Browsing by Subject "Genetik"

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Analyse komplexer Merkmale beim Schwein mittels SNP-Chip Genotypen, Darmmikrobiota- und Genexpressionsdaten
(2017) Maushammer, Maria; Bennewitz, Jörn
In the present scientific research, SNP chip genotypes, gut microbiota and gene expression data were used for analysing complex traits in a Piétrain population. These data were collected from around 200 performance tested sows and were used for genetic and microbial analyses of complex trait as well as for structural and functional meat quality traits. The gut microbiome plays a major role in the immune system development, state of health and energy supply of the host. Quantitative-genetic methods were applied to analyse the interrelationship between pig gut microbiota compositions, complex traits (daily gain, feed conversion and feed intake) and pig genomes. The specific aims were to characterize the gut microbiota of the pigs, to analyse the effects of host genetics on gut microbial composition, and to investigate the role of gut microbial composition on the host’s complex traits. The pigs were genotyped with a standard 60K SNP chip. Microbial composition was characterized by 16S rRNA gene amplicon sequencing technology. Ten out of 51 investigated bacterial genera showed a significant host heritability, ranging from 0.32 to 0.57. Conducting genome wide association analysis showed associations of 22 SNPs and six bacterial genera. The potential candidate genes identified are involved in the immune system, mucosa structure and secretion of digestive juice. These results show, that parts of the gut microbiota are heritable and that the gut microbiome can be seen as quantitative trait. Microbial mixed linear models were applied to estimate the microbiota variance for each of the investigated traits. The fraction of phenotypic variance explained by the microbial variance was 0.28, 0.21, and 0.16 for daily gain, feed conversion, and feed intake, respectively. The SNP data and the microbiota data were used to predict the phenotypes of the traits using both, genomic best linear unbiased prediction (G-BLUP) and microbial best linear unbiased prediction (M-BLUP) methods. The prediction accuracies of G-BLUP were 0.35, 0.23, and 0.20 for daily gain, feed conversion, and feed intake, respectively. The corresponding prediction accuracies of M-BLUP were 0.41, 0.33, and 0.33. Thus, the gut microbiota can be seen as an explaining variable for complex traits like daily gain, feed conversion and feed intake. In addition, in combination with meat quality traits, transcript levels of muscle tissue were analysed at time of slaughtering. This study should give an insight into the biological processes involved in meat quality characteristics. The aims were to functionally characterise differentially expressed genes, to link the functional information with structural information obtained from GWAS, and to identify potential candidate genes based on these results. An important meat quality trait is the intramuscular fat content, since it affects the juiciness, the taste and the tenderness of the meat. Another important trait is drip loss which causes not only a loss of weight but also a loss of important proteins. Both traits have an impact on the consumer acceptance of fresh meat products. For each of the two traits, eight discordant sibling pairs were selected out of the Piétrain sample and were used for genome-wide gene expression analyses. Thirty five and 114 genes were identified as differentially expressed and trait correlated genes for intramuscular fat content and drip loss, respectively. On the basis of functional annotation, gene groups belonging to the energy metabolism of the mitochondria, the immune response and the metabolism of fat, were associated with intramuscular fat content. Gene groups associated with protein ubiquitination, mitochondrial metabolism, and muscle structural proteins were associated with drip loss. Furthermore, genome-wide association analyses were carried out for these traits and their results were linked to the genome-wide expression analysis by functional annotation. In this context, intramuscular fat was related to muscle contraction, transmembrane transport and nucleotide binding. Drip loss was characterized by the endomembrane system, the energy generation of cells, and phosphorus metabolic processes. Three and four potential candidate genes were identified for intramuscular fat content and drip loss, respectively.
Analyses of quantitative traits in varying environments in pigs and Brown Swiss cattle
(2020) Imort-Just, Nina Annik; Bennewitz, Jörn
Complex breeding programmes are used worldwide to achieve genetic progress in quantitative traits. These programmes are basically similarly structured, independent of breed and species, and are characterised by successive steps. The adjustment and revision of breeding programmes is of ongoing interest due to several reasons, e.g. research findings and various political, economic, social and ethical aspects. For the long-term improvement of livestock populations, multiple traits are included in the breeding goals of such programmes. Unfavourable genetic correlations between economically important production traits and functional traits compromise the genetic progress in animal health and welfare. Novel functional and behavioural traits and the adjustment of relative economic weights for the optimisation of total merit indices are investigated in research projects. In addition, genotype by environment interactions (GxE) can influence the genetic improvement of livestock populations and their consideration is crucial due to the globalisation of breeding structures and associated varying production environments. The main objectives of this thesis were 1) to investigate novel behavioural traits in pig breeding, 2) to derive environmental-specific relative economic weights based on consumers preferences for Brown Swiss cattle, 3) to estimate GxE at a trait and an index level by applying bivariate sire models in Brown Swiss cattle and 4) to analyse GxE for different production and functional traits in Brown Swiss cattle using reaction norm models. In Chapter 1 genetic parameters for mothering ability traits were estimated. Heritabilities (h²) were estimated by applying a linear mixed- and a threshold model, ranging between 0.02 to 0.07 and 0.05 to 0.15, respectively. The slightly higher estimates for the repeatability ranged from 0.05 to 0.09 and from 0.08 to 0.17, indicating the influence of the permanent environment. Highest h² were found for the group- and nursing behaviour of the sows. Highest genetic correlations were found between group-/nursing behaviour and litter balance and piglet weaning weight with estimates between 0.71 and 0.86. Accelerating genetic gain for improved mothering ability in sows is possible. In Chapter 2, the importance of breeding traits of Brown Swiss cattle in terms of selection decisions of farm managers was evaluated by using a discrete choice experiment (DCE). Environment-specific relative economic weights (REW) and the marginal willingness to pay were estimated by using a conditional logit model. Several trait complexes, the semen price, interactions between these traits and specific characteristics of the farms were included. Farmers showed highest preferences for the milk value, conformation/udder and fitness. Interactions indicated a great importance of the fitness trait complex for organically managed farms compared to conventional farmers. The latter weighted the milk value and the trait complex conformation/udder high. The method is suitable to judge farmers’ preferences for specific traits, especially those which have not yet been monetarily evaluated. Chapter 3 investigated GxE at a trait and an index level for Brown Swiss sires. Bivariate sire models were used to estimate genetic correlations between organic and conventional production systems and two altitude level of the farms for milk production traits and several functional traits. Furthermore, to determine possible GxE and rerankings at an index level, total merit indices for the sires were calculated. The genetic correlations were high between the analysed environments, ranging from 0.79 (first insemination to conception between different altitude levels) to 0.99 (calving to first insemination, cystic ovaries, maternal stillbirth between production systems). The results indicate no severe GxE at a trait level. No putative GxE effects were found for the production system environments at an index level. In Chapter 4, GxE for various production and functional traits in Brown Swiss cattle were analysed using random regression reaction norm models. The continuous environmental descriptor milk energy yield (MEY) was calculated as a linear combination of average herd effects, obtained from the routine breeding value estimation, of milk-, fat- and protein yield. The applied reaction norm model included a random sire effect and a random sire slope effect (environmental sensitivity), i.e. the random regression coefficient of the regression of a specific sire on the environmental descriptor MEY. To investigate putative GxE effects, breeding values for the sires were estimated. Results showed no severe GxE for the functional traits but for the production trait fat yield. In addition, the slope variances as descriptors of the environmental sensitivity and the Spearman rank correlations between the estimated breeding values of the sires at different environmental levels indicate no severe GxE for the investigated traits.
