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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #377196

Research Project: Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: Investigation of ancestral alleles in the Bovinae subfamily

item NAJI, MAULANA - University Of Natural Resources & Applied Life Sciences - Austria
item UTSUNOMIYA, YURI - Sao Paulo State University (UNESP)
item SOLKNER, JOHANN - University Of Natural Resources & Applied Life Sciences - Austria
item Rosen, Benjamin - Ben
item MESZAROS, GABOR - University Of Natural Resources & Applied Life Sciences - Austria

Submitted to: Gigascience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/27/2021
Publication Date: 2/8/2021
Citation: Naji, M.M., Utsunomiya, Y.T., Solkner, J., Rosen, B.D., Meszaros, G. 2021. Investigation of ancestral alleles in the Bovinae subfamily. Gigascience. 22(1):108.

Interpretive Summary: The selection for specific traits in animal breeding leaves telltale marks within the genome. Identification of these selection signatures in the DNA can provide insight into traits of interest. Many methods used to identify signatures of selection require knowledge of the ancestral state of variants within the genome. This comprehensive report of ancestral states across the cattle genome has practical applications for the management and improvement of cattle populations by providing a standardized set of ancestral alleles for future studies identifying signatures of selection.

Technical Abstract: In evolutionary theory, divergence and speciation can arise from long periods of reproductive isolation, genetic mutation, selection and environmental adaptation. After divergence, alleles can either persist in their initial state (ancestral allele - AA), co-exist or be replaced by a mutated state (derived alleles -DA). In this study, we aligned whole genome sequences of individuals from the Bovinae subfamily to the cattle reference genome (ARS-UCD1.2) for defining ancestral alleles necessary for selection signatures study. Accommodating independent divergent of each lineage from the initial ancestral state, AA were defined based on fixed alleles on at least two groups of yak, bison and gayal-gaur-banteng resulting in ~32.4 million variants. Using non-overlapping scanning windows of 10 Kb, we counted the AA observed within taurine and zebu cattle. We focused on the extreme points, regions with top 0.1% (high count) and regions without any occurrence of AA (null count). High count regions preserved gene functions from ancestral states that are still beneficial in the current condition, while null counts regions were linked to mutated ones. For both cattle, high count regions were associated with basal lipid metabolism, essential for survival of various environmental pressures. Mutated regions were associated to productive traits in taurine, i.e. higher metabolism, cell development and behaviors and in immune response domain for zebu. Our findings suggest that retaining and losing AA in some regions are varied and made it species-specific with possibility of overlapping as it depends on the selective pressure they had to experience.