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View article: Bighorn sheep T2T genome assembly reveals differences in immune genes: a potential cause of high morbidity due to respiratory pathogens
Bighorn sheep T2T genome assembly reveals differences in immune genes: a potential cause of high morbidity due to respiratory pathogens Open
The bighorn sheep ( Ovis canadensis ), despite its close relation to domestic sheep, suffer higher morbidity and mortality from respiratory disease complexes, likely due to genetic differences in immune responses. Unraveling highly repetit…
View article: Genomic Tools for South American Camelids: Genotyping-by-Sequencing Is a Cost-Effective Tool for Alpaca Breeders in Peru
Genomic Tools for South American Camelids: Genotyping-by-Sequencing Is a Cost-Effective Tool for Alpaca Breeders in Peru Open
Peruvian alpacas represent 85% of the global population and are mainly bred for their fiber and adaptation to high-altitude Andean environments. Two distinct phenotypes exist: Huacaya and Suri. This study aimed to investigate the genetic p…
View article: Improved prediction using genomic relationships for farmed red deer in New Zealand
Improved prediction using genomic relationships for farmed red deer in New Zealand Open
View article: Bighorn Sheep T2T Genome Assembly Reveals Differences in Immune Genes: A Potential Cause of High Morbidity Due to Respiratory Pathogens
Bighorn Sheep T2T Genome Assembly Reveals Differences in Immune Genes: A Potential Cause of High Morbidity Due to Respiratory Pathogens Open
View article: Genome-Wide Association Study Revealed Putative SNPs and Candidate Genes Associated with Growth and Meat Traits in Japanese Quail
Genome-Wide Association Study Revealed Putative SNPs and Candidate Genes Associated with Growth and Meat Traits in Japanese Quail Open
The search for SNPs and candidate genes that determine the manifestation of major selected traits is one crucial objective for genomic selection aimed at increasing poultry production efficiency. Here, we report a genome-wide association s…
View article: Genotype-by-Sequencing (Gbs) – an Unintended Tool to Better Understand Pathogen Prevalence and Load in Aquaculture Breeding Programmes
Genotype-by-Sequencing (Gbs) – an Unintended Tool to Better Understand Pathogen Prevalence and Load in Aquaculture Breeding Programmes Open
View article: Aotearoa genomic data repository: An āhuru mōwai for taonga species sequencing data
Aotearoa genomic data repository: An āhuru mōwai for taonga species sequencing data Open
The Aotearoa Genomic Data Repository (AGDR) is an initiative to provide a secure within‐nation option for the storage, management and sharing of non‐human genomic data generated from biological and environmental samples originating in Aote…
View article: Additional file 3 of Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host
Additional file 3 of Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host Open
Additional file 3: Supplemental Table 5: Summary of the biological and systematic effects, including the variance explained by each effect, with cells coloured by effect size. Supplemental Table 6: Detailed parameters and results of F-test…
View article: Additional file 2 of Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits
Additional file 2 of Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits Open
Additional file 2: Table S2. Variance components and prediction accuracies for methane-related traits including variance component, accuracy and regression coefficient estimates for the traits related to methane emissions (CH4), methane ra…
View article: Additional file 4 of Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host
Additional file 4 of Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host Open
Additional file 4: Supplemental Table 7: Heritability and repeatability estimates and standard errors for the reference-based approach. Supplemental Table 8: Heritability and repeatability estimates and standard errors for genera from the …
View article: Additional file 1 of Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits
Additional file 1 of Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits Open
Additional file 1: Table S1a. Rumen sample information including SRA_number, sample ID, animal ID, flock, year of birth, sample date, diet, age, group, and cohort. Table S1b. Summary of Additional file 1 Table S1a, showing the number of sa…
View article: Additional file 6 of Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host
Additional file 6 of Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host Open
Additional file 6. Supplemental Table 9. The genomic relationship matrix for the New Zealand samples.
View article: Additional file 1 of Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host
Additional file 1 of Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host Open
Additional file 1: Supplemental Table 1. Information for each sample including: SampleID, AnimalID, Flock, Year of Birth (YOB), Sample Date, Diet, Age, Time Off Feed, Feeding, Group, Cohort, Batch, Shelf, Library and Well. Supplemental Tab…
View article: SheepGenomesDB run2 - list of animals
SheepGenomesDB run2 - list of animals Open
A list of all 935 animals used in run2 of the SheepGenomesDB (SGD). Featured are SGD_ID, SRA_sample, SRA_acc, Country_code, Breed_code, Sex_code, Country, Breed, Sex, Bioproject.
View article: Additional file 4 of Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits
Additional file 4 of Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits Open
Additional file 4: Table S4: Proportion of RF profiles (reads) and number of tags attributed to various taxonomies of interest separated by group.
