Selected tissues of two Polish goat breeds do not differ on genomic level

The aim of the study was to investigate differences in the gene expression profiles of selected tissues in two most popular goat’s breeds in Poland: Polish White Improved (PWI) and Polish Fawn Improved (PFI). Three different types of tissue samples were selected: somatic cells isolated from goats’ milk (MSC), milk fat globules (MFG) and peripheral nuclear blood cells (PBNC) Since there were no earlier genetic studies focused on genetic differences between these two goat breeds we decided to evaluate hypothetical genomic differences assuming that such a differences should be the consequence of genetic differences. We created the hypothesis that if genomic differences exist they should be revealed in hierarchical clustering of transcriptomic profiles of selected tissues. Should the genomic differences exist the clusters obtained are grouping goat breeds and not goat’s tissues. The results of hierarchical clustering however show something completely different. The clusters are grouping goat tissues (milk fat globules, milk somatic cells, peripheral blood nuclear cells) without any relation with goat breed. So the analytical tool does not recognize the goat breed as a driver of transcriptomic difference. Moreover, we were not able to find significantly regulated genes between two breeds The experiment was performed on 24 transcriptomic microarrays using a common reference design. The common reference comprised a pool of equal amounts of RNA from 7 healthy goats in 4th lactation from both Polish breeds (PWI n=4 and PFI n=3). Samples were taken after finishing of lactation period. Experimental samples were collected from healthy goats in 3rd lactation (PWI n=4, PFI n=4) and RNA was isolated from 3 different sources: MSC, MFG and nucleated blood cells