Potential causes of linkage disequilibrium in a European maize breeding program investigated with computer simulations

Abstract

Knowledge about the forces generating and conserving linkage disequilibrium (LD) is important for drawing conclusions about the prospects and limitations of association mapping. The objectives of our research were to examine the importance of (1) selection, (2) mutation, and (3) genetic drift for generating LD in a typical maize breeding program. We conducted computer simulations based on genotypic data of Central European maize open-pollinated varieties which have played an important role as founders of the European flint heterotic group. The breeding scheme and the dimensioning underlying our simulations reflect essentially the maize breeding program of the University of Hohenheim. Results suggested that in a plant breeding program of the examined dimension and breeding scheme, genetic drift and selection are major forces generating LD. The currently used population-based association mapping tests do not explicitly correct for LD caused by these two forces. Therefore, increased type I error rates are expected if these tests are applied to plant breeding populations. As a consequence, we recommend to use family-based association tests for association mapping approaches in plant breeding populations.

Unraveling the genetic architecture of subtropical maize (Zea mays L.) lines to assess their utility in breeding programs

“…The high LD regions were mostly interspersed with low LD regions, indicative of maize genome complexity and the random nature of recombination events across the genome [15,53]. However, extensive regions of high LD were found on chromosomes 3 and 8 from 94.6–95.1 Mb and 48.7–51.7 Mb, respectively; their presence may be due to recent allelic drift in the population (Figure 7) [54]. In almost all chromosomes, LD was lower near telomeric regions and higher in centromeric and pericentromeric regions.…”

QTL detection power of multi-parental RIL populations in Arabidopsis thaliana

“…Furthermore, the loci that explain the difference between subpopulations cannot be detected with such approaches. Therefore, the concept for mapping in multi-parental linkage mapping population was developed, which minimizes the effect of population structure by crossing diverse individuals, but still providing a high mapping resolution (Stich et al, 2007). Rebaï and Goffinet (1993) proposed the extension of the biparental population to a four-parental population, in which the parents were crossed in a half diallel.…”

Population genetic simulation and data analysis with Plabsoft

“…Further examples for simulation with Plabsoft are the studies conducted to evaluate the power of a new family-based association mapping test (Stich et al 2006b), simulate the breeding history of European maize for investigation of the causes of linkage disequilibrium in breeding programs (Stich et al 2007), and investigate the prediction error of markerbased predictions of the parental contribution to inbred lines derived from biparental crosses (Frisch and Melchinger 2006).…”