University of Oulu

Boby Mathew, Jens Léon, Said Dadshani, Klaus Pillen, Mikko J Sillanpää, Ali Ahmad Naz, Importance of correcting genomic relationships in single-locus QTL mapping model with an advanced backcross population, G3 Genes|Genomes|Genetics, Volume 11, Issue 6, June 2021, jkab105,

Importance of correcting genomic relationships in single-locus QTL mapping model with an advanced backcross population

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Author: Mathew, Boby1; Léon, Jens1; Dadshani, Said1;
Organizations: 1Institute of Crop Science and Resource Conservation, Department of Plant Breeding, University of Bonn, 53115 Bonn, Germany
2Department of Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
3Department of Mathematical Sciences, University of Oulu, FIN-90014 Oulu, Finland
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 1.6 MB)
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Language: English
Published: Genetics Society of America, 2021
Publish Date: 2021-09-21


Advanced backcross (AB) populations have been widely used to identify and utilize beneficial alleles in various crops such as rice, tomato, wheat, and barley. For the development of an AB population, a controlled crossing scheme is used and this controlled crossing along with the selection (both natural and artificial) of agronomically adapted alleles during the development of AB population may lead to unbalanced allele frequencies in the population. However, it is commonly believed that interval mapping of traits in experimental crosses such as AB populations is immune to the deviations from the expected frequencies under Mendelian segregation. Using two AB populations and simulated data sets as examples, we describe the severity of the problem caused by unbalanced allele frequencies in quantitative trait loci mapping and demonstrate how it can be corrected using the linear mixed model having a polygenic effect with the covariance structure (genomic relationship matrix) calculated from molecular markers.

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Series: G3. Genes, genomes, genetics
ISSN: 2160-1836
ISSN-E: 2160-1836
ISSN-L: 2160-1836
Volume: 11
Issue: 6
Article number: jkab105
DOI: 10.1093/g3journal/jkab105
Type of Publication: A1 Journal article – refereed
Field of Science: 112 Statistics and probability
1184 Genetics, developmental biology, physiology
Funding: The phenotyping and genotyping works were funded by the German Plant Genome Research Initiative (GABI) of the Federal Ministry of Education and Research (BMBF, project 312862) and by the Federal Ministry of Agriculture and Nutrition (Grant # IdMaRo-100203349), respectively.
Copyright information: © The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (, which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact