Sex and Parental Genome Effects on Bovine Fetal Development

Abstract

During fetal development, the process of forming organs and tissues is mediated by tissuespecific patterns of gene expression. Studying qualitative and quantitative changes in the transcriptome and understanding the mechanisms that regulate gene expression and the association with specific phenotypes in bovine fetal development will help us to explore the sex effect and breed effect. To carry out this work, a well-assembled cattle reference genome is essential, but the current cattle reference genome is incomplete and in particular, missing the Y chromosome. In this thesis I describe the first bovine sex chromosome assemblies for Bos taurus indicus and Bos taurus taurus cattle, that include the complete pseudoautosomal regions (PAR), which span 6.84 Mb and comprises 31 genes, and three Y chromosome X-degenerate (X-d) regions. The results show the ruminant PAR boundary is at a similar position to those of the pig and dog, but that the ruminant PAR extends further than those of human and horse. Differences in the PAR boundaries are consistent with evolutionary divergence times. A bovidae-specific expansion of members of the lipocalin gene family in the PAR reported here, may affect immune-modulation and anti-inflammatory responses in ruminants. Comparison of the X-d regions of Y chromosomes across species revealed that five of the X-Y gametologues, which are known to be global regulators of gene activity and candidate sexual dimorphism genes, are conserved. I report the transcriptome sequencing of 120 samples (60 males and 60 females) and analyzed differences in gene expression between male and female tissues derived from all three germ layers of the embryo, including brain, liver and lung, skeletal muscle and placenta. A remarkably small set of XY genes (gametologues) was identified that differentiate males and females across all tissues. Expression levels of paired gametologues in males and females are unbalanced and explain 18% - 96% of the phenotypic variance in organ weights attributed to the sex effect. Considering the significant programming events at the embryo-fetal stage, we propose that early differences in gametologue expression between females and males are fundamental drivers of phenotypic differences between the sexes.The 120 samples used in this study were from 4 genetic groups: pure Angus, pure Brahman and their reciprocal crosses. Differential gene expression between the pure breed individuals and between the reciprocal crosses was explored. There were 110 genes differentially expressed (DEGs) between pure Angus and pure Brahman in all tissues which were related to functions including immune response and stress response. The DEG between the purebred groups and in the reciprocal crosses showed an additive expression pattern, where both paternal and maternal genomes contributed to the gene expression levels. Only 5% of DEGs in each tissue showed a parent of origin driven expression, Angus or Brahman, and showed both maternal and paternal dominant effects. In summary, the newly assembled cattle sex chromosomes helped us to identify the PAR, X-degenerate region and the locations of gametologues which provide a clear reference for sex-specific study. Studies of sex-specific and breed-specific effects on fetal development showed gametologues play a major role in early female-male phenotypic differentiation which also provided solid evidence to support further parent of origin studies.