Browsing by Subject "Genkartierung"

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Genomic analyses of behavior traits in laying hen lines divergently selected for feather pecking
(2021) Iffland, Hanna; Bennewitz, Jörn
Feather pecking is a longstanding problem in commercial layer flocks. It often causes injured birds and even cannibalism. In the past, hens were beak trimmed to reduce feather pecking. Nevertheless, this procedure is already prohibited in some EU countries. Hence, a solution to this problem is urgently needed. The experimental populations analyzed in this thesis were formed by hens based on a White Leghorn layer strain which were divergently selected for high and low feather pecking since 1995. The first experimental population of this thesis was an F2 cross of about 900 hens which was established of the 10th generation of the pure selection lines. The second population consisted of about 500 hens of the 15th generation of these two lines. The aim of this thesis was to gain further knowledge of the genetic background of feather pecking and its relation to additional behavior traits and the gut microbiome. In chapter one, a novel model to detect extreme feather pecking hens was developed. Therefore, a mixture of two negative binomial distributions was fitted to feather pecking data of the F2 cross. With the estimated parameters, the trait posterior probability of a hen to belong to the extreme feather pecking subgroup (pEFP) was calculated. The fear tests tonic immobility and emerge box were conducted at juvenile and adult age of the hens to relate fearfulness to pEFP. After dichotomization, all traits were analyzed in a multivariate threshold model and subsequent genomewide association studies (GWAS) were performed. The fit revealed that extreme feather peckers made up a proportion of about one third of the hens. The new trait pEFP has a medium heritability of 0.35 and is positively correlated with the fear traits. Breeding for this new trait could be an option to reduce the proportion of extreme feather peckers. An index of fear related traits might serve as a proxy to breed indirectly against pEFP. In chapter two, the model to detect extreme feather pecking hens was applied to the pure selection lines. After calculation of the trait pEFP, GWAS with a subsequent post GWAS analysis were performed. Additionally, to find genomic regions influencing feather pecking, selection signatures were mapped by applying the intra-population iHS and the inter-population FST approach. Mapping of selection signatures revealed no clear regions under selection. GWAS revealed a region on chromosome one, where the existence of a quantitative trait locus (QTL) influencing feather pecking is likely. The candidate genes found in this region are a part of the GABAergic system. Despite the polygenic nature of feather pecking, selection on these candidate genes may reduce the extreme occurrence of it. In chapter three, the relation between agonistic behavior and feather pecking was analyzed. Therefore, the active parts of the traits (delivery of feather pecking, aggressive pecking or threatening) as well as the passive parts (reception of the traits) were considered. These groups of traits were additionally summarized by means of an index formation which led to the two additional traits Activity and Passivity, because all these behaviors are undesired in their excessive manifestations. Moreover, Indices were built by subtracting the passive traits from the respective active traits to obtain the feather pecking index, the aggression index and the threat index. Phenotypic correlations were estimated between all traits which were followed by heritability estimations and GWAS. Feather pecking is significantly positively correlated with the agonistic traits in both lines. The active traits and the feather pecking index show medium heritabilities. Hence, selection on high feather pecking leads to an increase of agonistic behavior whereas the correlation probably depends on the phase of establishing the social hierarchy and might disappear, after a stable ranking is established. GWAS revealed that the heritable traits in this study seem to be typical quantitative traits. Chapter four provides the analyses of the gut microbial composition of the two feather pecking lines, followed by the estimation of microbiabilities for feather pecking and the two agonistic behavior traits, to study the influence of the gut microbiome on behavior. Microbiota samples from digesta and mucosa were taken from ileum and caecum. The microbial communities were determined by using 16S RNA gene sequencing techniques. Although both lines differ significantly in some fractions of their gut microbial composition, the microbial animal effects were mostly negligibly small. Thus, the calculated microbiabilities were close to zero and not significant in both lines and for all traits investigated. Hence, trait variations were not affected by the gut microbial composition in both feather pecking lines. The thesis ends with a general discussion where additional results of a meta-analysis of pEFP and breeding strategies against feather pecking are considered.
Molecular genetic analysis of modified recurrent full-sib selection in two European F 2 flint maize populations
(2007) Falke, Karen Christin; Melchinger, Albrecht E.
