De novo assembly of the cattle reference genome with single-molecule sequencing.

BackgroundMajor advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies.ResultsWe present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use.ConclusionsWe demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species

Uncovering the architecture of selection in two Bos taurus cattle breeds

Abstract Directional selection alters the genome via hard sweeps, soft sweeps, and polygenic selection. However, mapping polygenic selection is difficult because it does not leave clear signatures on the genome like a selective sweep. In populations with temporally stratified genotypes, the Generation Proxy Selection Mapping (GPSM) method identifies variants associated with generation number (or appropriate proxy) and thus variants undergoing directional allele frequency changes. Here, we use GPSM on two large datasets of beef cattle to detect associations between an animal's generation and 11 million imputed SNPs. Using these datasets with high power and dense mapping resolution, GPSM detected a total of 294 unique loci actively under selection in two cattle breeds. We observed that GPSM has a high power to detect selection in the very recent past (<10 years), even when allele frequency changes are small. Variants identified by GPSM reside in genomic regions associated with known breed‐specific selection objectives, such as fertility and maternal ability in Red Angus, and carcass merit and coat color in Simmental. Over 60% of the selected loci reside in or near (<50 kb) annotated genes. Using haplotype‐based and composite selective sweep statistics, we identify hundreds of putative selective sweeps that likely occurred earlier in the evolution of these breeds; however, these sweeps have little overlap with recent polygenic selection. This makes GPSM a complementary approach to sweep detection methods when temporal genotype data are available. The selected loci that we identify across methods demonstrate the complex architecture of selection in domesticated cattle

A multi-breed reference panel and additional rare variants maximize imputation accuracy in cattle

International audienceAbstractBackgroundDuring the last decade, the use of common-variant array-based single nucleotide polymorphism (SNP) genotyping in the beef and dairy industries has produced an astounding amount of medium-to-low density genomic data. Although low-density assays work well in the context of genomic prediction, they are less useful for detecting and mapping causal variants and the effects of rare variants are not captured. The objective of this project was to maximize the accuracies of genotype imputation from medium- and low-density assays to the marker set obtained by combining two high-density research assays (~ 850,000 SNPs), the Illumina BovineHD and the GGP-F250 assays, which contains a large proportion of rare and potentially functional variants and for which the assay design is described here. This 850 K SNP set is useful for both imputation to sequence-level genotypes and direct downstream analysis.ResultsWe found that a large multi-breed composite imputation reference panel that includes 36,131 samples with either BovineHD and/or GGP-F250 genotypes significantly increased imputation accuracy compared with a within-breed reference panel, particularly at variants with low minor allele frequencies. Individual animal imputation accuracies were maximized when more genetically similar animals were represented in the composite reference panel, particularly with complete 850 K genotypes. The addition of rare variants from the GGP-F250 assay to our composite reference panel significantly increased the imputation accuracy of rare variants that are exclusively present on the BovineHD assay. In addition, we show that an assay marker density of 50 K SNPs balances cost and accuracy for imputation to 850 K.ConclusionsUsing high-density genotypes on all available individuals in a multi-breed reference panel maximized imputation accuracy for tested cattle populations. Admixed animals or those from breeds with a limited representation in the composite reference panel were still imputed at high accuracy, which is expected to further increase as the reference panel expands. We anticipate that the addition of rare variants from the GGP-F250 assay will increase the accuracy of imputation to sequence level

A simulation technique for radiating shock tube flows

We describe a numerical modelling technique used to simulate the gas flow in the complete X2 facility in non-reflected shock tube mode. The technique uses a one-dimensional model to simulate piston dynamics and diaphragm rupture and couples this to an axisymmetric simulation of the shock tube which captures viscous and finite-rate chemistry effects. This technique is used to simulate a nonequilibrium radiation condition relevant to a Titan atmospheric manoeuvre. The condition is a 7 km/s shock propagating into a N-2/CH4 Mixture at 80 Pa. The results show that the shock remains relatively planar at the exit of the shock tube such that there should be little difficulty for the optics. In terms of modelling, the finite-rate chemistry gas performs better than the equilibrium gas for these flows with regards to flow property estimates

