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

该项目旨在建立一个多代动物模型。该模型在跨代水平上允许研究妊娠后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甲基化谱相关，以分析不同的“组学水平”，包括表型组学、代谢组学、（表）基因组学和转录组学。具体的相关性是鉴定表观遗传印记的影响，这将是推断使用一个整体的方法。最初，遗传统计建模基于来自所谓的合同牛群的20，000多头基因型奶牛（包括多代），具有生产和健康性状的表型。可能的印迹效应和相应染色体片段的定位的估计基于特定基因组关系矩阵的生成，以及通过SNP标记数据的印迹效应的（协）方差矩阵的生成。该模型同时允许估计加性遗传和显性效应。定量遗传学和基因组统计分析由UGI的König教授（定量遗传学和基因组建模专家）进行。识别出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，通过靶向甲基化组和转录组测序方法进行DNA甲基化和基因表达分析。将在多代动物模型中研究DNA甲基化和基因表达模式的动态分析。在这方面，我们扩展了表型数据库，其中包含来自研究站“霍夫古特·诺伊米勒”（表型代谢组学数据专业知识）的创新奶牛表型。将在三代G0（母体）、G1（女儿）和G2（孙女）中采集血样，以描述多器官转录组和表观基因组。对于受表观遗传学影响的基因组区域，通过靶向测序方法，即使用下一代测序技术的亚硫酸氢盐或cDNA测序，对现有DNA甲基化模式和转录组谱进行特定分子遗传学分析。 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).