ArticleG3 (Bethesda, Md.)2019
Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models.
Article in G3 (Bethesda, Md.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Identification of race-specific QTL and candidate genes for Aphanomyces root rot resistance in alfalfa (Medicago sativa L.).G3 (Bethesda, Md.) · 2026Article
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- A public mid-density genotyping platform for cultivated cranberry (Vaccinium macrocarpon Aiton).The plant genome · 2025Article
- Tests for segregation distortion in higher ploidy F1 populations.G3 (Bethesda, Md.) · 2025Article
- Genetic linkage mapping in Megathyrsus maximus (Jacq.) with multiple dosage markers.G3 (Bethesda, Md.) · 2025Article
- Phased chromosome-level assembly provides insight into the genome architecture of hexaploid sweetpotato.Nature plants · 2025Article
- Exploring chromosomal variations in garden roses: Insights from high-density SNP array data and a new tool, Qploidy.The plant genome · 2025Article
- The integration of quantitative trait locus mapping and transcriptome studies reveals candidate genes for water stress response in St. Augustinegrass.BMC plant biology · 2025Article
- Combating Root-Knot Nematodes (Plants (Basel, Switzerland) · 2025Review
- Tests for segregation distortion in tetraploid F1 populations.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- A low-cost dpMIG-seq method for elucidating complex inheritance in polysomic crops: a case study in tetraploid blueberry.Horticulture research · 2024Article
- Discovery of a major QTL for resistance to the guava root-knot nematode (Meloidogyne enterolobii) in 'Tanzania', an African landrace sweetpotato (Ipomoea batatas).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
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- QTL identified that influence tuber length-width ratio, degree of flatness, tuber size, and specific gravity in a russet-skinned, tetraploid mapping population.Frontiers in plant science · 2024Article
- Meta-Analysis of Rose Rosette Disease-Resistant Quantitative Trait Loci and a Search for Candidate Genes.Pathogens (Basel, Switzerland) · 2023Article
- Smooth Descent: A ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errors.Frontiers in genetics · 2023Article
- Identification of QTL associated with plant vine characteristics and infection response to late blight, early blight, and Verticillium wilt in a tetraploid potato population derived from late blight-resistant Palisade Russet.Frontiers in plant science · 2023Article
- QTL discovery for resistance to black spot and cercospora leaf spot, and defoliation in two interconnected F1 bi-parental tetraploid garden rose populations.Frontiers in plant science · 2023Article
- Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps.GigaScience · 2022Article
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Abstract
Modern SNP genotyping technologies allow measurement of the relative abundance of different alleles for a given locus and consequently estimation of their allele dosage, opening a new road for genetic studies in autopolyploids. Despite advances in genetic linkage analysis in autotetraploids, there is a lack of statistical models to perform linkage analysis in organisms with higher ploidy levels. In this paper, we present a statistical method to estimate recombination fractions and infer linkage phases in full-sib populations of autopolyploid species with even ploidy levels for a set of SNP markers using hidden Markov models. Our method uses efficient two-point procedures to reduce the search space for the best linkage phase configuration and reestimate the final parameters by maximizing the likelihood of the Markov chain. To evaluate the method, and demonstrate its properties, we rely on simulations of autotetraploid, autohexaploid and autooctaploid populations and on a real tetraploid potato data set. The results show the reliability of our approach, including situations with complex linkage phase scenarios in hexaploid and octaploid populations.
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