View article: Additional file 3 of Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits
Additional file 3 of Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits Open
Additional file 3: Table S3. Variance components and prediction accuracies for selected health and production traits including variance component, accuracy and regression coefficient estimates for the traits of liveweight at 8 months of ag…
View article: Additional file 2 of Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host
Additional file 2 of Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host Open
Additional file 2. Supplemental Table 4. Sequencing statistics for all samples split by Group.
View article: Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits
Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits Open
Background Rumen microbes break down complex dietary carbohydrates into energy sources for the host and are increasingly shown to be a key aspect of animal performance. Host genotypes can be combined with microbial DNA sequencing to predic…
View article: Genome wide association study for growth in Pakistani dromedary camels using genotyping-by-sequencing
Genome wide association study for growth in Pakistani dromedary camels using genotyping-by-sequencing Open
Objective: Growth performance and growth-related traits have a crucial role in livestock due to their influence on productivity. This genome-wide association study (GWAS) in Pakistani dromedary camels was conducted to identify single nucle…
View article: Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host
Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host Open
Background Producing animal protein while reducing the animal’s impact on the environment, e.g., through improved feed efficiency and lowered methane emissions, has gained interest in recent years. Genetic selection is one possible path to…
View article: 378 Characterizing Functional Genetic Regulatory Elements in Sheep Reference Genome
378 Characterizing Functional Genetic Regulatory Elements in Sheep Reference Genome Open
Characterizing the locations of genetic regulatory elements is critical for understanding the regulatory mechanisms of complex phenotypic traits related to production traits and health in livestock species. The Ovine Functional Annotation …
View article: Hitchhiking Mapping of Candidate Regions Associated with Fat Deposition in Iranian Thin and Fat Tail Sheep Breeds Suggests New Insights into Molecular Aspects of Fat Tail Selection
Hitchhiking Mapping of Candidate Regions Associated with Fat Deposition in Iranian Thin and Fat Tail Sheep Breeds Suggests New Insights into Molecular Aspects of Fat Tail Selection Open
The fat tail is a phenotype that divides indigenous Iranian sheep genetic resources into two major groups. The objective of the present study is to refine the map location of candidate regions associated with fat deposition, obtained via t…
View article: Mapping of ISGC SNP chip probes
Mapping of ISGC SNP chip probes Open
Ovine SNP chips created by the International Sheep Genomics Consortium (ISGC, https://sheephapmap.org/) were mapped onto reference genomes. Results are reported per chip and include SNP_name, chrom, pos, ref_alt, flag, rsID.Probe sequences…
View article: Mapping of ISGC SNP chip probes
Mapping of ISGC SNP chip probes Open
Ovine SNP chips created by the International Sheep Genomics Consortium (ISGC, https://sheephapmap.org/) were mapped onto reference genomes. Results are reported per chip and include SNP_name, chrom, pos, ref_alt, flag, rsID.Probe sequences…
View article: ISGC run3 - metadata
ISGC run3 - metadata Open
Metadata for 3522 animals used in ISGC's run3 for variant detection. Data was retrieved from NCBI and manually curated.
View article: Beyond the genome: a perspective on the use of DNA methylation profiles as a tool for the livestock industry
Beyond the genome: a perspective on the use of DNA methylation profiles as a tool for the livestock industry Open
View article: Fine mapping of candidate regions associated with fat deposition in thin and fat tail sheep breeds suggests new insights into molecular aspects of fat tail selection
Fine mapping of candidate regions associated with fat deposition in thin and fat tail sheep breeds suggests new insights into molecular aspects of fat tail selection Open
Background Fatness related traits are economically very important in sheep production and are associated with serious diseases in humans. The fat tail is a phenotype that divides domesticated sheep into two major groups. The objective of t…
View article: A Multi-Omic Huntington’s Disease Transgenic Sheep-Model Database for Investigating Disease Pathogenesis
A Multi-Omic Huntington’s Disease Transgenic Sheep-Model Database for Investigating Disease Pathogenesis Open
Background: The pathological mechanism of cellular dysfunction and death in Huntington’s disease (HD) is not well defined. Our transgenic HD sheep model (OVT73) was generated to investigate these mechanisms and for therapeutic testing. One…
View article: Supplemental data
Supplemental data Open
Supplemental data for publication Klapste et al. (2021). The Use of ``Genotyping-by-Sequencing'' to Recover Shared Genealogy in Genetically Diverse Eucalyptus Populations. Forests
View article: Supplemental data
Supplemental data Open
Supplemental data for publication Klapste et al. (2021). The Use of ``Genotyping-by-Sequencing'' to Recover Shared Genealogy in Genetically Diverse Eucalyptus Populations. Forests