Analysis of phosphorus utilization using the host genome and microbiota variability in Japanese quail
(2021) Vollmar, Solveig Deniece; Bennewitz, Jörn
Phosphorus (P) is an essential element for growth and performance of avian species. It is predominantly bound as phytic acids and salts (phytate) in plant seeds. Phytases and other phosphatases can harness P by cleaving P groups. Nonruminants have low endogenous phytase activity in the gastrointestinal tract, and thus, the requirement of this element is not met from exclusive plant-based diets. Therefore, mineral P or phytase enzymes are supplemented in poultry feed. Due to the finite quantities of high quality mineral P worldwide, it is of great economic interest. P supplementation is increasingly causing environmental problems. Past studies investigated the P utilization (PU) of different poultry species. They revealed a high phenotypic variation in PU among individuals. Moderate heritabilities indicates that breeding for this trait is in principle possible. The overall aim of this thesis was to gain a deeper understanding of the variability of P utilization in relation to host genetics, ileal microbiota composition and their interaction in the model species Japanese quail. The objective of chapter two was to verify whether variation in PU in quail is a heritable trait conditioned by a few quantitative trait loci (QTL) with detectable effects. For this purpose, individuals were genome-wide genotyped with a 4k SNP chip, and a linkage map was generated. Based on this map, QTL linkage analysis was performed using multimarker regression analysis in a line-crossing model to map QTL for PU. We identified a few QTL regions with significant effects. Among them was a QTL peak at Coturnix japonica chromosome (CJA) 3 for PU. Several genes were found in the region surrounding this peak, which requires further functional gene analysis. Based on these results, we hypothesized that these traits are polygenically determined due to several small QTL effects, which we could not detect significantly. The overlap of the QTL regions indicated linkage of the traits and confirmed their genetic correlations. With the aim of predicting microbiota-related host traits, chapter three examined the composition of the ileum microbiota and differential abundance analysis (DAA). Based on this study, it was shown that a sex-specific influence on microbiota composition exists. The digesta samples of all animals were dominated by five genera, which contributed to more than 70% of the total ileum microbial community. In examining the microbiota composition of each of the 50 animals with the highest and lowest PU, DAA revealed genera significantly associated with PU. In chapter four, we characterized the influence of performance-related gut microbiota to unravel the microbial architecture of the traits evaluated. The aim of this study was to determine whether the variation in PU is partly driven by the microbial community in the ileum. We used microbial mixed linear models to estimate microbiabilities (m^2). This determines the fraction of phenotypic variance that can be explained by the gut microbiota. The estimation of m^2 was 0.15 for PU and was highly significant. It was also highly significant for feed intake, body weight gain and feed per gain. This model was bivariately extended and showed a high microbial correlation of the traits. Based on both results, the ileum microbiota composition plays a substantial role in PU as well as in performance traits, and there is a considerable animal microbiota correlation, showing that the microbiota affects multiple traits. The microbial drivers of this microbial fraction were identified by applying microbiome-wide association studies (MWAS). By back-solving the microbial linear mixed model, we approximated the effect of single OTUs on the phenotypic traits from the microbial model solutions. An MWAS at the genus level uncovered several traits associated with bacterial genera. Subsequently, we assessed whether the microbial community in the ileum is a heritable host trait that can be used for breeding individuals with improved PU. In chapter five we applied QTL analysis using specific genera to examine whether they are linked with genomic SNP markers. These QTL analyses revealed a link between some microbiota species and host genomic regions of chromosomes and SNP markers. By estimating significant heritabilities for some genera, we were able to provide evidence for the hypothesis that the microbial community and microbial features are at least partially related to host genetics. We predicted the animal microbial effects on PU and correlated performance traits by applying microbial best linear unbiased predictions (M-BLUP). In addition, genomic best linear unbiased predictions (G-BLUP) were used to predict the SNP effect for the predicted animal microbial effect. A combination of those two may help to predict genomic breeding values of the microbiota effects for future hologenomic breeding programs.
Characterization of dietary and genetic influences on the gastrointestinal microbiota
(2023) Bubeck, Alena Marie; Fricke, Florian W.
Although the gut microbiota is known to contribute fundamentally to human health, e.g. by promoting the maturation of the immune system and intestinal homeostasis, the factors shaping its composition are only poorly understood. Extrinsic and intrinsic influences can disturb the tightly controlled equilibrium between the microbiome and the host and induce dysbiosis, which has been linked to diverse health conditions such as obesity, atherosclerotic cardiovascular disease (ACVD) and inflammatory bowel disease (IBD). Therefore, understanding events leading to microbial perturbations and the prediction of associated health outcomes could aid in the prevention and treatment of these conditions. In this work, the impact of dietary and genetic factors on gastrointestinal microbiota compositions were determined, with the diet serving as an exemplary extrinsic, modifiable microbiota-relevant factor and with a genetic deficiency in a mouse model for intestinal inflammation serving as an exemplary intrinsic, non-modifiable microbiota-relevant factor. In both studies, microbial communities obtained from either a human or a murine cohort, respectively, were taxonomically characterized by 16S rRNA gene amplicon sequencing and analyzed in the context of metabolic and inflammatory implications for the host. In ACVD, the reduction of excess blood cholesterol, which is a main risk factor, is tackled by clinical interventions aiming to reduce cholesterol uptake from exogenous, dietary sources or by inhibiting endogenous cholesterol biosynthesis. Cholesterol-to-coprostanol conversion by the intestinal microbiota has also been suggested to reduce intestinal and serum cholesterol availability, but the dependencies of cholesterol conversion on specific bacterial taxa and dietary habits, as well as its association with serum lipid levels remain largely unknown. To study microbiota contributions to human cholesterol metabolism under varying conditions, fecal microbiota and lipid profiles, as well as serum lipid biomarkers, were determined in two independent human cohorts, including individuals with (CARBFUNC study) and without obesity (KETO study) on very low-carbohydrate high-fat diets (LCHF) for three to six months and six weeks, respectively. Across these two geographically independent studies, conserved distributions of cholesterol high and low-converter types were measured. Also, cholesterol conversion was most dominantly linked to the relative abundance of the cholesterol-converting bacterial species Eubacterium coprostanoligenes, which was further increased in low-converters by LCHF diets, shifting them towards a high-conversion state. Lean cholesterol high-converters, which were characterized by adverse serum lipid profiles even before the LCHF diet, responded to the intervention with increased LDL-C, independently of fat, cholesterol and saturated fatty acid intake. These findings identify the cholesterol high-converter type as a potential predictive biomarker for an increased LDL-C response to LCHF diet in metabolically healthy lean individuals. Although the etiology of IBD has not been fully resolved, an interplay between the intestinal microbiota, environmental factors and an individual’s genetic susceptibility is thought to trigger chronic inflammation by a dysregulation of the immune response in the gut. To identify colitis-associated microbiota alterations throughout the development of spontaneous colitis, mice with a genetic deficiency of the anti-inflammatory cytokine Interleukin-10 (IL-10) from different litters were co-housed with wild-type mice and monitored for 20 weeks. The scoring of mice based on their phenotype and stool consistency mirrored the state of mucosal inflammation as assessed based on histopathological examinations and cytokine expression profiles. Also, the state of colitis was characterized by global microbiota alterations and susceptibility to colitis was dependent on litter-specific microbiome compositions that mice adopted early on in their lives. Colitis development was further associated with the presence of the bacterial genus Akkermansia in mature mice shortly before symptoms manifested. This genus was also a good predictor of colitis-related mice withdrawal, suggesting the potential of Akkermansia to serve as an early onset, subclinical colitis marker. In summary, fecal microbiota characterizations in response to LCHF diets in humans and throughout the development of intestinal inflammation in a colitis mouse model highlight the potential of personalized microbiome-based patient classifications to predict clinical outcomes and improve treatment approaches.
Comparison of omics technologies for hybrid prediction
(2019) Westhues, Matthias; Melchinger, Albrecht E.
One of the great challenges for plant breeders is dealing with the vast number of putative candidates, which cannot be tested exhaustively in multi-environment field trials. Using pedigree records helped breeders narrowing down the number of candidates substantially. With pedigree information, only a subset of candidates need to be subjected to exhaustive tests of their phenotype whereas the phenotype of the majority of untested relatives is inferred from their common pedigree. A caveat of pedigree information is its inability to capture Mendelian sampling and to accurately reflect relationships among individuals. This shortcoming was mitigated with the advent of marker assays covering regions harboring causal quantitative trait loci. Today, the prediction of untested candidates using information from genomic markers, called genomic prediction, is a routine procedure in larger plant breeding companies. Genomic prediction has revolutionized the prediction of traits with complex genetic architecture but, just as pedigree, cannot properly capture physiological epistasis, referring to complex interactions among genes and endophenotypes, such as RNA, proteins and metabolites. Given their intermediate position in the genotype-phenotype cascade, endophenotypes are expected to represent some of the information missing from the genome, thereby potentially improving predictive abilities. In a first study we explored the ability of several predictor types to forecast genetic values for complex agronomic traits recorded on maize hybrids. Pedigree and genomic information were included as the benchmark for evaluating the merit of metabolites and gene expression data in genetic value prediction. Metabolites, sampled from maize plants grown in field trials, were poor predictors for all traits. Conversely, root-metabolites, grown under controlled conditions, were moderate to competitive predictors for the traits fat as well as dry matter yield. Gene expression data outperformed other individual predictors for the prediction of genetic values for protein and the economically most relevant trait dry matter yield. A genome-wide association study suggested that gene expression data integrated SNP interactions. This might explain the superior performance of this predictor type in the prediction of protein and dry matter yield. Small RNAs were probed for their potential as predictors, given their involvement in transcriptional, post-transcriptional and post-translational regulation. Regardless of the trait, small RNAs could not outperform other predictors. Combinations of predictors did not considerably improve the predictive ability of the best single predictor for any trait but improved the stability of their performance across traits. By assigning different weights to each predictor, we evaluated each predictors optimal contribution for attaining maximum predictive ability. This approach revealed that pedigree, genomic information and gene expression data contribute equally when maximizing predictive ability for grain dry matter content. When attempting to maximize predictive ability for grain yield, pedigree information was superfluous. For genotypes having only genomic information, gene expression data were imputed by using genotypes having both, genomic as well as gene expression data. Previously, this single-step prediction framework was only used for qualitative predictors. Our study revealed that this framework can be employed for improving the cost-effectiveness of quantitative endophenotypes in hybrid prediction. We hope that these studies will further promote exploring endophenotypes as additional predictor types in breeding.
