Quantitative Trait Loci (QTL) Detection in Multicross Inbred Designs

Abstract

Mapping quantitative trait loci in plants is usually conducted using a population derived from a cross between two inbred lines. The power of such QTL detection and the parameter estimates depend largely on the choice of the two parental lines. Thus, the QTL detected in such populations represent only a small part of the genetic architecture of the trait. In addition, the effects of only two alleles are characterized, which is of limited interest to the breeder, while common pedigree breeding material remains unexploited for QTL mapping. In this study, we extend QTL mapping methodology to a generalized framework, based on a two-step IBD variance component approach, applicable to any type of breeding population obtained from inbred parents. We then investigate with simulated data mimicking conventional breeding programs the influence of different estimates of the IBD values on the power of QTL detection. The proposed method would provide an alternative to the development of specifically designed recombinant populations, by utilizing the genetic variation actually managed by plant breeders. The use of these detected QTL in assisting breeding would thus be facilitated. T HE availability of molecular markers in the 1980scalled the fixed-model approach (Xu and Atchley 1995) since it considers a fixed number of distinct alleles opened a new scope for quantitative genetics and breeding. It was anticipated that the manipulation of (most often two) at each putative QTL. Statistical methods for the QTL analysis of biparental populations unloci underlying quantitative traits (QTL) would be as easily feasible as with Mendelian factors. This, however, derwent successive improvements through the advent of interval mapping (Lander and Botstein 1989) and has generally not been the case, despite the large corpus of theoretical studies on marker-assisted selection (MAS;

Quantitative Trait Loci Controlling Fruit Size and Other Horticultural Traits in Bell Pepper (Capsicum annuum)

“…Quantitative trait locus analyses are used to study complex traits by predicting the regions in the genome that affect the traits and estimating the effect of each region. The power to detect QTLs is determined by genetic and phenotypic distance between parental lines, population size, and experimental designs that affect heritability (Crepieux et al, 2004;Hackett, 2002). Fruit-related QTL studies in pepper have been reported in different pairs of parents, with both intraspecific and interspecific populations (Barchi et al, 2007(Barchi et al, , 2009Chaim et al, 2001;Dwivedi et al, 2013;Han et al, 2016;Rao et al, 2003;Yarnes et al, 2012;Zygier et al, 2005).…”

Mixed linear model approaches in mapping QTLs with epistatic effects by a simulation study

“…Different mixed models have been proposed to map QTLs in complex pedigrees. Crepieux et al (2004) proposed an identity by descent QTL mapping method using plant breeding data for self-pollinated crops. Crepieux et al (2005) used this method to identify one QTL for kernel hardness and two QTLs for dough strength from data available in a wheat breeding program.…”

Challenges for effective marker-assisted selection in plants

“…If MAS is more costly than phenotypic selection, as is generally the case for selection on a marker-phenotype index (see Moreau et al 2000), this is a disincentive to its use. One solution to the need to increase sample size at low cost is to use existing pedigrees, as opposed to designing new specific crosses (Crepieux et al 2004). More generally, that would be almost equivalent to considering the whole set of available commercial and wild resources in a species as a vast (structured) population, and applying strategies already undertaken in outbred populations (animals) and humans.…”