach to detect evidence of local adaptation in the alpine plant Biscutella laevigata. The two gene pools identified, experiencing limited gene flow along a 1‐km ridge, were different in regard to several habitat features derived from a very high resolution (VHR) digital elevation model (DEM). A correlative approach detected signatures of selection along environmental gradients such as altitude, wind exposure, and solar radiation, indicating adaptive pressures likely driven by fine‐scale topography. Using a large panel of DEM‐derived variables as ecologically relevant proxies, our results highlighted the critical role of spatial resolution. These high‐resolution multiscale variables indeed indicate that the robustness of associations between genetic loci and environmental features depends on spatial parameters that are poorly documented. We argue that the scale issue is critical in landscape genomics and that multiscale ecological variables are key to improve our understanding of local adaptation in highly heterogeneous landscapes.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Multiscale landscape genomic models to detect signatures of selection in the alpine plant Biscutella laevigata

Leempoel

Parisod

Geiser

et al. 2018

Ecology and Evolution

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“…If we would like to employ markers in our breeding program the answer is clearly yes, understanding the mode of inheritance is vital. Genotyping polyploids is in general more complex and less reliable than genotyping diploids (Mason, 2015). This could be caused by off-target amplification due to duplication of marker sequences at other loci (Limborg et al, 2016), but is also due in large part to the difficulty in correctly estimating the number of copies of a marker allele, also known as marker dosage assignment (Chapter 2).…”

Section: Understanding the Mode Of Inheritancementioning

confidence: 99%

Genetic mapping in polyploids

Bourke¹

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“…One of the most crucial aspects in the study of polyploid genetics is the generation of accurate genotypic data. However, it is also fraught with difficulties, not least the detection of multiple loci when only a single locus is targeted ( Mason, 2015 ; Limborg et al, 2016 ). Various technologies exist, with almost all current applications aimed at identifying single nucleotide polymorphisms (SNPs).…”

Section: Polyploid Genotypingmentioning

confidence: 99%

Tools for Genetic Studies in Experimental Populations of Polyploids

et al. 2018

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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.

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Challenges of Genotyping Polyploid Species

Cited by 20 publications

References 23 publications

Multiscale landscape genomic models to detect signatures of selection in the alpine plant Biscutella laevigata

Multiscale landscape genomic models to detect signatures of selection in the alpine plant Biscutella laevigata

Genetic mapping in polyploids

Tools for Genetic Studies in Experimental Populations of Polyploids

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