Signatures of Selection in the Genomes of Commercial and Non-Commercial Chicken Breeds

Identifying genomics regions that are affected by selection is important to understand the domestication and selection history of the domesticated chicken, as well as understanding molecular pathways underlying phenotypic traits and breeding goals. While whole-genome approaches, either high-density SNP chips or massively parallel sequencing, have been successfully applied to identify evidence for selective sweeps in chicken, it has been difficult to distinguish patterns of selection and stochastic and breed specific effects. Here we present a study to identify selective sweeps in a large number of chicken breeds (67 in total) using a high-density (58 K) SNP chip. We analyzed commercial chickens representing all major breeding goals. In addition, we analyzed non-commercial chicken diversity for almost all recognized traditional Dutch breeds and a selection of representative breeds from China. Based on their shared history or breeding goal we in silico grouped the breeds into 14 breed groups. We identified 396 chromosomal regions that show suggestive evidence of selection in at least one breed group with 26 of these regions showing strong evidence of selection. Of these 26 regions, 13 were previously described and 13 yield new candidate genes for performance traits in chicken. Our approach demonstrates the strength of including many different populations with similar, and breed groups with different selection histories to reduce stochastic effects based on single populations

Regions of Homozygosity in the Porcine Genome: Consequence of Demography and the Recombination Landscape

Inbreeding has long been recognized as a primary cause of fitness reduction in both wild and domesticated populations. Consanguineous matings cause inheritance of haplotypes that are identical by descent (IBD) and result in homozygous stretches along the genome of the offspring. Size and position of regions of homozygosity (ROHs) are expected to correlate with genomic features such as GC content and recombination rate, but also direction of selection. Thus, ROHs should be non-randomly distributed across the genome. Therefore, demographic history may not fully predict the effects of inbreeding. The porcine genome has a relatively heterogeneous distribution of recombination rate, making Sus scrofa an excellent model to study the influence of both recombination landscape and demography on genomic variation. This study utilizes next-generation sequencing data for the analysis of genomic ROH patterns, using a comparative sliding window approach. We present an in-depth study of genomic variation based on three different parameters: nucleotide diversity outside ROHs, the number of ROHs in the genome, and the average ROH size. We identified an abundance of ROHs in all genomes of multiple pigs from commercial breeds and wild populations from Eurasia. Size and number of ROHs are in agreement with known demography of the populations, with population bottlenecks highly increasing ROH occurrence. Nucleotide diversity outside ROHs is high in populations derived from a large ancient population, regardless of current population size. In addition, we show an unequal genomic ROH distribution, with strong correlations of ROH size and abundance with recombination rate and GC content. Global gene content does not correlate with ROH frequency, but some ROH hotspots do contain positive selected genes in commercial lines and wild populations. This study highlights the importance of the influence of demography and recombination on homozygosity in the genome to understand the effects of inbreeding

Genotype data of 480 chickens from 37 traditional Dutch chicken breeds

The folder contains the information for 52,232 markers genotyped in 480 samples using the Illumina Infinium iSelect 60K BeadChip. Markers are uniformly distributed across the Gallus_gallus5.0 chicken genome, comprising 29 autosomes (Gga 1-28 and Gga 33), two sex chromosomes (W,Z), and one linkage group (LGE64)

The utility of digital templating in Total Hip Arthroplasty with Crowe type II and III dysplastic hips

With the superiority of digital imaging, conventional preoperative acetate templating is gradually being replaced by digital templating in total hip arthroplasty (THA). The purpose of this study was to assess the utility of digital templating for patients with Crowe type II and III dysplastic hips. In this study, 41 THA patients with Crowe type II or III dysplastic hips and 48 THA patients with other primary diseases were retrospectively reviewed. All patients were fitted with cementless prostheses in 2008. For the THA patients with dysplastic hips, we attempted to restore their hip centres to the position of the true acetabulum. Digital templating was the method chosen to achieve hip centre restoration. The prosthesis prediction accuracy (within ± one size using digital templating) was 20 (48.8%) for the cup size and 30 (73.2%) for the stem size. Meanwhile, for patients with other primary diseases, the accuracy for the cup size within ± one size was 34 (70.8%) and for the stem size accuracy was within ± one size in 38 (79.2%). Between the two patient groups, there was a significant difference in the predicted cup size. In patients with dysplastic hips, the low accuracy of the predicted cup size may have resulted from difficulty in predicting the vertical location of the hip centre. Despite this limitation, preoperative planning using digital templating is a convenient technique for THA patients with Crowe type II and III dysplastic hips