ABSTRACT: Background: Transcriptome variability is due to genetic and environmental causes, much like any other complex phenotype. Ascertaining the transcriptome differences between individuals is an important step to understand how selection and genetic drift may affect gene expression. To that end, extant divergent livestock breeds offer an ideal genetic material. Results: We have analyzed with microarrays five tissues from the endocrine axis (hypothalamus, adenohypophysis, thyroid gland, gonads and fat tissue) of 16 pigs from both sexes pertaining to four extreme breeds (Duroc, Large White, Iberian and a cross with SinoEuropean hybrid line). Using a Bayesian linear model approach, we observed that the largest breed variability corresponded to the male gonads, and was larger than at the remaining tissues, including ovaries. Measurement of sex hormones in peripheral blood at slaughter did not detect any breed-related differences. Not unexpectedly, the gonads were the tissue with the largest number of sex biased genes. There was a strong correlation between sex and breed bias expression, although the most breed biased genes were not the most sex biased genes. A combined analysis of connectivity and differential expression suggested three biological processes as being primarily different between breeds: spermatogenesis, muscle differentiation and several metabolic processes. Conclusion: These results suggest that differences across breeds in gene expression of the male gonads are larger than in other endocrine tissues in the pig. Nevertheless, the strong presence of breed biased genes in the male gonads cannot be explained solely by changes in spermatogenesis nor by differences in the reproductive tract development. Experiment Overall Design: Sixteen animals, four from each of four breeds, Large White (LW), Duroc (DU), Youli (YL) and Iberian (IB) piglets were sampled. These breeds represent a wide genetic variability in current pig breeding schemes. There were two males and two females per breed except in Youli, represented by three males and one female. Animals were bought from three breeding companies and transferred to the University experimental farms at weaning, i.e., aged one month approximately. Pigs were housed simultaneously, fed the same diets during the fattening period, that lasted two months, and were weighed at weekly intervals. At the time of slaughter, the average ages were 87, 83, 80 and 89 days for Large White, Duroc, Youli and Iberian pigs, respectively. Their mean live weights at that time were 27.2 (LW), 23.1 (DU), 18.9 (YL) and 17.4 kg (IB). Experiment Overall Design: Animals were euthanized, after 24h fasting, by an overdose of intravenous sodium thiobarbital. At necropsy, tissue samples were collected, snap frozen in liquid nitrogen and stored at -80 ºC. The average time gap between euthanasia and tissue collection was ~ 15 minutes, maximum time was 25 minutes. The tissues collected were hypothalamus (HYPO), adenohypophysis (AHYP), which was separated from the neurohypophysis, thyroid gland (THYG), gonads (GONA) from both sexes, and back fat tissue (FATB). The hypothalamus included the mamillary body and grey tubercle but excluded the chiasma opticum. Throughout this work, each sample was identified by the acronym of the tissue followed by the animal id, e.g., FATBLWF1 refers to back fat tissue from female 1 Large White.
