An improved method for quantitative trait loci detection and identification of within-line segregation in F2 intercross designs.

Genetics
Lars RönnegårdOrjan Carlborg

Abstract

We present a new flexible, simple, and powerful genome-scan method (flexible intercross analysis, FIA) for detecting quantitative trait loci (QTL) in experimental line crosses. The method is based on a pure random-effects model that simultaneously models between- and within-line QTL variation for single as well as epistatic QTL. It utilizes the score statistic and thereby facilitates computationally efficient significance testing based on empirical significance thresholds obtained by means of permutations. The properties of the method are explored using simulations and analyses of experimental data. The simulations showed that the power of FIA was as good as, or better than, Haley-Knott regression and that FIA was rather insensitive to the level of allelic fixation in the founders, especially for pedigrees with few founders. A chromosome scan was conducted for a meat quality trait in an F(2) intercross in pigs where a mutation in the halothane (Ryanodine receptor, RYR1) gene with a large effect on meat quality was known to segregate in one founder line. FIA obtained significant support for the halothane-associated QTL and identified the base generation allele with the mutated allele. A genome scan was also performed in a previo...Continue Reading

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Citations

Jan 19, 2011·Genetics, Selection, Evolution : GSE·Francois BesnierOrjan Carlborg
Jun 30, 2009·BMC Genetics·Lars RönnegårdOrjan Carlborg
Jul 17, 2012·Developmental and Comparative Immunology·Weronica EkSusanne Kerje
Dec 13, 2016·Genetic Epidemiology·Hua ZhouEric M Sobel
Mar 27, 2009·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·L RönnegårdD von Rosen
Oct 15, 2013·G3 : Genes - Genomes - Genetics·Ronald M NelsonOrjan Carlborg
Mar 1, 2019·G3 : Genes - Genomes - Genetics·Jilun MengNorbert Reinsch

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