Browsing by Subject "Quantitative trait locus"

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Biometrical Analyses of Epistasis and the Relationship between Line per se and Testcross Performance of Agronomic Traits in Elite Populations of European Maize (Zea mays L.)
(2005) Mihaljevic, Renata; Melchinger, Albrecht E.
Relations of yield and other important agronomic traits of inbred lines to the same traits in hybrids have been studied from the time of initiation of hybrid breeding to the present. Because crossing lines to a tester and conducting yield trials are expensive and time-consuming, reliable information on inbred lines that is indicative of their testcross performance is crucial for optimum testing schemes in hybrid breeding as well as simultaneous improvement of commercial hybrids and their inbred parents. It has therefore been of great importance to determine the magnitude of correlation between line per se performance (LP) and testcross performance (TP) and investigate if epistasis influences this correlation. The comprehensive study on hand was performed with five populations (F3 to F6 lines) differing in size (ranging from 71 to 344), level of inbreeding, and the number of common parents. The populations employed were derived from three biparental crosses within the heterotic pool of European elite flint maize (Zea mays L.). All five populations were evaluated for TP (using an unrelated dent tester inbred) of five agronomically important quantitative traits: grain yield, grain moisture, kernel weight, protein concentration, and plant height. Four of these populations were also evaluated for LP of the same five traits. The objectives were to (i) estimate phenotypic and genotypic correlations between LP and TP within four populations for all five traits, (ii) map quantitative trait loci (QTL) for LP and TP in four and five populations, respectively, for all five traits, (iii) validate estimated QTL effects and positions for TP by assessing QTL congruency among testcross populations differing in size and genetic background, (iv) determine the value of LP-QTL for the prediction of TP, (v) estimate the importance of epistatic effects for LP and TP of grain yield and grain moisture by generation means analysis as well as genome-wide testing for epistatic marker pairs, and (vi) draw conclusions regarding the prospects of marker-assisted selection (MAS). Genotypic correlations between LP and TP, rg(LP, TP), estimated herein were comparable with those obtained for European flint or U.S. dent material. The magnitude of rg(LP, TP) was trait-specific: for traits of high heritability, i.e. grain moisture, kernel weight, protein concentration, and plant height, estimates were generally larger than 0.7 across all four populations, whereas for grain yield, estimates were consistently lower and did not exceed the intermediate level of 0.5. For grain yield, lowest rg(LP, TP) were estimated with lowest precision (largest confidence intervals). This requires testing for both LP and TP and/or combining the data in a selection index to ensure sufficient inbred performance (seed production) and yield improvement. However, combined selection for LP and TP proved less efficient than sole selection for TP unless unadapted material was employed. For kernel weight, protein concentration, and plant height, we detected "large" congruent QTL across testcross populations derived from the same cross, which individually explained up to 46% of the validated genotypic variance p. However, as the p values estimated from validation were still below the corresponding heritability estimates, MAS will be superior to phenotypic selection only if it is more cost-efficient. For the above traits, similar numbers of QTL for LP and TP were detected across populations. More than half of the QTL regions detected for LP were in common for LP and TP in the largest population (N = 280). To assess the value of QTL identified for LP in predicting TP, we calculated the genotypic correlation rg(MLP, YTP). This parameter assesses QTL congruency for LP and TP quantitatively and is thus the key parameter for assessing the prospects of MAS. The number of common QTL for LP and TP (qualitative QTL congruency) was generally not indicative of the magnitude of rg(MLP, YTP) due to the differences in the effect size of the respective QTL detected for LP and used for the prediction of TP. For all traits, rg(MLP, YTP) were smaller than rg(LP, TP). This is because rg(MLP, YTP) is only predictive for the validated proportion of genotypic variance explained by the QTL for LP, which was generally below 50% because of the limited power of QTL detection, in particular with small sample sizes below 100. Only if QTL detected for LP explain a substantial proportion of the genotypic variance, MAS based on these QTL can be applied, provided it is more cost-efficient than an indirect phenotypic selection for TP based on LP. QTL detection power was drastically reduced for the complex trait grain yield with a presumably large number of small QTL underlying its genetic architecture. Thus, the number of common QTL for LP and TP as well as the QTL congruency across testcross populations was much lower for grain yield than the other four traits. Estimated gene action of QTL detected for LP was primarily additive for grain yield. Evidence for dominance and/or epistasis, which may be a reason for the low rg(LP, TP) and the low number of common QTL for LP and TP was generally weak. Both generation means analysis for LP and TP and genome-wide search for epistatic marker pairs yielded no evidence for epistasis. This is not only because the detected epistatic effects could not be validated, but also because there is low chance to find epistasis unless the generation examined displays the full epistatic variance such as expected from doubled haploids produced from an F1 cross. Thus, it is anticipated that the relative importance of epistatic effects in hybrid maize breeding may strongly increase with the currently happening shift in line development from recurrent selfing towards the production of doubled haploids.
Joint QTL analysis of three connected F2-crosses in pigs
(2012) Rückert, Christine; Bennewitz, Jörn
Mapping Quantitative Trait Loci (QTL) has received considerable attention in livestock genetic research over the last two decades. Knowledge of the location, the mode of inheritance and the size of effects of QTL contribute to a deeper understanding of the genetic architecture of quantitative or complex traits. Furthermore, mapped QTL were envisaged for use in so-called marker assisted selection programs. Before the era of genomics started, microsatellites were usually used as genetic markers for QTL mapping. In pigs, F2-crosses were frequently established from divergently selected founder breeds. Usually, the sizes of these F2-experiments are in the range of 300 individuals, which is too small to obtain sufficient statistical power to map QTL precisely. One large F2-experiment was set up in the 90th of the last century at the University of Hohenheim. Three F2-crosses from three genetically different founder breeds (Meishan, Pietrain and European Wild Boar) with almost 1000 individuals were genotyped and phenotyped for around 50 quantitative traits. In further studies, each of the crosses were analysed separately and more complex modes of inheritance were ignored. However, several researchers showed that a combined analysis with several QTL experiments can boost statistical power. Additionally, the mode of inheritance is sometimes not restricted to additive and dominant gene action. The overall aim of this thesis was the joint analysis of these three F2-crosses with more appropriate statistical models and to draw more precise conclusions about the QTL segregating within these experimental designs.