ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2016
Integrating haplotype-specific linkage maps in tetraploid species using SNP markers.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 37 citations in OpenAlex.
- Identification, Elucidation and Deployment of a Cytoplasmic Male Sterility System for Hybrid Potato.Biology · 2024Article
- Multiallelic models for QTL mapping in diverse polyploid populations.BMC bioinformatics · 2022Article
- Article
- Using probabilistic genotypes in linkage analysis of polyploids.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Preferential Disomic Segregation andFrontiers in plant science · 2020Article
- High-Resolution Linkage Map With Allele Dosage Allows the Identification of Regions Governing Complex Traits and Apospory in Guinea Grass (Frontiers in plant science · 2020Article
- Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models.G3 (Bethesda, Md.) · 2019Article
- Quantifying the Power and Precision of QTL Analysis in Autopolyploids Under Bivalent and Multivalent Genetic Models.G3 (Bethesda, Md.) · 2019Article
- Genetic Mapping With Allele Dosage Information in TetraploidFrontiers in plant science · 2019Article
- Multi-allelic QTL analysis of protein content in a bi-parental population of cultivated tetraploid potato.Euphytica: Netherlands journal of plant breeding · 2019Article
- polymapR-linkage analysis and genetic map construction from F1 populations of outcrossing polyploids.Bioinformatics (Oxford, England) · 2018Article
- Multi-environment QTL analysis of plant and flower morphological traits in tetraploid rose.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018Article
- Tools for Genetic Studies in Experimental Populations of Polyploids.Frontiers in plant science · 2018Review
- An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Article
- Conclusive evidence for hexasomic inheritance in chrysanthemum based on analysis of a 183 k SNP array.BMC genomics · 2017Article
- High-density SNP-based genetic maps for the parents of an outcrossed and a selfed tetraploid garden rose cross, inferred from admixed progeny using the 68k rose SNP array.Horticulture research · 2016Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
key messageLinkage mapping can help unravel the complexities of polyploid genomes. Here, we integrate haplotype-specific linkage maps in autotetraploid potato and explore the possibilities for mapping in other polyploid species. High-density linkage mapping in autopolyploid species has become possible in recent years given the increasing number of molecular markers now available through modern genotyping platforms. Such maps along with larger experimental populations are needed before we can obtain sufficient accuracy to make marker-trait association studies useful in practice. Here, we describe a method to create genetic linkage maps for an autotetraploid species with large numbers of markers and apply it to an F1 population of tetraploid potato (Solanum tuberosum L.) of 235 individuals genotyped using a 20K SNP array. SNP intensity values were converted to allele dosages after which we calculated pairwise maximum likelihood estimates of recombination frequencies between all marker segregation types under the assumption of random bivalent pairing. These estimates were used in the clustering of markers into linkage groups and their subsequent ordering into 96 homologue maps. The homologue maps were integrated per chromosome, resulting in a total map length of 1061 cM from 6910 markers covering all 12 potato chromosomes. We examined the questions of marker phasing and binning and propose optimal strategies for both. We also investigated the effect of quadrivalent formation and preferential pairing on recombination frequency estimation and marker phasing, which is of great relevance not only for potato but also for genetic studies in other tetraploid species for which the meiotic pairing behaviour is less well understood.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.