Factors influencing the accuracy of genomic prediction in plant breeding
(2017) Schopp, Pascal; Melchinger, Albrecht E.
Genomic prediction (GP) is a novel statistical tool to estimate breeding values of selection candidates without the necessity to evaluate them phenotypically. The method calibrates a prediction model based on data of phenotyped individuals that were also genotyped with genome-wide molecular markers. The renunciation of an explicit identification of causal polymorphisms in the DNA sequence allows GP to explain significantly larger amounts of the genetic variance of complex traits than previous mapping-based approaches employed for marker-assisted selection. For these reasons, GP rapidly revolutionized dairy cattle breeding, where the method was originally developed and first implemented. By comparison, plant breeding is characterized by often intensively structured populations and more restricted resources routinely available for model calibration. This thesis addresses important issues related to these peculiarities to further promote an efficient integration of GP into plant breeding.
Gene mining in doubled haploid lines from European maize landraces with association mapping
(2014) Strigens, Alexander Carl Georg; Melchinger, Albrecht E.
Since the introduction of maize into Europe, open-pollinated varieties of flint maize were cultivated across the continent. Natural selection promoted adaptation to the climatic conditions prevailing in the different regions. With the advent of hybrid breeding in Europe during the 1950’s, some of the genes responsible for the specific adaptations of the landraces to abiotic and biotic stress were captured in the first developed inbred lines, but most of their genetic diversity is still untapped. Development of inbred lines out of this material by recurrent selfing is very tedious due to strong inbreeding depression. In contrast, the doubled-haploid (DH) technology allows producing fully homozygous lines out of landraces in only one step. This allows their precise characterization in replicated trials and identification of new genes by genome wide association (GWA) mapping. In this study we genotyped a set of 132 DH lines derived from European Flint landraces and 364 elite European flint (EU-F), European dent (EU-D) and North-American dent (NA-D) inbred lines with 56,110 single nucleotide polymorphism (SNP) markers. The lines were evaluated in field trials for morphologic and agronomic traits and GWA mapping was performed to identify underlying quantitative trait loci (QTL). In particular, our objectives were to (1) develop a robust method for quantifying early growth with a non-destructive remote-sensing platform, (2) evaluate the importance of early growth performance of inbred lines with regard to their testcross performance, (3) determine the potential of GWA mapping to identify genes underlying early growth and cold tolerance related traits, (4) evaluate the phenotypic and genotypic diversity recovered in the DH lines derived from the landraces, (5) estimate the effect of the DH method on the recovered genetic diversity, (6) identify new genes by GWA mapping in the DH lines derived from landraces, and (8) discuss the potential of DH lines derived from landraces to improve the genetic diversity and performance of elite maize germplasm. A phenotyping platform using spectral reflectance and light curtains was used to perform repeated measurements of biomass and estimate relative growth rates (RGR) of the DH and inbred lines, as well as of two testcrosses of 300 dent inbred lines. The DH lines derived from the landraces Schindelmeiser and Gelber Badischer had the highest RGR followed by EU-F lines, DH lines derived from Bugard, EU-D lines and, finally, NA-D lines. For inbred lines, whole plant dry matter yield (DMY) was positively correlated with RGR (r = 0.49), whereas this relation was weaker in the testcrosses (r = 0.29). RGR of the inbred lines correlated with RGR of their testcrosses (r = 0.42), but it had no influence on testcross DMY. A set of 375 EU-F, EU-D and NA-D lines were further evaluated in growth chambers under chilling (16/13°C) and optimal (27/25°C) temperatures. Photosynthetic and early growth performance were estimated for each treatment and an adaptation index (AI) built as the chilling to optimal performance ratio. Nineteen QTL were identified by GWA mapping for trait performance and AI. Candidate genes involved in ethylene signaling, brassinolide, and lignin biosynthesis were found in their vicinity. Several QTL for photosynthetic performance co-located with previously reported QTL and the QTL identified for shoot dry wieght under optimal conditions co-located with a QTL for RGR. Comparison of the DH lines derived from landraces with the EU-F lines showed that genotypic variances in single DH populations were greater than in the EU-F breeding population. A high average genetic distance among the DH lines derived from the same landrace as well as a rapid decay of linkage disequilibrium suggests a high effective population size of the landraces. Because no systematic phenotypic differences were observed between the landraces and synthetic landraces obtained by intermating the corresponding DH lines, the expected purge of lethal recessive alleles during the DH production did neither improve grain yield performance nor affect the recovered genetic diversity. Performing GWA in the DH lines derived from landraces as well as the EU-F, and EU-D lines allowed the identification of 49 QTL for 27 traits. A larger set of DH lines derived from more landraces might solve problems arising from population structure and allow a much higher power for the detection of new alleles. In conclusion, the introgression of DH lines derived from landraces into the elite breeding material would strongly broaden its genetic base. However, grain yield performance was 22% higher in EU-F lines than in the DH lines derived from landraces. Selection of the best DH lines would allow partially bridging this yield gap and marker-assisted selection may allow introgression of positive QTL without introducing negative features by linkage drag.
Genetic architecture of quality traits in wheat
(2021) Rapp, Matthias; Longin, Friedrich
Quality traits in wheat are of great importance, as they are required for the production of a wide range of food products. In Europe, bread wheat (Triticum aestivum ssp. aestivum) for human consumption is primarily used in pastries. For durum wheat (Triticum turgidum ssp. durum) that is used almost exclusively for pasta production, quality traits are at least as important as in bread wheat. In Central Europe, the bread wheat subspecies spelt (Triticum aestivum ssp. spelta) is characterized by a different quality compared to bread wheat. In addition, it is produced for a niche market with a particular focus on the final product quality. The high number of demanded quality traits of a wheat variety represents a great challenge for wheat breeders. Thus, knowledge about the genetic architecture and interrelation of quality traits is of high value for wheat breeding. Due to the long list of quality traits in wheat, we focused on currently important quality traits in each of the three wheat species. In durum wheat, I was interested in traits with a high importance for durum millers and pasta producers. The protein content and the sedimentation volume are of high importance for pasta producers as they influence the firmness of cooked pasta, better known as “al dente”. A low falling number may lead to brown instead of light yellow pasta, which goes back to an increased maillard reaction during pasta production and drying. The vitreousity, representing the glassy appearance of durum grains, and the thousand kernel mass influence the semolina yield and are therefore of great interest for durum millers. In the genome-wide association mapping, I identified several putative QTL for these quality traits. For the sedimentation volume, a genomic region on chromosome 1B appeared to be important. A BLAST search against the reference genomes of emmer and bread wheat revealed the Glu-B3 gene as a likely candidate. For vitreousity, genomic regions on chromosome 7A explained a larger proportion of the genotypic variance. One of these QTL, possibly related to the Pinb-2 locus, also slightly influenced the protein content. Thus, this genomic region might be a genomic reason for the positive correlation between vitreousity and protein content. For TKM we detected a putative QTL, which explained a large proportion of the genetic variance, but could not be attributed to a known gene. Besides a good performance for quality traits, a modern durum wheat variety should be complemented by a good agronomic performance, in particular a high grain yield. This poses a great challenge for plant breeders, since grain yield and protein content are negatively correlated. With regard to simultaneously improving grain yield and protein content, the protein yield or the grain protein deviation (GPD) were proposed. We evaluated those and further selection indices for their potential to be utilized for the simultaneous improvement of grain yield and protein content. Our results indicated that a simultaneous improvement of the two traits grain yield and protein content by means of an index seems possible. However, its efficiency largely depends on the weighting of the single traits. The selection for a high GPD would mainly increase the protein content whereas a selection based on protein yield would mainly improve the grain yield. Nevertheless, a combination of different indices allows balancing this selection. Compared to the primary traits grain yield and protein content, the selection indices did not essentially differ in the complexity of their genetic architecture. In bread wheat, we focused on the acrylamide precursor asparagine. Acrylamide is formed in potentially harmful concentrations when cereals are treated with high temperatures over a long period during the processing to food products. A promising strategy to reduce the acrylamide formation would be to decrease the precursors in the raw material. The wide range of variation for asparagine content showed that variety selection might have a large influence on the occurrence of acrylamide in the final product. In addition, the moderately high heritability suggested that successful breeding for lower asparagine content is possible. This conclusion is supported by the observation of no strong negative correlations between asparagine content and a number of other important traits. The genome-wide association mapping resulted in the detection of eight putative QTL, which jointly explained 78.5% of the genetic variance. A putative QTL on chromosome 7B explained with, 18.4%, the highest proportion of the genetic variance for a single marker. For spelt wheat, we assessed a high number of quality traits but placed a special emphasis on the flavor and odor of bread produced from 30 different varieties. Interestingly, we observed a significant genetic variation for bread flavor and a heritability estimate of moderate magnitude. This suggests that even for bread flavor a successful selection appears possible. Taken together, for most traits the genome-wide association mapping resulted in the detection of a high number of putative QTL. This indicates a complex genetic architecture, typical for predominantly quantitatively inherited traits. However, few of the putative QTL explained a large proportion of the genetic variance, so that they might have the potential to be used in marker-assisted selection. In order to examine the potential of genomic selection, I performed a five-fold cross validation for the different quality traits. I could confirm previous findings that the integration of QTL information as fixed effects in the genomic prediction model increased the prediction abilities considerably. The average prediction abilities for most traits suggested a high potential for genomic selection in breeding programs. In conclusion or results form a good basis for further research but more importantly already deliver valuable knowledge that can be used as guideline to advance wheat breeding programs for improved quality.
