Multi-omics-approach in dairy cattle to analyse the impact of intra-uterine heat stress during late pregnancy on production and health traits with special consideration of metabolomics and epigenetics

该项目旨在实施多代动物模型。这一跨代水平的模型允许研究妊娠晚期子宫热应激对母鼠及其后代的生产力、健康和代谢参数(代谢物)的影响。在这方面，表型将与基因组变异、基因表达和DNA甲基化情况有关，以分析不同的“组学水平”，包括表观组学、代谢组学、(表观)基因组学和转录组学。具体的相关性是确定表观遗传印记效应，这将使用整体方法进行推断。最初，遗传统计建模基于来自所谓合同牛群的20,000多头分型奶牛(包括多代奶牛)，具有生产和健康性状的表型。基于特定基因组关系矩阵的生成和通过SNP标记数据生成用于印记效应的(协方差)矩阵，来估计可能的印记效应和相应染色体片段的定位。该模型同时允许估计加性-遗传和显性效应。数量遗传和基因组统计分析是由UGI的König教授小组进行的(数量遗传和基因组建模方面的专业知识)。已确定的与印记效应相关的基因组区域是在序列水平上分析表观遗传过程的基础，即通过有针对性的甲基组和转录组测序方法进行DNA甲基化和基因表达分析。DNA甲基化和基因表达模式的动态分析将在多代动物模型中进行研究。在这方面，我们使用来自“Hofgut Neumühle”研究站(代谢组学表型鉴定方面的专业知识)的创新奶牛表型来扩展表型数据库。在G0代(Dam)、G1代(女儿)和G2代(孙女)三代中采集血液样本，以描绘多器官转录组和表观基因组。对于受表观遗传影响的基因组区域，现有DNA甲基化模式和转录组图谱的特定分子遗传分析是通过靶向测序方法进行的，即使用下一代测序技术进行亚硫酸盐测序或cDNA测序。序列分析主要由TUM的Krebs博士团队进行(下一代测序、转录组分析方面的专业知识)。

The project aims on the implementation of a multi-generation-animal-model. This model on a transgenerational level allows studying the impact of uterine heat stress during late pregnancy on productivity, health and metabolic parameters (metabolites) in dams and their offspring. In this regard, phenotypes will be related to genomic variants, gene expressions and DNA-methylation profiles, in order to analyse the different "omics Levels" including phenomics, metabolomics, (epi-)genomics and transcriptomics. Of specific relevance is the identification of epigenetic imprinting effects, which will be inferred using a holistic approach. Initially, genetic-statistical modelling bases on more than 20,000 genotyped dairy cows (including multiple generations) from so-called contract-herds, with phenotypes for production and health traits. Estimation of possible imprinting effects and the localisation of respective chromosome segments bases on the generation of a specific genomic relationship matrix, and of a (co)variance matrix for imprinting effects via SNP marker data. The modelling simultaneously allows an estimation of additive-genetic and dominance effects. The quantitative-genetic and genomic statistical analyses are carried out by the group of Prof. König from UGI (expertise in quantitative-genetic and genomic modelling). The identified genomic regions associated with imprinting effects are the basis for analyses on epigenetic processes at the sequence level, i.e., DNA-methylation and gene expression analyses via targeted methylome- and transcriptome-sequencing approaches. The analysis of dynamics in DNA-methylation and gene expression patterns will be studied in a multi-generation-animal-model. In this regard, we extend the phenome database with innovative dairy cow phenotypes from the research station “Hofgut Neumühle” (expertise in phenotyping metabolomics data). Blood samples will be collected in the three generations G0 (dam), G1 (daughter) and G2 (granddaughter), in order to depict the multi-organ transcriptome and epigenome. For epigenetically influenced genomic regions, the specific molecular genetic analyses of the existing DNA methylation patterns and transcriptome profiles are carried out via targeted-sequencing approaches, i.e. bisulphite- or cDNA-sequencing using next-generation sequencing technology. The sequence analyses are mainly carried out by the group of Dr. Krebs from TUM (expertise in next-generation-sequencing, transcriptome analysis).