An improved pig reference genome sequence to enable pig genetics and genomics research
Abstract Background The domestic pig (Sus scrofa) is important both as a food source and
as a biomedical model given its similarity in size, anatomy, physiology, metabolism …
as a biomedical model given its similarity in size, anatomy, physiology, metabolism …
The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000
Hi-C contact maps are valuable for genome assembly (;;). Recently, we developed Juicebox,
a system for the visual exploration of Hi-C data, and 3D-DNA, an automated pipeline for …
a system for the visual exploration of Hi-C data, and 3D-DNA, an automated pipeline for …
[HTML][HTML] Symposium review: Advances in sequencing technology herald a new frontier in cattle genomics and genome-enabled selection
The cattle reference genome assembly has underpinned major innovations in beef and
dairy genetics through genome-enabled selection, including removal of deleterious …
dairy genetics through genome-enabled selection, including removal of deleterious …
Evaluation of the accuracy of imputed sequence variant genotypes and their utility for causal variant detection in cattle
Background The availability of dense genotypes and whole-genome sequence variants from
various sources offers the opportunity to compile large datasets consisting of tens of …
various sources offers the opportunity to compile large datasets consisting of tens of …
Genome sequence analysis reveals selection signatures in endangered trypanotolerant West African Muturu cattle
Like most West African Bos taurus, the shorthorn Muturu is under threat of replacement or
crossbreeding with zebu. Their populations are now reduced to a few hundred breeding …
crossbreeding with zebu. Their populations are now reduced to a few hundred breeding …
Genetic dissection of bread wheat diversity and identification of adaptive loci in response to elevated tropospheric ozone
Rising tropospheric ozone affects the performance of important cereal crops thus
threatening global food security. In this study, genetic variation of wheat regarding its …
threatening global food security. In this study, genetic variation of wheat regarding its …
SNPrune: an efficient algorithm to prune large SNP array and sequence datasets based on high linkage disequilibrium
MPL Calus, J Vandenplas - Genetics Selection Evolution, 2018 - Springer
Background High levels of pairwise linkage disequilibrium (LD) in single nucleotide
polymorphism (SNP) array or whole-genome sequence data may affect both performance …
polymorphism (SNP) array or whole-genome sequence data may affect both performance …
A PLAG1 mutation contributed to stature recovery in modern cattle
The recent evolution of cattle is marked by fluctuations in body size. Height in the Bos taurus
lineage was reduced by a factor of~ 1.5 from the Neolithic to the Middle Ages, and increased …
lineage was reduced by a factor of~ 1.5 from the Neolithic to the Middle Ages, and increased …
Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
The role of chromosome rearrangements in driving evolution has been a long-standing
question of evolutionary biology. Here we focused on ruminants as a model to assess how …
question of evolutionary biology. Here we focused on ruminants as a model to assess how …
Detection of breeding signatures in wheat using a linkage disequilibrium-corrected mapping approach
Marker assisted breeding, facilitated by reference genome assemblies, can help to produce
cultivars adapted to changing environmental conditions. However, anomalous linkage …
cultivars adapted to changing environmental conditions. However, anomalous linkage …