Decker, J. E. | bioRxiv Science

bioRxiv2018

CRUMBLER: A tool for the Prediction of Ancestry in Cattle

BackgroundIn many beef and some dairy production systems, crossbreeding is used to take advantage of breed complementarity and heterosis. Admixed animals are frequently identified by their coat color and body conformation phenotypes, however, without pedigree information it is not possible to identify the expected breed composition of an admixed animal and in the presence of selection, the actual composition may differ from expectation.\n\nResultsWe tested an approach to estimate the global ancestry of individuals using ADMIXTURE and SNPweights. ADMIXTURE estimates ancestry using a model-based approach applied to large single nucleotide polymorphism (SNP) genotype datasets. Individuals are assumed to be unrelated and a supervised analysis can be performed using reference animals sampled to represent ancestral populations. SNPweights infers ancestry using weights estimated by principal component analysis for genome-wide SNP panels that have been genotyped in the reference panel animals. We constructed analysis pipelines to determine the ancestry of individuals with potentially complex ancestries using both methods and a specified reference population SNP dataset. The reference population was constructed using breed association pedigree information and an iterative analysis to identify sets of purebred individuals representative of each breed.\n\nConclusionThe finally adopted CRUMBLER pipeline extracts a subset of genotypes that are common to all current commercially available genotyping platforms and processes these into the file formats required for the analysis software and predicts admixture proportions using the reference population dataset.

genomics↗

bioRxiv2017

Lethal Haplotypes And Candidate Casual Mutations In Angus Cattle

BackgroundIf unmanaged, high rates of inbreeding in livestock populations adversely impact their reproductive fitness. In beef cattle, historical selection strategies have increased the frequency of several segregating fatal autosomal recessive polymorphisms. Selective breeding has also decreased the extent of haplotypic diversity genome-wide. By identifying haplotypes for which homozygotes are not observed but would be expected based on their frequency, developmentally lethal recessive loci can be localized. This analysis comes without the need for observation of the loss-associated phenotype (e.g., failure to implant, first trimester abortion, deformity at birth). In this study, haplotypes were estimated for 3,961 registered Angus individuals using 52,545 SNP loci using findhap v2, which exploited the complex pedigree among the individuals in this population.\n\nResultsSeven loci were detected to possess haplotypes that were not observed in homozygous form despite a sufficiently high frequency and pedigree-based expectation of homozygote occurrence. These haplotypes were identified as candidates for harboring autosomal recessive lethal alleles. Of the genotyped individuals, 109 were resequenced to an average 27X depth of coverage to identify putative loss-of-function alleles genome-wide and had variants called using a custom in-house developed pipeline. For the candidate lethal-harboring haplotypes present in these bulls, sequence-called genotypes were used to identify concordant variants. In addition, whole-genome sequence imputation of variants was performed into the set of 3,961 genotyped animals using the 109 resequenced animals to identify candidate lethal recessive variants at the seven loci.\n\nConclusionsSelective breeding programs could utilize the predicted lethal haplotypes associated with SNP genotypes. Sequencing and other methods for identifying the causal variants underlying these haplotypes can allow for more efficient methods of management such as gene editing. These two methods in total will reduce the negative impacts of inbreeding on fertility and maximize overall genetic gains.

genomics↗