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.
Genomic and microbial analyses of quantitative traits in poultry
(2023) Haas, Valentin Peter; Bennewitz, Jörn
Feed and nutrient efficiency will become increasingly important in poultry production in the coming years. In addition to feed efficiency, particular attention is paid to phosphorus (P) in nonruminants. Especially growing animals have a high demand of P but through the low usability of plant-based P sources for nonruminants, mineral P is added to their feeds. Due to worldwide limited mineral P sources, the high environmental impact of P in excretions and high supplementation costs, a better utilization of P from feed components is required. Animals’ P utilization (PU) is known to be influenced by the host genetics and by gastrointestinal microbiota. The overall aim of this thesis was to investigate the relationships between host genetics, gastrointestinal microbiota composition and quantitative traits with the focus on PU and related traits in F2 cross Japanese quail (Coturnix japonica). Japanese quail represent a model species for agriculturally important poultry species. In Chapter one, a genetic linkage map for 4k genome-wide distributed SNPs in the study design was constructed and quantitative trait loci (QTL) linkage mapping for performance as well as bone ash traits using a multi-marker regression approach was conducted. Several genome-wide significant QTL were mapped, and subsequent single marker association analyses were performed to find trait associated marker within the significant QTL regions. The analyses revealed a polygenic nature of the traits with few significant QTL and many undetectable QTL. Some overlapping QTL regions for different traits were found, which agreed with the genetic correlations between the traits. Potential candidate genes within the discovered QTL regions were identified and discussed. Chapter two provided a new perspective on utilization and efficiency traits by incorporating gastrointestinal microbiota and investigated the links between host genetics, gastrointestinal microbiota and quantitative traits. We demonstrated the host genetic influences on parts of the microbial colonization localized in the ileum by estimating heritabilities and mapping QTL regions. From 59 bacterial genera, 24 showed a significant heritability and six genome-wide significant QTL were found. Structural equation models (SEM) were applied to determine causal relationships between the heritable part of the microbiota and efficiency traits. Furthermore, accuracies of different microbial and genomic trait predictions were compared and a hologenomic selection approach was investigated based on the host genome and the heritable part of the ileum microbiota composition. This chapter confirmed the indirect influence of host genetics via the microbiota composition on the quantitative traits. Chapter three further extended the approaches to identify causalities from chapter two. Bayesian learning algorithms were used to discover causal networks. In this approach, microbial diversity was considered as an additional quantitative trait and analyzed jointly with the efficiency traits in order to model and identify their directional relationships. The detected directional relationships were confirmed using SEM and extended to SEM association analyses to separate total SNP effects on a trait into direct or indirect SNP effects mediated by upstream traits. This chapter showed that up to one half of the total SNP effects on a trait are composed of indirect SNP effects via mediating traits. A method for detecting causal relationships between microbial and efficiency traits was established, allowing separation of direct and indirect SNP effects. Chapter four includes an invited review on the major genetic-statistical studies involving the gut microbiota information of nonruminants. The review discussed the analyses conducted in chapter one to three and places the analyses published in these chapters in the context of other statistical approaches. Chapter four completed the microbial genetic approaches published to date and discussed the potential use of microbial information in poultry and pig breeding. The general discussion includes further results not presented in any of the chapters and discusses the general findings across the chapters.
Genomische und mikrobielle Analysen von Effizienzmerkmalen beim Schwein
(2022) Weishaar, Ramona Ribanna; Bennewitz, Jörn
Most traits in animal breeding, including efficiency traits in pigs, are influenced by many genes with small effect and have moderate heritabilities between 0.1 and 0.5, which enables efficient selection. These so-called quantitative traits are influenced by genetic factors and environmental factors. The use of next-generation sequencing methods, such as 16S rRNA sequencing to analyse the gut microbiome of livestock, allows identification and analysis of the gut microbiota. It has been shown that the composition of the microbiota in the gastrointestinal tract is heritable and has an influence on efficiency traits. Thus, the animal genome influences the phenotype not only directly by altering metabolic pathways, but also indirectly by changing the composition of the microbiota. This increases the interest in implementing gut microbiota into existing breeding strategies as an explanatory variable. The potential of an efficient utilization and absorption of nutrients varies between individuals. Differences in nutrient absorption depend on feed intake, digestion of dietary components in the stomach and intestine, and intake of digested nutrients from the gastrointestinal tract into blood and lymphatic vessels. Undigested nitrogen is excreted as urea and can be detected by blood urea nitrogen (BUN). The BUN is correlated with efficiency traits and there exist differences between pig breeds. Thus, therefore the BUN would be conceivable as an easier recordable trait for nitrogen utilisation efficiency in pig breeding. In the first chapter of this study, an existing data set of the Department for Animal Genetics and Breeding of the University of Hohenheim was used. This is a data set with 207 phenotyped and genotyped Piétrain sows. The relationship between gut microbial composition, efficiency traits and the porcine genome is investigated using quantitative genetic methods. The heritabilities of the traits FVW, RFI, TZ, and FI ranged from 0.11 to 0.47. The microbiabilities of the traits were significant and ranged from 0.16 to 0.45. In a further step, the previously generated microbial animal effects were used as observation vector for a genomic mixed model. Subsequently, heritabilities for the microbial animal effect were estimated, ranging from 0.20 to 0.61. The similarity of the heritabilities and microbiabilities suggests that the traits are influenced to a similar extent by both genetics and gut microbiota and that the microbial animal effect is determined by the host. These results are underlined by the identification of genera and phyla with significant effects on efficiency traits. The microbial architecture of the traits demonstrated a poly-microbial nature, there are many OTUs with small effects involved in the variation of the observed traits. Genomic Best Linear Unbiased Predictions (G-BLUP) and Microbial Best Linear Unbiased Predictions (M-BLUP) were performed to predict complex traits. The accuracies of M-BLUP and G-BLUP were all in a similar range between 0.14-0.41. This shows that gut microbiota could be used to predict performance traits or be included as a variable in the existing models of breeding value estimation to realize an increase in accuracies. The second part of the paper analysed a dataset from a research project called "ProtiPig". The data set included 475 sows and castrates of crossbreds of German Landrace x Piétrain and was analysed for protein utilization efficiency and nitrogen(N)-utilization efficiency. N-utilization efficiency is a trait that is difficult to record. Because conventional metabolic cage methods are a very complex procedure and difficult to integrate in the standard recording, it was tested whether the BUN is suitable as a proxy trait. Moderate to medium heritabilities could be estimated for all traits and ranged from 0.13 to 0.49. The genome-wide association studies showed that the traits were polygenic. For the BUN, SNPs could be detected that were above the genome-wide significance level. Significant genetic and phenotypic correlations were found between some traits. In particular, the heritabilities of BUNs and the significant genetic correlation between BUN and N-utilization efficiency indicate an opportunity to use the BUN to select for improved N-utilization efficiency. Before the research results generated here can be implemented in breeding practice, further questions must be clarified. In addition, a larger number of animals is needed to validate the results. The results presented here demonstrate the potential of microbial-assisted breeding value estimation and the use of BUN to identify selection candidates for breeding for increased efficiency.
Implementation and optimization of the doubled haploid technology for tropical maize (Zea mays L.) breeding programs
(2012) Prigge, Vanessa; Melchinger, Albrecht E.
