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Genetics. 2014 Sep;198(1):117-28. doi: 10.1534/genetics.114.167577.

Characterizing uncertainty in high-density maps from multiparental populations.

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School of Mathematics and Physics, University of Queensland, St. Lucia, Queensland, Australia 4072.
Plant Industry and Food Futures National Research Flagship, Commonwealth Scientific and Industrial Research Organization, Acton, Australian Capital Territory, Australia, 2601.
Computational Informatics and Food Futures National Research Flagship, Commonwealth Scientific and Industrial Research Organization, Dutton Park, Queensland, Australia 4102


Multiparental populations are of considerable interest in high-density genetic mapping due to their increased levels of polymorphism and recombination relative to biparental populations. However, errors in map construction can have significant impact on QTL discovery in later stages of analysis, and few methods have been developed to quantify the uncertainty attached to the reported order of markers or intermarker distances. Current methods are computationally intensive or limited to assessing uncertainty only for order or distance, but not both simultaneously. We derive the asymptotic joint distribution of maximum composite likelihood estimators for intermarker distances. This approach allows us to construct hypothesis tests and confidence intervals for simultaneously assessing marker-order instability and distance uncertainty. We investigate the effects of marker density, population size, and founder distribution patterns on map confidence in multiparental populations through simulations. Using these data, we provide guidelines on sample sizes necessary to map markers at sub-centimorgan densities with high certainty. We apply these approaches to data from a bread wheat Multiparent Advanced Generation Inter-Cross (MAGIC) population genotyped using the Illumina 9K SNP chip to assess regions of uncertainty and validate them against the recently released pseudomolecule for the wheat chromosome 3B.


High-density genotyping, Multiparent Advanced Generation Inter-Cross (MAGIC); MPP; Multiparental populations; Single nucleotide polymorphism (SNP); linkage map; multiparental populations; recombinant inbred line; recombination fraction; variability

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