ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2012
QTL linkage analysis of connected populations using ancestral marker and pedigree information.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Early Response QTLs and DEGs Underlying Oil Palm Resistance toMicroorganisms · 2026Article
- Pedigree-based QTL analysis of flower size traits in two multi-parental diploid rose populations.Frontiers in plant science · 2023Article
- Identification of novel genetic regions associated with resistance to European canker in apple.BMC plant biology · 2022Article
- Modeling allelic diversity of multiparent mapping populations affects detection of quantitative trait loci.G3 (Bethesda, Md.) · 2022Article
- Pedigree-based analysis in multi-parental diploid rose populations reveals QTLs for cercospora leaf spot disease resistance.Frontiers in plant science · 2022Article
- Mapping and characterization QTLs for phenological traits in seven pedigree-connected peach families.BMC genomics · 2021Article
- Fire blight QTL analysis in a multi-family apple population identifies a reduced-susceptibility allele in 'Honeycrisp'.Horticulture research · 2021Article
- RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops.Horticulture research · 2020Review
- Quantifying the Power and Precision of QTL Analysis in Autopolyploids Under Bivalent and Multivalent Genetic Models.G3 (Bethesda, Md.) · 2019Article
- FaRCa1: a major subgenome-specific locus conferring resistance to Colletotrichum acutatum in strawberry.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
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- Application of a Bayesian ordinal animal model for the estimation of breeding values for the resistance toBreeding science · 2017Article
- Genomic dissection of a 'Fuji' apple cultivar: re-sequencing, SNP marker development, definition of haplotypes, and QTL detection.Breeding science · 2016Article
- Choice of models for QTL mapping with multiple families and design of the training set for prediction of Fusarium resistance traits in maize.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2016Article
- Article
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- Bayesian QTL analyses using pedigreed families of an outcrossing species, with application to fruit firmness in apple.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2014Article
- Clusthaplo: a plug-in for MCQTL to enhance QTL detection using ancestral alleles in multi-cross design.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2014Article
- Combined linkage and linkage disequilibrium QTL mapping in multiple families of maize (Zea mays L.) line crosses highlights complementarities between models based on parental haplotype and single locus polymorphism.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2013Article
- The first genetic map of the American cranberry: exploration of synteny conservation and quantitative trait loci.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2013Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The common assumption in quantitative trait locus (QTL) linkage mapping studies that parents of multiple connected populations are unrelated is unrealistic for many plant breeding programs. We remove this assumption and propose a Bayesian approach that clusters the alleles of the parents of the current mapping populations from locus-specific identity by descent (IBD) matrices that capture ancestral marker and pedigree information. Moreover, we demonstrate how the parental IBD data can be incorporated into a QTL linkage analysis framework by using two approaches: a Threshold IBD model (TIBD) and a Latent Ancestral Allele Model (LAAM). The TIBD and LAAM models are empirically tested via numerical simulation based on the structure of a commercial maize breeding program. The simulations included a pilot dataset with closely linked QTL on a single linkage group and 100 replicated datasets with five linkage groups harboring four unlinked QTL. The simulation results show that including parental IBD data (similarly for TIBD and LAAM) significantly improves the power and particularly accuracy of QTL mapping, e.g., position, effect size and individuals' genotype probability without significantly increasing computational demand.
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Registered trials
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.