Published in Genetics, selection, evolution : GSE
Alongside substantially expanding the ruminant lncRNA repertoire, the outcomes of our analysis demonstrate that stochastic sampling can be partly overcome by combining RNA-seq datasets from related species. This has practical implications for the future discovery of lncRNAs in other species.
Published in Genetics, selection, evolution : GSE
Our findings provide an empirical comparison of the efficacy of pedigree and genomic predictions in broiler chickens and examine the effects of fitting GRM with coefficients regressed back to a reference anchored to the pedigree, either A or [Formula: see text]. For the analysed dataset, the best results were obtained when [Formula: see text] was c...
Published in Genetics, selection, evolution : GSE
These results suggest that natural selection has, at least partially, a role in shaping the genome of Valle del Belice sheep and that ROH in the ovine genome may help to detect genomic regions involved in the determinism of traits under selection.
Published in Genetics, selection, evolution : GSE
Various SNPs that are significantly associated with calving performance are located within or nearby genes with potential roles in tight junction, oxytocin signaling, and MAPK signaling. Combining the significant SNPs or SNPs within or nearby gene(s) from the HD panel with the BovineSNP50 panel yielded a marginal increase in the accuracy of predict...
Published in Genetics, selection, evolution : GSE
Here, we report the mapping and genetic variation of 18 selection signatures that were identified between Australian Merino and Spanish Churra sheep breeds, which were validated by an additional contrast between Spanish Merino and Churra genotypes. Analysis of whole-genome sequencing datasets allowed us to identify divergent variants that may be vi...
Published in Genetics, selection, evolution : GSE
The low levels of genomic inbreeding observed in the original Swiss cattle populations ER, OB and SI compared to the other breeds are explained by a lesser use of artificial insemination and greater use of natural service. Natural service results in more sires having progeny at each generation and thus this breeding practice is likely the major rea...
Published in Genetics, selection, evolution : GSE
Large differences in estimated ASE were observed for low MAF SNPs when allele counts were scaled or not scaled because there is less shrinkage towards the mean for scaled allele counts. We derived a theoretical framework that shows that the difference in ASE due to shrinkage is heavily influenced by the power of the data. Increasing the power resul...
Published in Genetics, selection, evolution : GSE
In this paper, we describe a new strategy for incorporating genetic interactions into genomic prediction and association models. This strategy results in accurate models, with sometimes significantly higher accuracies than that of a standard additive model.
Published in Genetics, selection, evolution : GSE
Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selec...
Published in Genetics, selection, evolution : GSE
We present an efficient approach to approximate analysis of whole-sequence data with a Bayesian variable selection model. The lack of increase in prediction accuracy when applied to real data could be due to imputation errors, which demonstrates the importance of developing more accurate methods of imputation or directly genotyping sequence variant...
