Genetic diversity analyses reveal first insights into breed-specific selection signatures within Swiss goat breeds
ANIMAL GENETICS
Authors: Burren, A.; Neuditschko, M.; Signer-Hasler, H.; Frischknecht, M.; Reber, I.; Menzi, F.; Drogemuller, C.; Flury, C.
Abstract
We used genotype data from the caprine 50k Illumina BeadChip for the assessment of genetic diversity within and between 10 local Swiss goat breeds. Three different cluster methods allowed the goat samples to be assigned to the respective breed groups, whilst the samples of Nera Verzasca and Tessin Grey goats could not be differentiated from each other. The results of the different genetic diversity measures show that Appenzell, Toggenburg, Valais and Booted goats should be prioritized in future conservation activities. Furthermore, we examined runs of homozygosity (ROH) and compared genomic inbreeding coefficients based on ROH (F-ROH) with pedigree-based inbreeding coefficients (F-PED). The linear relationship between F-ROH and F-PED was confirmed for goats by including samples from the three main breeds (Saanen, Chamois and Toggenburg goats). F-ROH appears to be a suitable measure for describing levels of inbreeding in goat breeds with missing pedigree information. Finally, we derived selection signatures between the breeds. We report a total of 384 putative selection signals. The 25 most significant windows contained genes known for traits such as: coat color variation (MITF, KIT, ASIP), growth (IGF2, IGF2R, HRAS, FGFR3) and milk composition (PITX2). Several other putative genes involved in the formation of populations, which might have been selected for adaptation to the alpine environment, are highlighted. The results provide a contemporary background for the management of genetic diversity in local Swiss goat breeds.
Atlas of tissue- and developmental stage specific gene expression for the bovine insulin-like growth factor (IGF) system
PLOS ONE
Authors: Ghanipoor-Samami, Mani; Javadmanesh, Ali; Burns, Brian M.; Thomsen, Dana A.; Nattrass, Greg S.; Estrella, Consuelo Amor S.; Kind, Karen L.; Hiendleder, Stefan
Abstract
The insulin-like growth factor (IGF) axis is fundamental for mammalian growth and development. However, no comprehensive reference data on gene expression across tissues and pre- and postnatal developmental stages are available for any given species. Here we provide systematic promoter- and splice variant specific information on expression of IGF system components in embryonic (Day 48), fetal (Day 153), term (Day 277, placenta) and juvenile (Day 365-396) tissues of domestic cow, a major agricultural species and biomedical model. Analysis of spatiotemporal changes in expression of IGF1, IGF2, IGF1 R, IGF2R, IGFBP1-8 and IR genes, as well as IncRNAs H19 and AIRN, by qPCR, indicated an overall increase in expression from embryo to fetal stage, and decrease in expression from fetal to juvenile stage. The stronger decrease in expression of IncRNAs (average -16-fold) and ligands (average -12.1-fold) compared to receptors (average -5.7-fold) and binding proteins (average -4.3-fold) is consistent with known functions of IGF peptides and supports important roles of IncRNAs in prenatal development. Pronounced overall reduction in postnatal expression of IGF system components in lung (-12.9-fold) and kidney (-13.2-fold) are signatures of major changes in organ function while more similar hepatic expression levels (-2.2-fold) are evidence of the endocrine rather than autocrine/paracrine role of IGFs in postnatal growth regulation. Despite its rapid growth, placenta displayed a more stable expression pattern than other organs during prenatal development. Quantitative analyses of contributions of promoters PO-P4 to global IGF2 transcript in fetal tissues revealed that P4 accounted for the bulk of transcript in all tissues but skeletal muscle. Demonstration of IGF2 expression in fetal muscle and postnatal liver from a promoter orthologous to mouse and human promoter PO provides further evidence for an evolutionary and developmental shift from placenta-specific PO-expression in rodents and suggests that some aspects of bovine IGF expression may be closer to human than mouse.