Browsing by Subject "Maize elite germplasm"

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    Linkage disequilibrium and association mapping in elite germplasm of European maize
    (2006) Stich, Benjamin; Melchinger, Albrecht E.
    Linkage mapping has become a routine tool for the identification of quantitative trait loci (QTL) in plants. An alternative, promising approach is association mapping, which has been successfully applied in human genetics to detect QTL coding for diseases. The objectives of this research were to examine the feasibility of association mapping in elite maize breeding populations and develop for this purpose appropriate biometric methods. The feasibility of association mapping depends on the extent of linkage disequilibrium (LD) as well as on the forces generating and conserving LD in the population under consideration. The objectives of our studies were to (i) examine the extent and genomic distribution of LD between pairs of simple sequence repeat (SSR) marker loci, (ii) compare these results with those obtained with amplified fragment length polymorphism (AFLP) markers, and (iii) investigate the forces generating and conserving LD in plant breeding populations. Our studies were based on experimental data of European elite maize inbreds as well as on computer simulations modeling the breeding history of the European flint heterotic group. The experimental results on European elite maize germplasm suggested that the extent of LD between SSR markers as well as AFLP markers are encouraging for the detection of marker-phenotype associations in genomewide scans. In populations with a short history of recombination, SSRs are advantageous over AFLPs in that they have a higher power to detect LD. In contrast, in populations with a long history of recombination, for which no LD is expected between pairs of SSR markers, AFLP markers should be favored over SSRs because then their higher marker density that is generated with a fixed budget can be used. Furthermore, the results of our experimental and simulation studies indicated that not only physical linkage is a cause of LD in plant breeding populations, but also relatedness, population stratification, genetic drift, and selection. So far, in plant genetics the logistic regression ratio test (LRRT) has been applied as a population-based association mapping approach. However, this test does only correct for LD caused by population stratification. The objectives of the presented study were to (i) adapt the quantitative pedigree disequilibrium test to typical pedigrees of inbred lines produced in plant breeding programs and (ii) compare the newly developed quantitative inbred pedigree disequilibrium test (QIPDT) and the commonly employed LRRT with respect to the power and type I error rate of QTL detection. This study was based on computer simulations modeling the breeding history of the European maize heterotic groups. In QIPDT the power of QTL detection was higher with 75 extended pedigrees than in LRRT with 75 independent inbreds. Furthermore, while the type I error rate of LRRT surpassed the nominal ® level, the QIPDT adhered to it. These results suggested that the QIPDT is superior to the LRRT for genome-wide association mapping if data collected routinely in plant breeding programs are available. Epistatic interactions among QTL contribute substantially to the genetic variation in complex traits. The main objectives of our study were to (i) investigate by computer simulations the power and proportion of false positives for detecting three-way interactions among QTL involved in a metabolic pathway in populations of recombinant inbred lines (RILs) derived from a nested design and (ii) compare these estimates to those obtained for detecting three-way interactions among QTL in RIL populations derived from diallel and different partial diallel mating designs. The computer simulations of this study were based on single nucleotide polymorphism haplotype data of 26 diverse maize inbreds. The power and proportion of false positives to detect three-way interactions with 5000 RILs derived from a nested design was relatively high for both the 4 QTL and the 12 QTL scenario. Higher power to detect three-way interactions was observed for RILs derived from optimally allocated distancebased designs than for RILs derived from a nested or diallel design. Our results suggested that association mapping methods adapted to the special features of plant breeding populations have the potential to overcome the limitations of classical linkage mapping methods.