ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2021
An IBD-based mixed model approach for QTL mapping in multiparental populations.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 15 citations in OpenAlex.
- Genetic dissection of grain yield and correlated proxy traits under suboptimal conditions.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Dissecting the genetic basis of relevant fruit quality traits in interspecific grapevines (Horticulture research · 2026Article
- An olive parentage atlas: founder cultivars, regional diversification, and implications for breeding programs.BMC plant biology · 2026Article
- MAGIC populations: a next-generation framework for dissecting complex quantitative traits and accelerating molecular breeding in crops.Frontiers in plant science · 2026Review
- Optimization of crossing strategy based on the usefulness criterion in interpopulation crosses considering different marker effects among populations.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Unveiling yellow rust resistance in the near-Himalayan region: insights from a nested association mapping study.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Article
- Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea.The plant genome · 2024Article
- Modeling QTL-by-environment interactions for multi-parent populations.Frontiers in plant science · 2024Article
- Association Mapping and Expression Analysis of the Genes Involved in the Wood Formation of Poplar.International journal of molecular sciences · 2023Article
- Multi-parental fungal mapping population study to detect genomic regions associated with Pyrenophora teres f. teres virulence.Scientific reports · 2023Article
- A multi-locus linear mixed model methodology for detecting small-effect QTLs for quantitative traits in MAGIC, NAM, and ROAM populations.Computational and structural biotechnology journal · 2023Article
- statgenMPP: an R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of multi-parent populations.Bioinformatics (Oxford, England) · 2022Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
key messageThe identity-by-descent (IBD)-based mixed model approach introduced in this study can detect quantitative trait loci (QTLs) referring to the parental origin and simultaneously account for multilevel relatedness of individuals within and across families. This unified approach is proved to be a powerful approach for all kinds of multiparental population (MPP) designs. Multiparental populations (MPPs) have become popular for quantitative trait loci (QTL) detection. Tools for QTL mapping in MPPs are mostly developed for specific MPPs and do not generalize well to other MPPs. We present an IBD-based mixed model approach for QTL mapping in all kinds of MPP designs, e.g., diallel, Nested Association Mapping (NAM), and Multiparental Advanced Generation Intercross (MAGIC) designs. The first step is to compute identity-by-descent (IBD) probabilities using a general Hidden Markov model framework, called reconstructing ancestry blocks bit by bit (RABBIT). Next, functions of IBD information are used as design matrices, or genetic predictors, in a mixed model approach to estimate variance components for multiallelic genetic effects associated with parents. Family-specific residual genetic effects are added, and a polygenic effect is structured by kinship relations between individuals. Case studies of simulated diallel, NAM, and MAGIC designs proved that the advanced IBD-based multi-QTL mixed model approach incorporating both kinship relations and family-specific residual variances (IBD.MQMkin_F) is robust across a variety of MPP designs and allele segregation patterns in comparison to a widely used benchmark association mapping method, and in most cases, outperformed or behaved at least as well as other tools developed for specific MPP designs in terms of mapping power and resolution. Successful analyses of real data cases confirmed the wide applicability of our IBD-based mixed model methodology.
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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.