Doubled haploid (DH) technology is currently the fastest way to achieve homozygosity in maize and it offers numerous quantitative genetic, operational, and economic advantages. Hybrid maize breeding with DH lines is common in temperate areas, yet adoption of this technology is still to be realized in tropical areas. Therefore, the main goal of my thesis project was to establish and validate the DH technology for tropical maize breeding programs at the International Maize and Wheat Improvement Center (CIMMYT) in Mexico. In vivo production of maternal haploids and DH lines involves four steps: (i) inducing haploidy by pollinating source germplasm with pollen of a haploid inducer; (ii) identifying seeds with haploid embryos based on a visually scorable marker; (iii) duplicating chromosomes of putative haploids by treating the seedlings with a mitotic inhibitor; and (iv) self-pollinating DH plants to multiply their seed. To impart knowledge on each of the above steps, we compiled a detailed protocol and produced a publicly available video which will be very useful for capacity building. Lack of reliable information on the performance of temperate inducers under nontemperate conditions is one reason for the slow adoption of DH technology in tropical maize breeding programs. Therefore, we assessed haploid induction rates (HIR) and agronomic performance of three temperate inducers in tropical lowland environments in Mexico. HIR obtained under tropical conditions were similar to those previously reported from evaluations under temperate conditions, indicating that temperate inducers can be used for initiation of DH breeding programs in the tropics. However, the inducers showed poor pollen production, poor seed set, and strong susceptibility to tropical leaf diseases. Hence, better adapted inducers would be advantageous for large-scale induction of haploidy in tropical DH programs. To develop better adapted haploid inducers, segregating populations were generated from crosses between temperate inducers and eight tropical CIMMYT maize lines (CML) from Mexico and Zimbabwe. Mass selection of individual F2 plants was conducted for visually scorable and highly heritable traits, followed by family-based selection for HIR and agronomic traits. Several tropical inducer candidates (TIC) were identified with HIR of up to 10% and notably improved agronomic performance under tropical lowland conditions. Compared to backcrosses to the inducers, backcrosses to the CML showed similar HIR combined with a significantly later anthesis date and improved plant vigor. Hence, backcrossing to the adapted parent may be a suitable approach to improve adaptation of new inducers while maintaining high HIR levels. Furthermore, we screened randomly chosen South American maize accessions and observed HIR of up to 3%, suggesting that novel sources of haploid induction ability may be present in CIMMYT?s vast germplasm collection. Although extensively exploited in DH line production, the genetic mechanisms underlying in vivo induction of maternal haploids in maize are still largely unknown. We conducted comparative quantitative trait locus (QTL) mapping for HIR to explore the genetic architecture of this phenomenon. Segregating populations were generated from four crosses composed of two temperate haploid inducer lines and three non-inducer lines. One major QTL on chromosome 1 (qhir1; bin 1.04) explaining up to 66% of the genotypic variance was detected in the three populations involving non-inducer lines. Hence, bin 1.04 represents an interesting region for map-based cloning. Further, qhir1 was affected by strong segregation distortion against the inducer allele, indicating that natural selection disfavors haploid induction ability. Seven QTL with smaller effects were detected in the CAUHOI×UH400 population. Further, we proposed a conceptual genetic framework for inheritance of in vivo haploid induction ability in maize. Common methods for artificial duplication of haploid chromosome sets mostly involve toxic and costly reagents and are extremely labor-intensive. This leads to serious bottlenecks during DH line development. When screening haploid populations derived from 260 diverse temperate and tropical source germplasm, we observed significant genetic variation for fertility-related traits, suggesting that haploid fertility can be effectively improved by recurrent selection. This may facilitate abolishment of artificial chromosome doubling during DH production, which seems particularly relevant for enabling small national maize breeding programs and seed companies in developing countries to adopt the DH technology. To study the suitability of different population types for DH line extraction, we developed 131 DH lines from five tropical elite single crosses (SC) and five tropical open-pollinated populations (OP) and evaluated them for testcross performance in Mexico. While testcross grain yield means of the two population types did not differ significantly, significant genetic variance was only revealed for OP-derived DH lines. Several DH lines from OP excelled in testcross performance and may be useful for tropical hybrid breeding programs. In addition, tropical OP may harbor valuable untapped genetic variation that can effectively be exploited with DH technology. This thesis work demonstrated that established protocols for in vivo DH line development can be readily applied to tropical maize breeding programs. Adoption of the DH technology promises to greatly increase the efficiency of breeding programs and DH lines are also an exciting tool to (i) immortalize genetic resources, (ii) conduct high-resolution genetic analyses of important traits, and (iii) accelerate the arrival of improved varieties to farmers? fields.
Lockerbeerigkeit bei Klonen von Spätburgunder (Pinot noir) : Analyse von molekularen Markern und der Einfluss von Gibberellin auf die Traubenmorphologie
(2014) Hoffmann, Petra; Blaich, Rolf
In viticulture, the architecture of the grape cluster affects the quality of the grapes. Compact grape clusters are more prone to B. cinerea infection, which reduces yield (Vail et al. 1998, Vail et al. 1991). Loose clusters have longer pedicel and rachis structures (Alleweldt 1959) and are less susceptible to B. cinerea. For this reason, the cultivation of clones with the loose cluster trait is of great interest. Loose clusters can result from the application of phytohormones, the spacing of the flower clusters, the thinning of fruit, or a reduced pruning. These treatments reduce berry set and promote pedicle elongation when applied to clones with compact clusters (Alleweldt 1959). Genetically based loose clustered grape phenotypes occur among grapevine cultivars. In this study we are able to differentitate between losse and compact clones using the marker FlExp2 on the basis of sequence data. The loose cluster clones show a 4 bp deletion at 219-222 bp and a C/T transition at 231 bp, unlike the compact cluster clones. In all tested Pinot ssp. clones, the sequence correlated to the phenotype. The marker was tested on other varieties such as Riesling, Gewurztraminer, Chardonnay, Chenin blanc, Cardinal and White Chasselas. The phenotypes were again consistent with the sequence. In the case of loose clustered table grapes, a deletion occurs instead of the transition at 231 bp. Additionally, the variety White Gutedel demonst- rated a C/T transition at 217 bp. These results were confirmed by sequencing 30 clo- nes (loose and compact clusters) in two repetitions in both directions. Both markers shwoed two fragments with a four bp difference. The amplification products are a In- del/SNP mutation for loose cluster and a „CTTT“ mutation for copmact cluster grapes.The CAPS and the SCAR marker identified that the trait of bunch architecture is heterozygous. The sequence of the amplification products was distinct for loose and compact cluster types. The SCAR marker shows two amplification products at 162 bp and 166 bp and the CAPS marker at 283 bp and 287 bp. The heterozygosity didn ́t produce a molecular marker for the MAS. In silico, analysis shows that the identified locus is in the Exon in the Vlexp1 gene. This gene is an expansin gene which is responsible for cell elongation (McQueen- Mason 1992). A part of the role which the hormones play in grape Morphology was analyzed in this study. The inflorescences of the genetically loose clustered clone 1-84 Gm did not show increased gibberellin concentration, indicating that gibberellin does not have a influence on the genetic based loose clone (1-84 Gm). However, the auxin concentra- tion in inflorescences of loose cluster clones increases earlier and remains high lon- ger than in those of the compact cluster clone 18 Gm. After a treatment with gib- berellin, the clone 1-84 Gm exhibited increased concentration of both gibberellin and auxin and formed even looser clusters. Similarly, the same treatment applied to the compact clone 18 Gm resulted in looser clusters and increased concentration of gib- berellin and auxin with a higher concentration of auxin for a longer period of time. It remains unclear precisely how the gibberellin treatment induces looser clusters. It may be that there is an interaction between gibberellin and auxin or that the auxin alone causes the cell extension. It remains an open question whether expansin toge- ther with gibberellin or auxin is responsible for the development of loose clusters, or if it is caused by a gibberellin auxin interaction. The growth pattern of the stalks and inflorescences were identified in order to put these results in context with the results of the hormone and genetic analysis. The stalks and inflorescences of the treated and untreated clones were measured weekly before GA3-application and continued four weeks after application. The growth of the flower clusters ended three weeks af- ter anthesis while the stalks grew continuously. In the loose cluster clone 1-84 Gm, the growth of stalks and flower clusters was significantly larger than in the compact cluster clone 18 Gm. The growth behavior of the peclone 18 Gm when treated with gibberellin was identical to the clone 1-84 Gm without gibberellin treatment. Gib- berellin treatment caused a significant increase in the growth of the stalk and flower clusters. The treated loose cluster clones formed the largest stalks while the untrea- ted compact cluster clone 18 Gm the smallest. Such clone growth behavior results in loose cluster architecture.
Optimum schemes for hybrid maize breeding with doubled haploids
(2011) Wegenast, Thilo; Melchinger, Albrecht E.
