Model selection for quantitative trait loci mapping in a full-sib family

Abstract

Statistical methods for mapping quantitative trait loci (QTLs) in full-sib forest trees, in which the number of alleles and linkage phase can vary from locus to locus, are still not well established. Previous studies assumed that the QTL segregation pattern was fixed throughout the genome in a full-sib family, despite the fact that this pattern can vary among regions of the genome. In this paper, we propose a method for selecting the appropriate model for QTL mapping based on the segregation of different types of markers and QTLs in a full-sib family. The QTL segregation patterns were classified into three types: test cross (1:1 segregation), F2 cross (1:2:1 segregation) and full cross (1:1:1:1 segregation). Akaike’s information criterion (AIC), the Bayesian information criterion (BIC) and the Laplace-empirical criterion (LEC) were used to select the most likely QTL segregation pattern. Simulations were used to evaluate the power of these criteria and the precision of parameter estimates. A Windows-based software was developed to run the selected QTL mapping method. A real example is presented to illustrate QTL mapping in forest trees based on an integrated linkage map with various segregation markers. The implications of this method for accurate QTL mapping in outbred species are discussed.

QTL associated with resistance to cassava brown streak and cassava mosaic diseases in a bi-parental cross of two Tanzanian farmer varieties, Namikonga and Albert

“…It is known to have a large deleterious genetic load and suffers high levels of inbreeding depression (Ceballos et al 2010 ). For these reasons, QTL mapping is largely done in F 1 populations (Hayashi and Awata 2004 ), although occasionally F 2 populations have been generated (Tong et al 2012 ). The advantages of an F 1 population are that it is relatively quick to generate (one season/year) and a reasonable population size can be obtained, although it is difficult to detect purely recessive QTL that requires the homozygous state for expression.…”

Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing

“…deltoides and P . simonii [ 46 , 47 ]. The two linkage maps will also allow for comparative genomics among different species of Populus , and provide additional information on evolution in poplar.…”

Genetic Map and QTL Analysis of Agronomic Traits in a Diploid Potato Population using Single Nucleotide Polymorphism Markers

“…In general, the estimation of the recombination frequencies has been based on two‐point (Maliepaard et al, 1997; Ritter et al, 1990; Ritter and Salamini, 1996), three‐point (Ridout et al, 1998; Wu et al, 2002), and different multipoint maximum likelihood methods (Tong et al, 2010; Van Ooijen, 2011). Similarly, QTL models for complex pedigree and biparental outbreed populations have been developed and described (Gazaffi et al, 2014; Tong et al, 2012). The QTL detection and estimation of allelic effects are based on conditional QTL probabilities segregating for up to four genotypic classes in 1:1:1:1 and their linkage phases.…”