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A computationally feasible multi-trait single-step genomic prediction model with trait-specific marker weights Open
Background Regions of genome-wide marker data may have differing influences on the evaluated traits. This can be reflected in the genomic models by assigning different weights to the markers, which can enhance the accuracy of genomic predi…
Investigating the benefits and perils of importing genetic material in small cattle breeding programs via simulation Open
Supplementary tables and figures for the paper "Investigating the benefits and perils of importing genetic material in small cattle breeding programs via simulation"
465. Full-scale simulation of the Norwegian red dairy cattle breeding programme to enable testing future breeding directions Open
A full-scale simulation that can cover all aspects of an ongoing breeding programme is a useful tool to test future breeding decisions. For example, dairy breeding is facing new challenges to include feed efficiency and methane emission tr…
The benefits and perils of import in small cattle breeding programs Open
Small breeding programs are limited in achieving competitive genetic gain and prone to high rates of inbreeding. Thus, they often import genetic material to increase genetic gain and to limit the loss of genetic variability. However, the b…
Genomic Selection for Any Dairy Breeding Program via Optimized Investment in Phenotyping and Genotyping Open
This paper evaluates the potential of maximizing genetic gain in dairy cattle breeding by optimizing investment into phenotyping and genotyping. Conventional breeding focuses on phenotyping selection candidates or their close relatives to …
Pedigrees Open
The file Pedigrees.zip includes pedigrees for all the scenarios we ran. Each file is named after the type of selection it ran (Gen for genomic and Class for conventional) followed by the availability of the initial training population (Tru…
Genomic selection for any dairy breeding program via optimized investment in phenotyping and genotyping Open
This paper evaluates the potential of maximizing genetic gain in dairy cattle breeding by optimizing investment into phenotyping and genotyping. Conventional breeding focuses on phenotyping selection candidates or their close relatives to …
Additional file 9 of Meta-analysis for milk fat and protein percentage using imputed sequence variant genotypes in 94,321 cattle from eight cattle breeds Open
Additional file 9: Table S6. DAVID analysis for protein percentage. Three clusters with the highest enrichment scores according to DAVID functional annotation clustering for genes associated with significant variants in the meta-analysis f…
Additional file 3 of Meta-analysis for milk fat and protein percentage using imputed sequence variant genotypes in 94,321 cattle from eight cattle breeds Open
Additional file 3: Table S2. QTL detected for protein percentage in the meta-analysis. chr = chromosome, pos = position in base pair on UMD3.1 assembly, ARS-UCD2.1 = position in base pair on ASR-UCD2.1 assembly, p = p-value in the meta-ana…
Additional file 8 of Meta-analysis for milk fat and protein percentage using imputed sequence variant genotypes in 94,321 cattle from eight cattle breeds Open
Additional file 8: Table S5. DAVID analysis for fat percentage. Three clusters with the highest enrichment scores according to DAVID functional annotation clustering for genes associated with significant variants in the meta-analysis for f…
Additional file 2 of Meta-analysis for milk fat and protein percentage using imputed sequence variant genotypes in 94,321 cattle from eight cattle breeds Open
Additional file 2: Table S1. QTL detected for fat percentage in the meta-analysis. chr = chromosome, pos = position in base pair on UMD3.1 assembly, ARS-UCD2.1 = position in base pair on ASR-UCD2.1 assembly, p = p-value in the meta-analysi…
Efficient use of genomic information for sustainable genetic improvement in small cattle populations Open
In this study, we compared genetic gain, genetic variation, and the efficiency of converting variation into gain under different genomic selection scenarios with truncation or optimum contribution selection in a small dairy population by s…
Efficient use of genomic information for sustainable genetic improvement in small cattle populations Open
This paper compares genetic gain, genetic variation, and the efficiency of converting variation into gain under different genomic selection scenarios with truncation or optimum contribution selection in a small dairy population by simulati…
A Strategy To Exploit Surrogate Sire Technology in Livestock Breeding Programs Open
In this work, we performed simulations to develop and test a strategy for exploiting surrogate sire technology in animal breeding programs. Surrogate sire technology allows the creation of males that lack their own germline cells, but have…
Extending long-range phasing and haplotype library imputation algorithms to very large and heterogeneous datasets Open
Background This paper describes the latest improvements to the long-range phasing and haplotype library imputation algorithms that enable them to successfully phase both datasets with one million individuals and datasets genotyped using di…
Analysis of a large data set reveals haplotypes carrying putatively recessive lethal alleles with pleiotropic effects on economically important traits in beef cattle Open
Background Deleterious recessive alleles can result in reduced economic performance in livestock in multiple ways in homozygous individuals: from early embryonic death, death soon after birth, to being non-lethal but causing reduced viabil…
Removal of alleles by genome editing – RAGE against the deleterious load Open
Background In this paper, we simulate deleterious load in an animal breeding program, and compare the efficiency of genome editing and selection for decreasing load. Deleterious variants can be identified by bioinformatics screening method…
Can genomic data enable genetic evaluation with phenotypes recorded on smallholder farms Open
The huge increases in dairy cattle milk yield in advanced economies over the past century is a powerful example of the role of breeding in improving livestock productivity. However, breeding practices have had poor efficacy and penetrance …
A strategy to exploit surrogate sire technology in livestock breeding programs Open
In this work, we performed simulations to develop and test a strategy for exploiting surrogate sire technology in animal breeding programs. Surrogate sire technology allows the creation of males that lack their own germline cells, but have…
Potential of gene drives with genome editing to increase genetic gain in livestock breeding programs Open
Genome editing in livestock breeding results in short-, medium- and long-term increases in genetic gain. The increase in genetic gain occurs because editing increases the frequency of favourable alleles in the population. Gene drives accel…
Cow genotyping strategies for genomic selection in a small dairy cattle population Open
This study compares how different cow genotyping strategies increase the accuracy of genomic estimated breeding values (EBV) in dairy cattle breeds with low numbers. In these breeds, few sires have progeny records, and genotyping cows can …
Genomic evaluation, breed identification, and population structure of Guernsey cattle in North America, Great Britain, and the Isle of Guernsey Open
As of December 2015, 2,376 Guernsey bulls and cows had genotypes from collaboration between the United States, Canada, the United Kingdom, and the Isle of Guernsey. Of those, 439 bulls and 504 cows had traditional US evaluations, which pro…
Initiating maize pre-breeding programs using genomic selection to harness polygenic variation from landrace populations Open
Results of this study provide guidelines for SeeD and similar initiatives on how to initiate pre-breeding programs that aim to harness polygenic variation from landraces.
Additional file 3: of Initiating maize pre-breeding programs using genomic selection to harness polygenic variation from landrace populations Open
Simulation outputs and accompanying R code for its analysis. Analysis and decision support system for comparing simulation outputs of different designs of initiating a pre-breeding program from maize landrace populations. The ZIP file cont…