In hybrid maize breeding, the doubled haploid technique is increasingly replacing conventional recurrent selfing for the development of new lines. In addition, novel statistical methods have become available as a result of enhanced computing facilities. This has opened up many avenues to develop more efficient breeding schemes and selection strategies for maximizing progress from selection. The overall aim of the present study was to compare the selection progress by employing different breeding schemes and selection strategies. Two breeding schemes were considered, each involving selection in two stages: (i) developing DH lines from S0 plants and evaluating their testcrosses in stage one and testcrosses of the promising DH lines in stage two (DHTC) and (ii) early testing for testcross performance of S1 families before production of DH lines from superior S1 families and then evaluating their testcrosses in the second stage (S1TC-DHTC). For both breeding schemes, we examined different selection strategies, in which variance components and budgets varied, the cross and family structure was considered or ignored, and best linear unbiased prediction (BLUP) of testcross performance was employed. The specific objectives were to (1) maximize through optimum allocation of test resources the progress from selection, using the selection gain (ΔG) or the probability to select superior genotypes (P(q)) as well as their standard deviations as criteria, (2) investigate the effect of parental selection, varying variance components and budgets on the optimum allocation of test resources for maximizing the progress from selection, (3) assess the optimum filial generation (S0 or S1) for DH production, (4) compare various selection strategies - sequential selection considering or ignoring the cross and family structure - for maximizing progress from selection, (5) examine the effect of producing a larger number of candidates within promising crosses and S1 families on the progress from selection, and (6) determine the effect of BLUP, where information from genetically related candidates is integrated in the selection criteria, on the progress from selection. For both breeding schemes, the best strategy was to select among all S1 families and/or DH lines ignoring the cross structure. Further, in breeding scheme S1TC-DHTC, the progress from selection increased with variable sizes of crosses and S1 families, i.e., larger numbers of DH lines devoted to superior crosses and S1 families. Parental cross selection strongly influenced the optimum allocation of test resources and, consequently, the selection gain ΔG in both breeding schemes. With an increasing correlation between the mean testcross performance of the parental lines and the mean testcross performance of their progenies, the superiority in progress from selection compared to randomly chosen parents increased markedly, whereas the optimum number of parental crosses decreased in favor of an increased number of test candidates within crosses. With BLUP, information from genetically related test candidates resulted in more precise estimates of their genotypic values and the progress from selection slightly increased for both optimization criteria ΔG and P(q), compared with conventional phenotypic selection. Analytical solutions to enable fast calculations of the optimum allocation of test resources were developed. This analytical approach superseded matrix inversions required for the solution of the mixed model equations. In breeding scheme S1TC-DHTC, the optimum allocation of test resources involved (1) 10 or more test locations at both stages, (2) 10 or fewer parental crosses each with 100 to 300 S1 families at the first stage, and (3) 500 or more DH lines within a low number of parental crosses and S1 families at the second stage. In breeding scheme DHTC, the optimum number of test candidates at the first stage was 5 to 10 times larger, whereas the number of test locations at the first stage and the number of DH lines at the second stage was strongly reduced compared with S1TC-DHTC. The possibility to reduce the number of parental crosses by selection among parental lines is of utmost importance for the optimization of the allocation of test resources and maximization of the progress from selection. Further, the optimum allocation of test resources is crucial to maximize the progress from selection under given economic and quantitative-genetic parameters. By using marker information and BLUP-based genomic selection, more efficient selection strategies could be developed for hybrid maize breeding.
Pedigreeanalysen zur Beschreibung der populations- und quantitativgenetischen Situation von baden-württembergischen Lokalrinderrassen
(2014) Hartwig, Sonja; Bennewitz, Jörn
The challenge of a conservation breeding program is to solve a conflict of goals: genetic variability and genetic autonomy should be maintained, and on time a certain amount of breeding progress has to be realized to ensure the ability to compete. The aim of the present study was to analyse the situation concerning the targets mentioned above for traditional cattle breeds of Baden-Württemberg. Furthermore, methods for the consolidation and development of these breeds should be reconsidered. In chapter 1 the organisation of a breeding program for small cattle breeds is discussed. The challenge of such a program is the conservation of agrobiodiversity, culture and traditions and the progress of traditional local breeds. Number and extend of these breeds declined due to the increasing popularity of high-yielding breeds. Additionally, some of the local breeds are used in different branches of production compared to their original usage. Breeding programs have to be fitted. The establishment of individual adapted breeding methods is required for a sophisticated solution of the conflict mentioned above. Federal support is requested. Nowadays the implementation of genomic selection is not yet practicable for small breeds. But future opportunities should be analysed. The establishment of performance tests concerning breed specific product and efforts is demanded to improve these characteristics. In the following genetic variability of Vorderwald, Hinterwald and Limpurg cattle was examined. In chapter 2 for each breed two reference populations were defined that enable to observe the development over the years. Animals within the reference population comply with restrictions concerning racial origin and completeness of pedigree. Effective population size and the effective number of founders, and ancestors were estimated. The interpretation of the results was done with regard to the history of the breeds. The absolute population size of Vorderwald cattle is the biggest one. The number of Hinterwald cattle is intermediate; Limpurg cattle have the smallest population size. Whereas the management of Hinterwald cattle seemed to maintain genetic variability, the management of Vorderwald cattle was not that target-orientated. With an effective population size greater than 100 there is enough genetic variability within Vorderwald and Hinterwald. In contrast the values of Limpurg cattle are too low. Besides genetic variability, genetic autonomy and breeding progress are the targets of a conservation breeding program. Cross-breeding was carried out to mitigate the risk of inbreeding depression and to improve the performance of local breeds. However, breeding activities for local breeds were not as intensive and target oriented as for popular high yielding breeds. While the gap between the performance of high-yielding and local breeds increase, genetic autonomy of local breeds declined due to migrant influences. Chapter 3 examined the importance of migrant breed influences for the realization of breeding progress of beef traits of Vorderwald and Hinterwald cattle. The results show that there is a high amount of migrant contributions and their effects on performance are substantial for most traits. Breeding values adjusted for the effects of the migrant breeds showed little genetic trend for beef traits. The subject of chapter 4 is the development of milk yield and the associated migrant influences. Yield deviations for milk, fat, and protein content were analysed. Migrant contributions to Vorderwald cattle were high and even rose in the latest past. All the effects of foreign breeds were positive and in most cases highly significant. Most influential breed was Montbéliard. The influences of migrant breeds were substantial for the development of milk performance. However, the trend of milk yield traits for both breeds was positive even without foreign breeds’ influences. In comparison the number of analysed Hinterwald cows was small due to the reason that just a few Hinterwald husbandries take part at the official milk performance recording. Migrant breed contributions were moderate and nearly constant over the time. The most influential migrant breed was the Vorderwald cattle. The development of milk yield shows a flat trend. Influences of migrant breeds were low. The thesis ends with a general discussion.
Physiologische und genetische Einflüsse auf die Qualität von Schweinefleisch aus baden-württembergischen Gebrauchskreuzungen
(2012) Fecke, Anna; Weiler, Ulrike
What genotypes, basing on the genetic lines supplied by German Genetic, guarantees both a high-value carcass and excellent pork quality and high eating quality and also how the criteria of fertility, weight development and yield at slaughter, relate to the criteria of pork quality. 10 genotypes were studied. Therefore the sows crossbred represent typically genotypes in Baden-Württemberg as well as the Leicoma hybrid sows. These sows were bred at the LSZ Boxberg with Pietrain and Duroc boars. The sows of the LW*(LC*DL) had the highest fertility rate. The boar lines showed no influence on either the birth weight or fertility parameters. The boar line, however, did reflect a highly significant influence on the daily gain in all further production periods (Duroc vs. Pietrain: suckling +8%; rearing +3,8%; fattening +6,5%).The offspring from the sows LW*(LC*DL) had the greatest daily gain in the suckling period and had a higher weaning weight (+6%, p<0.05) than the offspring from the LW*(SH*DL), which achieved the lowest overall weaning weight. On analyzing the relationship between the development weights in the various production periods and the birth weight, it was obvious that the birth weight provides a significant positive influence on the performance in every production period, except for rearing. Indeed, in the rearing period the animals with a high birth weight tended to show low daily gains, whereas the piglets with a low birth weight were able to partially compensate for the early growth deficit during this period. The Pietrain offspring had more lean meat content than the Duroc offspring. The dissection in Trial #2 shows that the Pietrain offspring had 3.3% more ham content and 4.0% more of the valuable cuts. The Duroc offspring had less lean meat content in the belly (-4.2%, Gruber Formula), more back fat (+13.7%), more leaf fat (+14.6%), and 12.5% more corrected fat area than the Pietrain offspring. The offspring of the sows LC*LW had a significantly shorter carcass than the offspring of the other sows. The offspring from the 50% Leicoma sows showed the greatest corrected fat area. The offspring from the sows LW*(LC*DL) had 17.1% less corrected fat area. The correlation analysis resulted in the established relationships. Especially of a practical interest, is the close relationship between lean meat content (FOM) and the pork underbelly (Gruber Formula) (r=0.92; n=240; p<0.001). For nearly every parameter the results of the pork quality grading under practical conditions (Trial #1) tended toward improved values for the pigs with Duroc genes, which showed a significantly lower drip loss. The influence of the sows on pork quality parameters was negligible. Besides these parameters, some carcasses were also characterized with PSE qualities (pH1<5.8; conductivity 24hr p.m.>8.0mS/cm). In Trial #1, based on the pH-readings at the slaughterhouse, almost no carcasses (0.15%) were identified with PSE, whereas the conductivity measurements in ham, 5.79% of the carcasses were identified as PSE. In Trial #2, 15.0% of the animals were PSE based on pH1 or conductivity measurements in the loin and ham. There were 5 carcasses which have PSE after both measurements in loin and ham. In the histochemical analysis of the muscle fiber classification the only difference between the boar lines was found in the percentage of red fibers. The eating quality tests revealed an influence from the boar line. In general, all genotypes produced a high quality lean meat content according to the market requirements. As to expectation the improved pork quality of the Duroc breed was justified by the best eating quality, an improved water-holding capacity and a higher intramuscular fat content. An acceptable overall pork quality can be achieved by pairing the offspring from the Pietrain*LW*(LC*DL). The offspring with some Schwäbisch-Hall genes have an opportunity to establish a regional market. However, their performance was not convincing because in fertility, in daily gain, and even in pork quality they attained below average values. Nevertheless, an optimal pork quality can be achieved more efficiently with other genotypes. On establishing predicting criteria, the percentage of PSE of the pork carcasses is quite positive. The superiority of the 24hr p.m. conductivity value for the drip loss predict is evident here. The measurement of the conductivity subsume the effects of slaughtering and cooling and is more appropriate than the pH1 value, especially, for the incoming inspection in the deboning area as well as for quality assurance.
