Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions

There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the “Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)” to identify putative regulatory regions in flash-frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest-, average-, and largest-sized male piglets from each litter through five developmental time points. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs

Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions

There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the "Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)" to identify putative regulatory regions in flash-frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest-, average-, and largest-sized male piglets from each litter through five developmental time points. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs

Molecular characterisation of ichthyosis fetalis and Niemann-pick type C disease in cattle and brachygnathia, cardiomegaly and renal hypoplasia syndrome and pulmonary hypoplasia with anasarca in sheep

Since the domestication of cattle and sheep, these species have been extensively farmed to produce food and fibre for human consumption and use. The move from natural breeding to selective breeding has enabled for desired production traits to be selected, and has facilitated accelerated genetic gain within these populations. The presence of deleterious alleles is not a new phenomenon in animal breeding, yet inherited diseases continue to impact animal welfare, productivity and profitability. The advancement in molecular genetics, sequencing technologies and bioinformatics over the past few decades has facilitated the wide generation of genomes for cattle and sheep, and has allowed for improved variant discovery. Despite these advances, reporting of inherited diseases in cattle and sheep is not commonplace in Australia. This thesis utilised several approaches that included SNP genotyping, Sanger sequencing, candidate gene analysis and whole genome sequencing for initially ten inherited diseases, to identify causal mutations. These approaches were used successfully for four inherited diseases: ichthyosis fetalis in Shorthorn cattle, Niemann-Pick type C disease in Angus/Angus-cross cattle, brachygnathia, cardiomegaly and renal hypoplasia syndrome in Merino sheep and pulmonary hypoplasia with anasarca in Persian sheep, which forms the basis of this thesis. Diagnostic DNA tests were developed for these four diseases, and were used to improve breeding management. The communication of the results from this thesis will help provide awareness of emerging inherited diseases in Australian livestock populations, as well as highlighting the importance of taking a proactive approach for reporting and managing inherited diseases in livestock