Maulana M Naji1, Yuri T Utsunomiya2,3,4,5, Johann Sölkner1, Benjamin D Rosen6, Gábor Mészáros1. 1. University of Natural Resources and Life Sciences (BOKU), Vienna, Austria. 2. São Paulo State University (Unesp), School of Veterinary Medicine, Department of Production and Animal Health, Araçatuba, São Paulo, Brazil. 3. International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, São Paulo, Brazil. 4. AgroPartners Consulting. R. Floriano Peixoto, 120-Sala 43A-Centro, Araçatuba, SP, 16010-220, Brazil. 5. Personal-PEC. R. Sebastiao Lima, 1336-Centro, Campo Grande, MS, 79004-600, Brazil. 6. Agricultural Research Service USDA, Beltsville, MD, USA. ben.rosen@usda.gov.
Abstract
BACKGROUND: 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.UCD-1.2) for defining ancestral alleles necessary for selection signatures study. RESULTS: 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. CONCLUSIONS: 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.
BACKGROUND: 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.UCD-1.2) for defining ancestral alleles necessary for selection signatures study. RESULTS: 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. CONCLUSIONS: 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.
Authors: Laercio R Porto-Neto; Tad S Sonstegard; George E Liu; Derek M Bickhart; Marcos V B Da Silva; Marco A Machado; Yuri T Utsunomiya; Jose F Garcia; Cedric Gondro; Curtis P Van Tassell Journal: BMC Genomics Date: 2013-12-13 Impact factor: 3.969
Authors: Kun Wang; Lizhong Wang; Johannes A Lenstra; Jianbo Jian; Yongzhi Yang; Quanjun Hu; Deyong Lai; Qiang Qiu; Tao Ma; Zheng Du; Richard Abbott; Jianquan Liu Journal: Gigascience Date: 2017-04-01 Impact factor: 6.524
Authors: Maulana M Naji; Yuri T Utsunomiya; Johann Sölkner; Benjamin D Rosen; Gábor Mészáros Journal: Genet Sel Evol Date: 2021-12-18 Impact factor: 4.297
Authors: Maulana M Naji; Yifan Jiang; Yuri T Utsunomiya; Benjamin D Rosen; Johann Sölkner; Chuduan Wang; Li Jiang; Qin Zhang; Yi Zhang; Xiangdong Ding; Gábor Mészáros Journal: Front Genet Date: 2022-09-27 Impact factor: 4.772