Reproductive success and escape behaviour in urban greylag geese (Anser anser)
(2023) Mai, Sabrina; Steidle, Johannes
Urbanisation and its effect on animals and plants is an important factor to analyse in behavioural studies. Warmer temperatures and an increased availability of food provide benefits to animals occurring in urban habitats. In contrast, these animals also have to tolerate the disturbance caused by artificial lights or noise. This work studies an urban local population of greylag geese Anser anser. Greylag geese live in wetland landscapes, but also in urban parks with wide lawns and water bodies. Since the nineties, the city of Stuttgart in southwest Germany is home to a breeding population of greylag geese. As a result of a long-term ringing project, a large percentage of the population is ringed. This data shows that the population is non-migratory, as the geese generally remain in the area year-round. The individual identification offers the opportunity of tracing data, such as reproduction or behaviour, for the same animal over a longer period. This data can then be individually connected to genetic information, which is a large benefit in behavioural studies. The first chapter of this work focuses on reproductive success as one of the two key parameters which influence population change. As reproductive success itself is influenced by a variety of factors, this study analysed the effect of factors such as population size, brood size or dispersal by using two different measures of reproductive success: fledging success (the relation between hatched and fledged young of a brood ) and hatchling survival (the likelihood of a hatchling to survive to fledging). Fledging success of pairs initially increased with the number of times pairs bred together but decreased again in later broods. While the experience of a pair is therefore beneficial for their reproductive success, the subsequent decrease may be caused by the increasing age of the parents. The brood size also influenced reproductive success, as fledging success was higher in larger broods and hatchling survival was also positively influenced by brood size. In some years, several goose families dispersed from the breeding ground to a different brood rearing area. Hatchling survival was higher in these families, though this effect decreased again when the broods were large. The total population size had a negative effect on hatchling survival, indicating density dependence. To determine if there is a genetic basis for escape behaviour in greylag geese, the second chapter of this work compares Stuttgart’s urban local population of greylag geese with a rural local population in the countryside near Ludwigsburg. Animals occurring in urban habitats need a higher tolerance towards disturbance. This tolerance may be due to the animal’s personality. Animal personality is defined as consistent behaviour across time or context and is expressed for example through risk-prone behaviour. Urban animals are likely more risk-prone than their rural counterparts and thus have a bolder personality. There is increasing evidence that personality and thus behaviour have a genetic basis. This study analyses the dopamine D4 receptor (DRD4) as a candidate gene associated with boldness / shyness and fear. The gene showed a high variation with eleven alleles and 35 genotypes being detected in the analysed greylag geese. Allele and genotype frequencies were skewed, with one allele and two genotypes occurring more often than the others. Based on the detected frequencies, these two genotypes were defined as common and the remaining 33 as rare genotypes. Common genotypes were found more frequently in geese from urban areas, while rare genotypes were found more frequently in geese from rural areas. To determine if the detected genotypes could be associated with behaviour, the flight initiation distance (FID) of individual geese was measured. As the geese are ringed, FID measurements could be directly assigned to a specific goose and thus to its genotype. A high FID indicates geese which are more cautious, while a low FID indicates boldness. Indeed, greylag geese of the rural location show increased FID, while those in urban areas in Stuttgart have lower FIDs and thus a bolder personality. Despite these results, there was no significant correlation between DRD4 genotype frequency and FID. This may be explained by methodological effects. Alternatively, DRD4 has also been associated with other behaviours such as novelty seeking and exploratory behaviour. These behaviours may also differ between urban and rural animals and may thus be the reason for the detected frequencies. It is therefore likely that local habitat selection may be influenced by the DRD4 genotype. Overall, this work demonstrates that different factors, including genetics, should be taken into account when managing urban populations of wild animals, as their behaviour can differ significantly from their rural counterparts, even within a single species.
Resistance gene analogues as a tool for basic and applied resistance genetics exemplified by sugarcane mosaic virus resistance in maize (Zea mays L.)
(2003) Quint, Marcel; Melchinger, Albrecht E.
With the recent cloning of a number of plant disease resistance genes (R genes) it became apparent that R genes share certain homologies in conserved amino acid domains. PCR amplification of genomic DNA using degenerate primers on the basis of these conserved amino acid domains identified sequences with homologies to plant disease R genes - resistance gene analogues (RGAs). RGAs exist in large numbers in plant genomes and provide new possibilities for the investigation of resistance genetics in general and also for the analysis of certain plant disease resistances. The overall objective of this thesis was to evaluate the use of RGAs for plant breeding for the example of sugarcane mosaic virus (SCMV) resistance in maize. SCMV is one of the most important virus diseases of maize and causes serious yield losses in susceptible cultivars. Owing to the non-persistent manner of transmission, control of aphid vectors by chemical means is not effective and therefore, cultivation of resistant maize varieties is the most efficient method of virus control. Previous studies on the inheritance of oligogenic SCMV resistance located two major quantitative trait loci (QTLs) - Scmv1 and Scmv2 - on chromosomes 6S and 3L, respectively. The objectives of this study were to (1) give an overview on the current status of breeding for virus resistance in maize, (2) identify and genetically map candidate genes for Scmv1 and Scmv2, (3) use potential sequence homologies of linked RGAs for targeted increase of the number of candidate genes in the target regions, (4) convert closely linked amplified fragment length polymorphism (AFLP) markers into codominant, simple PCR-based markers as a tool for marker-assisted selection (MAS) and map-based cloning, (5) evaluate RGAs for the development of molecular markers, MAS, and map-based cloning, and (6) investigate the consequences of duplicate markers for the construction of linkage maps and their implications for MAS and map-based cloning. Three previously published RGAs, pic13, pic21, and pic19 were cloned from six maize inbred lines, converted to cleaved amplified polymorphic sequence (CAPS) markers, and mapped in relation to SCMV R genes (Scmv1, Scmv2) in maize. Pairwise sequence alignments among the six inbreds revealed a frequency of one single nucleotide polymorphism (SNP) per 33 bp for the three RGAs, indicating a high degree of polymorphism and a high probability of success in converting RGAs into codominant CAPS markers compared to other sequences. Therefore, RGAs meet important requirements for the development of molecular markers, i.e., a high degree of polymorphism and availability in great numbers throughout the genome. In contrast to this, the degree of polymorphism for AFLPs closely linked to Scmv1 an Scmv2 was significantly lower in the same six inbred lines compared to RGAs. Only two of eight AFLP markers could be converted into one CAPS and one indel (insertion/deletion) marker. By genetic mapping, pic21 was shown to be different from Scmv2, whereas pic19 and pic13 could be mapped as single-copy markers to the target regions and are candidates for Scmv1 and Scmv2, respectively, due to genetic mapping and consistent restriction patterns of ancestral lines. Subsequently, pic19 was used as candidate for Scmv1 to screen a maize BAC library to identify homologous sequences in the maize genome and to investigate their genomic organisation. Fifteen positive BAC clones were identified and classified into five physically independent contigs consisting of overlapping clones. Genetic mapping clustered three contigs into the same genomic region as Scmv1 on chromosome 6S. The two remaining contigs mapped to the same region as a QTL for SCMV resistance on chromosome 1. Thus, RGAs mapping to a target region can be successfully used to identify further linked candidate sequences. The pic19 homologous sequences of these clones revealed a sequence similarity of 94-98% at the nucleotide level. The high sequence similarity and the multi-locus character of the previously single-copy mapped RGA pic19 show potential problems for the use of RGAs as molecular markers. The existence of ghost markers analogous to ghost QTL was suggested to be a result of simultaneous mapping of several homologous gene family members which cannot be distinguished at the level of PCR. The idea of ghost loci derived by potentially duplicated sequences such as expressed sequence tags (ESTs), AFLPs, or simple sequence repeats (SSRs) was the subject of a theoretical and computer simulation study. Simultaneous amplification of homologous sequences results in an excess of heterozygotes causing distorted segregation ratios. We were able to theoretically prove the existence of such ghost markers resulting in changes of the correct marker orders. If these fictive ghost markers are part of a genetic map which is the subject of MAS or map-based cloning this may have fatal effects like locating a target gene into an incorrect marker interval. This incorrect locus order caused by duplicate marker loci can negatively affect the assignment of target genes to chromosome regions in a map-based cloning experiment, hinder indirect selection for a favourable allele at a QTL, and decrease the efficiency of reducing the chromosome segment attached to the target gene in marker-assisted backcrossing. In conclusion, this thesis demonstrates the use of RGAs for plant breeding and resistance genetics in general. RGAs provide a good source for the development of simple PCR-based markers. Furthermore, RGAs are an excellent tool for MAS, the identification of candidate genes and effective increase of such candidates in target regions using sequence homologies between RGAs. The duplicate nature of RGAs revealed potential problems for genetic mapping of potentially duplicated sequences which are widespread in eukaryote genomes and existent for several types of molecular markers. For resistance genetics in general, investigation of RGAs is important for the understanding of R gene organisation and evolutionary genetics of plant disease resistance.
