ArticleGenetics, selection, evolution : GSE2024
Ancestral alleles defined for 70 million cattle variants using a population-based likelihood ratio test.
Article in Genetics, selection, evolution : GSE, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed.
- Genetic basis of immunity in Indian cattle as revealed by comparative analysis of Bos genome.Scientific reports · 2026Article
- Genomic Insights into the Origins, Population Structure, and Local Adaptation of Philippine Visayan Native Cattle.Animals : an open access journal from MDPI · 2026Article
- Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain.Genome research · 2025Article
- Admixture and selection offer insights for the conservation and breeding of Guyuan cattle.BMC biology · 2025Article
- Taurine pangenome uncovers a segmental duplication upstream ofGenome research · 2025Article
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Authors and funding
7 authors.
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Abstract
backgroundThe study of ancestral alleles provides insights into the evolutionary history, selection, and genetic structures of a population. In cattle, ancestral alleles are widely used in genetic analyses, including the detection of signatures of selection, determination of breed ancestry, and identification of admixture. Having a comprehensive list of ancestral alleles is expected to improve the accuracy of these genetic analyses. However, the list of ancestral alleles in cattle, especially at the whole genome sequence level, is far from complete. In fact, the current largest list of ancestral alleles (~ 42 million) represents less than 28% of the total number of detected variants in cattle. To address this issue and develop a genomic resource for evolutionary studies, we determined ancestral alleles in cattle by comparing prior derived whole-genome sequence variants to an out-species group using a population-based likelihood ratio test.
resultsOur study determined and makes available the largest list of ancestral alleles in cattle to date (70.1 million) and includes 2.3 million on the X chromosome. There was high concordance (97.6%) of the determined ancestral alleles with those from previous studies when only high-probability ancestral alleles were considered (29.8 million positions) and another 23.5 million high-confidence ancestral alleles were novel, expanding the available reference list to improve the accuracies of genetic analyses involving ancestral alleles. The high concordance of the results with previous studies implies that our approach using genomic sequence variants and a likelihood ratio test to determine ancestral alleles is appropriate.
conclusionsConsidering the high concordance of ancestral alleles across studies, the ancestral alleles determined in this study including those not previously listed, particularly those with high-probability estimates, may be used for further genetic analyses with reasonable accuracy. Our approach that used predetermined variants in species and the likelihood ratio test to determine ancestral alleles is applicable to other species for which sequence level genotypes are available.
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