Genome-Wide Association Analyses of Fertility Traits in Beef Heifers

The ability of livestock to reproduce efficiently is critical to the sustainability of animal agriculture. Antral follicle count (AFC) and reproductive tract scores (RTS) can be used to estimate fertility in beef heifers, but the genetic mechanisms influencing variation in these measures are not well understood. Two genome-wide association studies (GWAS) were conducted to identify the significant loci associated with these traits. In total, 293 crossbred beef heifers were genotyped on the Bovine GGP 50K chip and genotypes were imputed to 836,121 markers. A GWAS was performed with the AFC phenotype for 217 heifers with a multi-locus mixed model, conducted using the year, age at time of sampling and principal component analysis groupings as the covariates. The RTS GWAS was performed with 289 heifers using an additive correlation/trend test comparing prepubertal to pubertal heifers. The loci on chromosomes 2, 3 and 23 were significant in the AFC GWAS and the loci on chromosomes 2, 8, 10 and 11 were significant in the RTS GWAS. The significant region on chromosome 2 was similar between both analyses. These regions contained genes associated with cell proliferation, transcription, apoptosis and development. This study proposes candidate genes for beef cattle fertility, although future research is needed to elucidate the precise mechanisms

Exploring genetic variation and population structure in a threatened species, <i>Noturus placidus</i>, with whole-genome sequence data

AbstractThe Neosho madtom (Noturus placidusIctalurus punctatus)Danio reri

DataSheet_3_Validation of a minimally-invasive method for sampling epithelial-associated microorganisms on the rumen wall.csv

The rumen microbiome provides approximately 70% of the required energy for the host by converting low-quality feedstuffs into usable energy for ruminants. The energy produced by the microorganisms is subsequently absorbed through the rumen epithelium and used towards growth and energy maintenance. There is evidence that ruminal epimural microbes directly interact with the rumen epithelium, acting as an intermediary communicator between the rumen liquid fraction and the host. Epimural microbiota have been demonstrated to be distinct from the ruminal liquid microbiome and perform unique roles within the rumen environment. However, methods to sample epimural communities from the rumen wall are limited and typically invasive, requiring animal fistulation or harvesting. To characterize the epimural communities present on the rumen wall, a novel and minimally-invasive surgical method was developed to swab the epithelium of the ventral sac of the rumen. The objective of this study was to validate this sampling method by comparing epimural and liquid fraction bacterial communities. During a 70-day feeding trial, Angus steers (n = 45) were sampled on day 35 using the novel surgery method and tubed on day 70 to sample rumen liquid content. Genomic DNA was used to generate amplicon libraries of the V4 region of the 16S rRNA gene. There were no differences between alpha diversity indices when comparing rumen versus epimural bacterial communities (P > 0.05). The Bray-Curtis dissimilarity was used to ordinate ASV counts, and then tested for differences between rumen and epimural communities using a PERMANOVA with 999 permutations (P < 0.05). Differential abundances of bacterial communities were tested using ANCOM-BC and MaAsLin2, where significance was determined by Q < 0.05 and overlap between both analysis methods. Within the 91 taxa that differed in abundance, 451 ASVs were found to be different between sample types (Q < 0.05). Unique ASVs associated with Prevotella, Succinivibrio, family-level Eubacterium, and family-level Succinivibrio were in greater abundance for the rumen epithelial-associated bacterial communities (Q < 0.05). The results demonstrate that the novel method of sampling from the rumen wall can capture differences between epimural and ruminal fluid bacterial communities, thus facilitating studies investigating the interactions between epimural bacteria with the host.</p

DataSheet_2_Validation of a minimally-invasive method for sampling epithelial-associated microorganisms on the rumen wall.csv

The rumen microbiome provides approximately 70% of the required energy for the host by converting low-quality feedstuffs into usable energy for ruminants. The energy produced by the microorganisms is subsequently absorbed through the rumen epithelium and used towards growth and energy maintenance. There is evidence that ruminal epimural microbes directly interact with the rumen epithelium, acting as an intermediary communicator between the rumen liquid fraction and the host. Epimural microbiota have been demonstrated to be distinct from the ruminal liquid microbiome and perform unique roles within the rumen environment. However, methods to sample epimural communities from the rumen wall are limited and typically invasive, requiring animal fistulation or harvesting. To characterize the epimural communities present on the rumen wall, a novel and minimally-invasive surgical method was developed to swab the epithelium of the ventral sac of the rumen. The objective of this study was to validate this sampling method by comparing epimural and liquid fraction bacterial communities. During a 70-day feeding trial, Angus steers (n = 45) were sampled on day 35 using the novel surgery method and tubed on day 70 to sample rumen liquid content. Genomic DNA was used to generate amplicon libraries of the V4 region of the 16S rRNA gene. There were no differences between alpha diversity indices when comparing rumen versus epimural bacterial communities (P > 0.05). The Bray-Curtis dissimilarity was used to ordinate ASV counts, and then tested for differences between rumen and epimural communities using a PERMANOVA with 999 permutations (P < 0.05). Differential abundances of bacterial communities were tested using ANCOM-BC and MaAsLin2, where significance was determined by Q < 0.05 and overlap between both analysis methods. Within the 91 taxa that differed in abundance, 451 ASVs were found to be different between sample types (Q < 0.05). Unique ASVs associated with Prevotella, Succinivibrio, family-level Eubacterium, and family-level Succinivibrio were in greater abundance for the rumen epithelial-associated bacterial communities (Q < 0.05). The results demonstrate that the novel method of sampling from the rumen wall can capture differences between epimural and ruminal fluid bacterial communities, thus facilitating studies investigating the interactions between epimural bacteria with the host.</p