The continuous improvement of breeding material is a main goal in plant breeding. However, many breeding methods result in a reduction of the genetic variation of the breeding material. The primary objective of recurrent selection (RS) methods is to assure a long-term selection response for the target traits while maintaining the genetic variability of the germplasm for continued selection. The main goal of this thesis research was the molecular evaluation of two European F2 flint maize populations under modified recurrent full-sib selection. In detail, the objectives were to (1) investigate linkage mapping with intermating populations, (2) verify the decay of parental linkage disequilibrium (LD) present in the F2 base population through three generations of intermating, (3) identify quantitative trait loci (QTL) of traits under selection, (4) separate the effects of random genetic drift and selection on allele frequency changes during the selection procedure in QTL regions, (5) determine the extent of LD build-up by selection, and (6) analyze the effects of LD on the selection response. Four homozygous inbred lines (A, B, C, and D) were crossed to developed 380 F2:3 lines of population A × B and 140 F3:4 lines of population C × D. The F2 generations of both populations were intermated for three generations by chain crossing to produce F2Syn3 populations. Starting from the F2Syn3 populations, four (A × B) and seven (C × D) cycles of modified recurrent full-sib selection were conducted using a pseudo-factorial mating design. The selection procedure was based on a selection index. For the marker assays, a total of 104 (A × B) and 101 (C × D) SSRs were employed to genotype random subsets of 146 F2:3 lines in A × B and 110 F3:4 lines C × D, 148 F2Syn3 plants and the parents of the 36 selected full-sib families in each cycle of both RS programs. Genetic linkage maps were constructed for population F2:3 (A × B) and F3:4 (C × D) and of both intermated populations F2Syn3. In contrast to earlier studies, mapping methods developed specifically for intermated populations were applied and, thus, the estimated recombination frequencies referred to a single meiosis. Consequently, the map expansion reported in earlier studies was neither expected nor observed. To verify the expected higher mapping resolution of intermated compared with the respective base population, the precision of estimates of the recombination frequencies r was quantified with the average information per individual ir relative to an F2 individual. For infinite population sizes of intermated populations ir > 1 when r < 0.142, however, with a population size of N = 240, as used in our mapping study, ir >1 only when r < 0.04. Therefore, we conclude that random genetic drift has a sizeable effect on ir and, thus, can overrule the advantages of intermating mapping populations. Three generations of intermating were primarily conducted to reduce the initial parental LD between linked loci in the F2 populations and its negative influence on the selection response. Our results demonstrated that the observed decay of LD agreed well with the theoretical expectations. In our modified recurrent full-sib selection program, a comparatively high selection response was reached. An evaluation at the molecular level revealed that further selection response can be expected, because neither fixation nor extinction of alleles was observed at the investigated marker loci. However, using SSR markers we also detected migration effects since the first selection cycles. Selection and random genetic drift are main forces affecting changes in allele frequencies and, therefore, the selection response of RS programs. In our study, we analyzed changes in allele frequencies employing a test that allows the separation of selection and random genetic drift. Significant allele frequency changes due to selection were observed for 23% (C0 vs. C1) and 20% (C0 vs. C4) of all loci in population A × B and for 6% (C0 vs. C1) and 13% (C0 vs. C7) in population C × D. In the base populations F2:3 (A × B) and F3:4 (C × D), several QTL for selection index and its components were detected. At some of them, loci displayed significant allele frequency changes due to selection. Selection is expected to increase the frequency of favorable alleles and simultaneously build up a negative LD between them, which causes a reduction in and, hence, a decline in the selection response. However, the development of LD in our study displayed an erratic change over the selection cycles with only slight increases in positive and negative LD. The reduction in due to a build-up of negative LD is expected only if negative LD is observed at many marker loci. Therefore, we concluded that LD due to selection did not limit the selection response in our RS programs.
Phänotypische und molekulare Analyse von Kreuzungsnachkommen auf Resistenz gegen Ährenfusariosen bei Triticale (x Triticosecale Wittmack)
(2011) Großmann, Maren; Großmann, Maren
Fusarium head blight (FHB) is an epidemic disease of cereals but disease control still is insufficiently possible. Resistance breeding can be addressed as one approach to reduce the mycotoxin contents. Since 2006 the European Union had strict rules governing the values for Desoxinivalenol (DON) in food products. The extraordinary loads through mycotoxins in triticale, which are caused by FHB, lead to large reductions in grain yield and quality. Beyond the fact that it can cause health issues in animals, especially in pig feed, it may induce financial burdens for farming industries. Resistance against FHB is inherited quantitatively with mainly additive effects and therefore is only recorded by complex field experiments. Molecular markers accelerate resistance breeding and enable specific introgressions of favorable QTL. The main topic of this thesis is to show the application possibilities of molecular markers for the investigation of FHB resistance in triticale. In detail this study aims to analyze factors leading to a minimized mycotoxin accumulation in perennial field trials at several locations. Furthermore genetic maps of two different crossing populations were compiled and QTL mapping for ear appearance, plant height, DON content and FHB resistance was implemented. For all populations significant varieties had been displayed for all characteristics. The average values for FHB rate were between 8 and 43 % depending on year and location. The heritability?s showed high values for each population (h2 = 0.7 ? 0.82). The substantial genotype-environment-interaction pointed out the importance of field experiments. Furthermore no significant correlation was obtained between ear appearance and plant height. Due to the fact that the correlation factor between DON-content and FHB rate was very low (r = 0.32) to moderate (r = 0,65). Therefore no assumption about the DON-content subjected to the FHB rate could be made. The mapping of both populations LASKO x ALAMO and LASKO x TRIMESTER has been accomplished with SSR- and DArT-markers. The rate of polymorphism could be increased from 7 - 12 % respectively to 9 - 18 %. Genetic maps were constructed with length of 1.815 and 1.407 cM. They indicated 5.19 and 4.54 cM in their average marker distances. Throughout the QTL mapping several QTL were detected (6 QTL for ear appearance, 4 QTL for plant height, 1 QTL for DON-content and 4 QTL for FHB rate). These QTL explained 8 to 66 % of the phenotypical variance. In addition crossing populations of LASKO x TRIMESTER showed 2 QTL for ear appearance, 1 for plant height and 2 QTL for FHB resistance, which could explain 3 to 41 % of the phenotypical variance. This was also observed in several other QTL-surveys for wheat. Prospectively using molecular markers and genetically engineered methods will increase the research and development of resistant varieties and lead to a reduced mycotoxin accumulation. So far neither genetic maps nor any QTL studies for FHB resistance or DON-content in triticale have been published. Due to the fact that resistance is transmitted by several genes numerous artificial inoculations have to be carried out during breeding. Additive gene effects are useful to combine several resistance genes from different parents. Established methods in plant breeding such as recurrent selection, phenotypical and marker-based selection are successfully in use to reduce FHB- symptoms and to reduce the mycotoxin value but these methods have to be improved. The results of this thesis are promising for a superior resistance breeding in the future.