Sorghum breeding strategies for phosphorus-limited environments in Western Africa : from field to genome level
(2014) Leiser, Willmar Lukas; Haussmann, Bettina
A growing world population juxtaposed with dwindling phosphorus (P) resources present new challenges to current and future global agricultural production. The burden of depleting phosphorus resources is particularly felt in sub-Saharan Africa (SSA). The expected doubling of its population by 2050 and the widespread poor soil fertility will pose an enormous task to future food security in SSA. Plant breeding can be considered as one major factor to improve agricultural production under these harsh low-input conditions. Nevertheless, until recently there have been no thorough breeding efforts to enhance crop production for low-P soil conditions in SSA. Sorghum (Sorghum bicolor L. Moench) is the world’s fifth and Africa’s second most grown cereal crop. Sorghum is a staple crop of SSA and is mostly grown in resource poor regions under low-input cropping conditions, with the largest share in West Africa (WA). Its good adaptation to harsh environmental conditions makes it an important crop for the arid and semi-arid regions, hence a crop vital for food security and increasingly farm income in WA. Breeding sorghum specifically targeting P-limited soils is considered as one of the major challenges for future food production and can serve millions of smallholder farmers in WA. Nevertheless, plant breeders are mostly reluctant to conduct breeding experiments under low-input conditions due to a higher spatial variability of soil properties leading to a lower response to selection. In an unprecedented large scale multi-environment experiment from 2006-2012 in three WA countries, namely Mali, Senegal and Niger, 187 WA sorghum genotypes were evaluated for their performance under P-sufficient and P-deficient conditions. The main goal of this study was to establish a breeding strategy for sorghum targeting P-limited environments. In order to establish such a strategy, the following objectives were defined: (I) to evaluate the impact of spatial models on genotypic selection in low-input field trials, (II) to develop a selection strategy for sorghum targeting P-limited environments, based on quantitative genetic parameters and (III) to identify genomic regions influencing sorghum performance in P-limited environments using modern genomic tools. The major findings of this study can be summarized as follows: Spatial models can increase the precision and efficiency especially of low-input field trials and may lead to different genotype rankings. Hence spatial models and/or adequate field designs are necessary tools for efficient genotype selection under low-input conditions and must be considered in a breeding program targeting P-limited conditions. Sorghum performance is severely impeded by low-P soil conditions and shows large grain yield and plant height reductions and delayed flowering. Nevertheless, WA sorghum is generally well adapted to low-P soil conditions and shows a large exploitable genetic variation for P efficiency. Direct selection under low-P conditions is feasible, necessary and more efficient than indirect selection under high-P conditions and should be pursued in a breeding program targeting P-limited environments. Landrace genotypes are more specifically adapted to low-P conditions and show a higher P acquisition capacity, Durra and Guinea race sorghums show a similar specific low-P adaptation, hence these genotype groups are very promising source germplasm for further breeding efforts. Photoperiod sensitive genotypes show less delay in heading, a higher P acquisition rate and a specific low-P adaptation, hence should be considered for climate and low-P resilience breeding. Selection for low P concentration of grain can be used to enhance internal P use efficiency, therefore decreasing further soil P mining. WA sorghum shows a large genetic diversity, hence providing a valuable source for genetic studies examining the underlying genetics of low-P adaptation. There are many genomic regions involved in sorghum adaptation to low-P soil conditions. Nevertheless, some regions could be identified as major contributors, showing large effects on and strong associations to genotypic performance. Molecular markers in sorghum homologs of the major P efficiency gene PSTOL1 from rice stably enhanced P uptake and crop performance through an increased root growth of sorghum under low-P soil conditions and can be used in marker assisted selection for grain yield production under P-limited conditions. Furthermore, it was observed that grain yield production under P-limited conditions and Al-tolerance are pleiotropically regulated by the same genomic region and most probably the same gene SbMATE. Molecular markers of this region and within the gene SbMATE should be used for marker assisted selection to simultaneously enhance the tolerance to two of the most serious abiotic stresses for sorghum in WA, Al toxicity and P deficiency. WA Guinea race sorghums are an excellent source not only for low-P specific alleles, but also for Al-tolerance and represent therefore an excellent source germplasm for allele mining and marker assisted selection. Genomic selection appears to be a very promising approach to further increase the response to selection. But methods giving more weight to single molecular markers linked to Al-tolerance should be considered. The laid out results show that breeding sorghum specifically targeting P-limited conditions is necessary and feasible using advanced statistical models and modern genetic tools, and should be pursued as a major selection criterion in WA sorghum breeding programs. Nevertheless, only by combining agronomic and socio-economic measures with plant breeding efforts, millions of WA smallholder farmers can be reached and major yield increases can be expected in the near future.
The genetic basis of heat tolerance in temperate maize (Zea mays L.)
(2016) Frey, Felix P.; Stich, Benjamin
The global mean temperature and probability of heat waves are expected to increase in the future, which has the potential to cause severe damages to maize production. To elucidate the genetic mechanisms of the response of temperate maize to heat stress and for the tolerance to heat stress, in a first experiment I applied gene expression profiling. Therewith, I investigated the transcriptomic response of temperate maize to linearly increasing heat levels. Further, I identified genes associated with heat tolerance in a set of eight genotypes with contrasting heat tolerance behavior. I identified 607 heat responsive genes, which elucidate the genetic pathways behind the response of maize to heat stress and can help to expand the knowledge of plant responses to other abiotic stresses. Further, I identified 39 genes which were differentially regulated between heat tolerant and heat susceptible inbreds and, thus, are putative heat tolerance candidate genes. Two of these candidate genes were located in genome regions which were associated with heat tolerance during seedling and adult stage that have been detected in QTL studies in the frame of this thesis. Their exact molecular functions, however, are still unknown. The statistical approach to identify heat tolerance genes, presented in my thesis, enables researchers to investigate the transcriptomic response of multiple genotypes to changing conditions across several experiments, considering their natural variation for a quantitative trait. In order to develop more heat tolerant cultivars, knowledge of natural variation for heat tolerance in temperate maize is indispensable. Therefore, heat tolerance was assessed in a set of intra- and interpool Dent and Flint populations on a multi-environment level. Usually, heat stress in temperate Europe occurs during the adult stage of maize. However, as maize is of increasing importance as a biogas crop, farmers can reduce the growth period by postponed sowing after the harvest of the winter cereals in early summer and, thus, sensitive maize seedlings can be exposed to heat stress. Therefore, I aimed to assess heat tolerance in six connected segregating Dent and Flint populations during both developmental stages considering besides multiple environments also multiple traits. At heat stress, I observed an average decrease of 20% of the shoot dry weight during seedling stage and an average of 50% of yield loss, when heat stress was present during adult stage. At the heat locations heat stress was present in the year, when the experiments were conducted as temperatures exceeded 32°C there for more than 400 hours during the growing period in contrast to less than 30 hours at the standard locations. This emphasizes that maize crop production can suffer with the increasing number and intensity of summer heat waves. Furthermore, the study revealed strong differences between genotypes, which was indispensable to differentiate between heat tolerant and heat susceptible inbred lines. The tested genotypes originating from the Flint pool turned out to possess higher heat tolerance during seedling stage, whereas the genotypes derived from the Dent pool possessed higher heat tolerance during adult stage. This fact could be exploited by the maintenance of two pools with contrasting heat tolerance and could be beneficial for hybrid breeding. A direct selection of more heat tolerant genotypes in terms of grain yield is expensive and time-consuming. To facilitate the selection process in order to develop more heat tolerant cultivars, breeders could make use of marker assisted selection. To lay the foundation for this technique, in my thesis, QTL for heat tolerance during adult and during seedling stage were identified with the previously mentioned populations. Two QTL explained 19% of the total variance for heat tolerance with respect to grain yield in a simultaneous fit. Furthermore each two QTL were identified for two principal components, which accounted for heat tolerance during seedling stage. They explained 14 and 12% of the respective variance. The results can be used by breeding companies to develop marker assays in order to select heat tolerant genotypes from their proprietary genetic material during both stages in an initial screening. This would reduce the field capacities considerably, which are needed to test heat tolerance on a field level.