Use of locally weighted scatterplot smoothing (LOWESS) regression to study selection signatures inPiedmontese andItalianBrown cattle breeds

Abstract

Selection is the major force affecting local levels of genetic variation in species. The availability of dense marker maps offers new opportunities for a detailed understanding of genetic diversity distribution across the animal genome. Over the last 50 years, cattle breeds have been subjected to intense artificial selection. Consequently, regions controlling traits of economic importance are expected to exhibit selection signatures. The fixation index (Fst ) is an estimate of population differentiation, based on genetic polymorphism data, and it is calculated using the relationship between inbreeding and heterozygosity. In the present study, locally weighted scatterplot smoothing (LOWESS) regression and a control chart approach were used to investigate selection signatures in two cattle breeds with different production aptitudes (dairy and beef). Fst was calculated for 42 514 SNP marker loci distributed across the genome in 749 Italian Brown and 364 Piedmontese bulls. The statistical significance of Fst values was assessed using a control chart. The LOWESS technique was efficient in removing noise from the raw data and was able to highlight selection signatures in chromosomes known to harbour genes affecting dairy and beef traits. Examples include the peaks detected for BTA2 in the region where the myostatin gene is located and for BTA6 in the region harbouring the ABCG2 locus. Moreover, several loci not previously reported in cattle studies were detected.

Genome wide association study on beef production traits in Marchigiana cattle breed

“…Significant markers found in this study identify a QTL region where MSTN and other neighbouring genes, such as collagen, type V, alpha 2 (COL5A2) and solute carrier family 40, member A1 (SLC40A1), involved in muscle biology and collagen biosynthesis were located. This result is in agreement with previous reports for beef cattle (Pintus et al 2014;Saatchi et al 2014).…”

“…This result is in agreement with previous reports for beef cattle ( Pintus et al . ; Saatchi et al . ).…”

Impact of the Publication of Appropriate Use Criteria on Utilization Rates of Myocardial Perfusion Imaging Studies in Ontario, Canada: A Population‐Based Study

“…To graphically represent the overall trend and any change in the rates before and after the intervention, we estimated a smoothing line using robust locally weighted regression (LOESS). 24,25 Reductions in numbers of MPI scans as a potential result of publication of the AUC were estimated by multiplying the change in monthly rate between the periods of any statistically significant intervention by the yearly population of Ontario aged ≥20 years. That number was then…”

Selection signatures in worldwide sheep populations

“…Another region harbors the HMGA2 gene, involved in selection for stature in dogs [19] and associated to body size in horses [20] and height in humans [21]. The last region includes two interesting candidate genes: ABCG2, which has been associated to a strong QTL for milk production in cattle [22], and NCAPG, which has been associated to fetal growth [23] and calving ease [24] in cattle and which is located in several selection signatures in this species [25][26][27][28]. In our analysis, populations with a selection signature in this region belong to three European groups (SWE, ITA and CEU) and our results suggest that selection in these different groups might imply distinct genes ( Table 2).…”