QTL linkage analysis of connected populations using ancestral marker and pedigree information
| Autor: | O. S. Smith, L. Radu Totir, Martin P. Boer, Cajo J. F. ter Braak, Christopher R. Winkler, Marco C. A. M. Bink |
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| Jazyk: | angličtina |
| Rok vydání: | 2012 |
| Předmět: |
Genetic Markers
Linkage disequilibrium Breeding program Genotype Quantitative Trait Loci selection Quantitative trait locus Biology Breeding maize Genes Plant Identity by descent Wiskundige en Statistische Methoden - Biometris Zea mays Linkage Disequilibrium kernel hardness Family-based QTL mapping Genetic linkage Inclusive composite interval mapping wheat Genetics Mathematical and Statistical Methods - Biometris identity Alleles Crosses Genetic Linkage (software) Original Paper model Models Genetic food and beverages Chromosome Mapping Bayes Theorem General Medicine families PE&RC Biometris Genetics Population Haplotypes plant-populations quantitative trait loci Agronomy and Crop Science dough strength Biotechnology |
| Zdroj: | TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik Theoretical and Applied Genetics, 124(6), 1097-1113 Theoretical and Applied Genetics 124 (2012) 6 |
| ISSN: | 1432-2242 0040-5752 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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