pSBVB: A Versatile Simulation Tool To Evaluate Genomic Selection in Polyploid Species.

Genomic Selection (GS) is the procedure whereby molecular information is used to predict complex phenotypes and it is standard in many animal and plant breeding schemes. However, only a small number of studies have been reported in horticultural crops, and in polyploid species in particular. In this paper, we have developed a versatile forward simulation tool, called polyploid Sequence Based Virtual Breeding (pSBVB), to evaluate GS strategies in polyploids; pSBVB is an efficient gene dropping software that can simulate any number of complex phenotypes, allowing a very flexible modeling of phenotypes suited to polyploids. As input, it takes genotype data from the founder population, which can vary from single nucleotide polymorphisms (SNP) chips up to sequence, a list of causal variants for every trait and their heritabilities, and the pedigree. Recombination rates between homeologous chromosomes can be specified, so that both allo- and autopolyploid species can be considered. The program outputs phenotype and genotype data for all individuals in the pedigree. Optionally, it can produce several genomic relationship matrices that consider exact or approximate genotype values. pSBVB can therefore be used to evaluate GS strategies in polyploid species (say varying SNP density, genetic architecture or population size, among other factors), or to optimize experimental designs for association studies. We illustrate pSBVB with SNP data from tetraploid potato and partial sequence data from octoploid strawberry, and we show that GS is a promising breeding strategy for polyploid species but that the actual advantage critically depends on the underlying genetic architecture. Source code, examples and a complete manual are freely available in GitHub https://github.com/lauzingaretti/pSBVB.

Plant polyphenol intake alters gene expression in canine leukocytes.

BACKGROUND/AIMS: Polyphenol compounds may explain most of the health-related beneficial effects of plants and vegetables, mainly through their antioxidant properties. The aim of the study was to assess the main changes on leukocyte gene expression of dogs caused by intake of three natural polyphenol-rich extracts and to compare them with caloric restriction. METHODS: 20 female dogs were divided into 5 groups: control fed ad libitum (C), caloric-restricted to 30% less than control (CR), and 3 groups fed ad libitum supplemented with citrus extract (CE), green tea extract (GTE) or grape seed extract (GSE). Leukocytes gene expression was analyzed in a specially designed microarray. RESULTS: CE treatment mainly downregulated genes related to inflammative (IL-8, VLA-4) and cytotoxic response (GRP 58) as well as proliferation of leukocytes. GTE induced gene expression related to leukocyte proliferation and signaling (GNAQ, PKC-B). GSE upregulated some of the genes increased by CE treatment. CR downregulated genes related with energy metabolism (ATP5A1, COX7C) and inflammatory markers (VLA-4). CONCLUSION: A chronic ingestion of citric, grape seed and green tea polyphenols is able to modulate canine leukocyte functions through changes in gene expression. CE ingestion reduces expression of some genes also diminished by a 30% caloric restriction.

Impact of breed and sex on porcine endocrine transcriptome: a bayesian biometrical analysis.

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.