Using genome-wide association studies to map genes for complex traits in porcine F2 crosses
(2018) Schmid, Markus; Bennewitz, Jörn
In the era of genomics, genome-wide association studies (GWASs) have become the method of choice for gene mapping. This is still of great interest to infer the genetic architecture of quantitative traits and to improve genomic selection in animal breeding. Formerly, linkage analyses were conducted in order to map genes. Therefore, many F2 cross populations were generated by crossing genetically divergent lineages in order to create informative experimental populations. However, a small number of markers and the limited meiotic divisions led to imprecise mapping results. The main objective of the present study was to investigate the use of existing porcine F2 cross data, extended towards single nucleotide polymorphism (SNP) chip genotype information, for quantitative trait loci (QTL) mapping in the genomic era. A special focus was on mapping genes that also segregate within the Piétrain breed since this is an important sire line and genomic selection is applied in this breed. Chapter 1 is a review article of statistical models and experimental populations applied in GWASs. This chapter gives an overview of methods to conduct GWASs using single-marker models and multi-marker models. Further, approaches taking non-additive genetic effects or genotype-by-environment interactions into account are described. Finally, post-GWAS analysis possibilities and GWAS mapping populations are discussed. In chapter 2, the power and precision of GWASs in different F2 populations and a segregating population was investigated using simulated whole-genome sequence data. Further, the effect of pooling data was determined. GWASs were conducted for simulated traits with a heritability of 0.5 in F2 populations derived from closely and distantly related simulated founder breeds, their pooled datasets, and a sample of the common maternal founder breed. The study showed that the mapping power was high (low) in F2 crosses derived from distantly (closely) related founder breeds and highest when several F2 datasets were pooled. By contrast, a low precision was observed in the cross with distantly related founder breeds and the pooling of data led to a precision that was between the two crosses. For genes that also segregated within the common founder breed, the precision was generally elevated and, at equal sample size, the power to map QTL was even higher in F2 crosses derived from closely related founder breeds compared with the founder breed itself. Within and across linkage disequilibrium (LD) structures of such F2 populations were examined in chapter 3 by separately and jointly (pooled dataset) analyzing four F2 datasets generated from different founder breeds. All individuals were genotyped with a 62k SNP chip. The LD decay was faster in crosses derived from closely related founder breeds compared with crosses from phylogenetically distantly related founder populations and fastest when the data of all crosses were pooled. The pooled dataset was also used to map QTL for the economically important traits dressing out and conductivity applying single-marker and Bayesian multi-marker regressions. For these traits, several genome-wide significant association signals were mapped. To infer the suitability of F2 data to map genes in a segregating breeding population, GWAS results of a pooled F2 cross were validated in two samples of the German Piétrain population (chapter 4). All individuals were genotyped using standard 62k SNP chips. The pooled cross contained the data of two F2 crosses, both had Piétrain as one founder breed, and consisted of 595 individuals. Initially, GWASs were conducted in the pooled F2 cross for the production traits dressing yield, carcass length, daily gain and drip loss. Subsequently, QTL core regions around significant trait associated peaks were defined. Finally, SNPs within these core regions were tested for association in the two samples of the current Piétrain population (771 progeny tested boars and 210 sows) in order to validate them in this breed. In total, 15 QTL were mapped and 8 (5) of them were validated in the boar (sow) validation dataset. This approach takes advantage of the high mapping power in F2 data to detect QTL that may not be found in the segregating Piétrain population. The findings showed that many of the QTL mapped in F2 crosses derived from Piétrain still segregate in this breed, and thus, these F2 datasets provide a promising database to map QTL in the Piétrain breed. The thesis ends with a general discussion.