DataSheet_1_Validation of a minimally-invasive method for sampling epithelial-associated microorganisms on the rumen wall.csv

The rumen microbiome provides approximately 70% of the required energy for the host by converting low-quality feedstuffs into usable energy for ruminants. The energy produced by the microorganisms is subsequently absorbed through the rumen epithelium and used towards growth and energy maintenance. There is evidence that ruminal epimural microbes directly interact with the rumen epithelium, acting as an intermediary communicator between the rumen liquid fraction and the host. Epimural microbiota have been demonstrated to be distinct from the ruminal liquid microbiome and perform unique roles within the rumen environment. However, methods to sample epimural communities from the rumen wall are limited and typically invasive, requiring animal fistulation or harvesting. To characterize the epimural communities present on the rumen wall, a novel and minimally-invasive surgical method was developed to swab the epithelium of the ventral sac of the rumen. The objective of this study was to validate this sampling method by comparing epimural and liquid fraction bacterial communities. During a 70-day feeding trial, Angus steers (n = 45) were sampled on day 35 using the novel surgery method and tubed on day 70 to sample rumen liquid content. Genomic DNA was used to generate amplicon libraries of the V4 region of the 16S rRNA gene. There were no differences between alpha diversity indices when comparing rumen versus epimural bacterial communities (P > 0.05). The Bray-Curtis dissimilarity was used to ordinate ASV counts, and then tested for differences between rumen and epimural communities using a PERMANOVA with 999 permutations (P < 0.05). Differential abundances of bacterial communities were tested using ANCOM-BC and MaAsLin2, where significance was determined by Q < 0.05 and overlap between both analysis methods. Within the 91 taxa that differed in abundance, 451 ASVs were found to be different between sample types (Q < 0.05). Unique ASVs associated with Prevotella, Succinivibrio, family-level Eubacterium, and family-level Succinivibrio were in greater abundance for the rumen epithelial-associated bacterial communities (Q < 0.05). The results demonstrate that the novel method of sampling from the rumen wall can capture differences between epimural and ruminal fluid bacterial communities, thus facilitating studies investigating the interactions between epimural bacteria with the host.</p

Image_1_Validation of a minimally-invasive method for sampling epithelial-associated microorganisms on the rumen wall.tiff

The rumen microbiome provides approximately 70% of the required energy for the host by converting low-quality feedstuffs into usable energy for ruminants. The energy produced by the microorganisms is subsequently absorbed through the rumen epithelium and used towards growth and energy maintenance. There is evidence that ruminal epimural microbes directly interact with the rumen epithelium, acting as an intermediary communicator between the rumen liquid fraction and the host. Epimural microbiota have been demonstrated to be distinct from the ruminal liquid microbiome and perform unique roles within the rumen environment. However, methods to sample epimural communities from the rumen wall are limited and typically invasive, requiring animal fistulation or harvesting. To characterize the epimural communities present on the rumen wall, a novel and minimally-invasive surgical method was developed to swab the epithelium of the ventral sac of the rumen. The objective of this study was to validate this sampling method by comparing epimural and liquid fraction bacterial communities. During a 70-day feeding trial, Angus steers (n = 45) were sampled on day 35 using the novel surgery method and tubed on day 70 to sample rumen liquid content. Genomic DNA was used to generate amplicon libraries of the V4 region of the 16S rRNA gene. There were no differences between alpha diversity indices when comparing rumen versus epimural bacterial communities (P > 0.05). The Bray-Curtis dissimilarity was used to ordinate ASV counts, and then tested for differences between rumen and epimural communities using a PERMANOVA with 999 permutations (P < 0.05). Differential abundances of bacterial communities were tested using ANCOM-BC and MaAsLin2, where significance was determined by Q < 0.05 and overlap between both analysis methods. Within the 91 taxa that differed in abundance, 451 ASVs were found to be different between sample types (Q < 0.05). Unique ASVs associated with Prevotella, Succinivibrio, family-level Eubacterium, and family-level Succinivibrio were in greater abundance for the rumen epithelial-associated bacterial communities (Q < 0.05). The results demonstrate that the novel method of sampling from the rumen wall can capture differences between epimural and ruminal fluid bacterial communities, thus facilitating studies investigating the interactions between epimural bacteria with the host.</p