ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2014
QTL mapping in autotetraploids using SNP dosage information.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Genetic linkage mapping in Megathyrsus maximus (Jacq.) with multiple dosage markers.G3 (Bethesda, Md.) · 2025Article
- 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
- 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
- Metabolite profiling of tubers of an early- and a late-maturing potato line and their grafts.Metabolomics : Official journal of the Metabolomic Society · 2022Article
- Identification of Long-Distance Transport Signal Molecules Associated with Plant Maturity in Tetraploid Cultivated Potatoes (Plants (Basel, Switzerland) · 2022Article
- Article
- Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR.Bioinformatics (Oxford, England) · 2021Article
- Article
- High-density linkage map construction and identification of loci regulating fruit quality traits in blueberry.Horticulture research · 2021Article
- The recombination landscape and multiple QTL mapping in a Solanum tuberosum cv. 'Atlantic'-derived FHeredity · 2021Article
- A tetrasomic inheritance model and likelihood-based method for mapping quantitative trait loci in autotetraploid species.The New phytologist · 2021Article
- Sampling Variation of RAD-Seq Data from Diploid and Tetraploid Potato (Plants (Basel, Switzerland) · 2021Article
- QTL Mapping for Resistance to Cankers Induced byPathogens (Basel, Switzerland) · 2020Article
- Multiple QTL Mapping in Autopolyploids: A Random-Effect Model Approach with Application in a Hexaploid Sweetpotato Full-Sib Population.Genetics · 2020Article
- Genome-wide association study identifies various loci underlying agronomic and morphological traits in diversified potato panel.Physiology and molecular biology of plants : an international journal of functional plant biology · 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
- Development of an Axiom Sugarcane100K SNP array for genetic map construction and QTL identification.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- Quantifying the Power and Precision of QTL Analysis in Autopolyploids Under Bivalent and Multivalent Genetic Models.G3 (Bethesda, Md.) · 2019Article
- In the name of the rose: a roadmap for rose research in the genome era.Horticulture research · 2019Article
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3 authors.
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Abstract
key messageDense linkage maps derived by analysing SNP dosage in autotetraploids provide detailed information about the location of, and genetic model at, quantitative trait loci. Recent developments in sequencing and genotyping technologies enable researchers to generate high-density single nucleotide polymorphism (SNP) genotype data for mapping studies. For polyploid species, the SNP genotypes are informative about allele dosage, and Hackett et al. (PLoS ONE 8:e63939, 2013) presented theory about how dosage information can be used in linkage map construction and quantitative trait locus (QTL) mapping for an F1 population in an autotetraploid species. Here, QTL mapping using dosage information is explored for simulated phenotypic traits of moderate heritability and possibly non-additive effects. Different mapping strategies are compared, looking at additive and more complicated models, and model fitting as a single step or by iteratively re-weighted modelling. We recommend fitting an additive model without iterative re-weighting, and then exploring non-additive models for the genotype means estimated at the most likely position. We apply this strategy to re-analyse traits of high heritability from a potato population of 190 F1 individuals: flower colour, maturity, height and resistance to late blight (Phytophthora infestans (Mont.) de Bary) and potato cyst nematode (Globodera pallida), using a map of 3839 SNPs. The approximate confidence intervals for QTL locations have been improved by the detailed linkage map, and more information about the genetic model at each QTL has been revealed. For several of the reported QTLs, candidate SNPs can be identified, and used to propose candidate trait genes. We conclude that the high marker density is informative about the genetic model at loci of large effects, but that larger populations are needed to detect smaller QTLs.
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