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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 #343318

Research Project: ENHANCING GENETIC MERIT OF RUMINANTS THROUGH GENOME SELECTION AND ANALYSIS

Location: Animal Genomics and Improvement Laboratory

Title: Signatures of selection for environmental adaptation and zebu × taurine hybrid fitness in East African shorthorn zebu

Author
item Bahbahani, Hussain - Kuwait University
item Tijjani, Abdulfatai - University Of Nottingham
item Mukasa, Christopher - Collaborator
item Wragg, David - Collaborator
item Almathen, Faisal - Collaborator
item Nash, Oyekanmi - Collaborator
item Akpa, Gerald - Ahmadu Bello University
item Mbole-kariuki, Mary - University Of Nottingham
item Malla, Sunir - University Of Nottingham
item Woolhouse, Mark - University Of Edinburgh
item Sonstegard, Tad - Recombinetics, Inc
item Van Tassell, Curtis - Curt
item Blythe, Martin - University Of Nottingham
item Huson, Heather
item Hanotte, Olivier - University Of Nottingham

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/12/2017
Publication Date: 6/8/2017
Citation: Bahbahani, H., Tijjani, A., Mukasa, C., Wragg, D., Almathen, F., Nash, O., Akpa, G., Mbole-Kariuki, M., Malla, S., Woolhouse, M., Sonstegard, T.S., Van Tassell, C.P., Blythe, M., Huson, H.J., Hanotte, O. 2017. Signatures of selection for environmental adaptation and zebu × taurine hybrid fitness in East African Shorthorn Zebu. Frontiers in Genetics. 8:68.

Interpretive Summary: The goal of this paper is to better understand the dynamics of selection when crossing native cattle. Genomic regions containing evidence of selection were compared in crossbred cattle from Kenya, Nigeria, and Uganda were compared. Cattle from Uganda and Nigeria show that 25 of these regions are shared between cattle from Kenya and Uganda, and seven regions are shared across cattle from all three countries. The identification of common candidate regions allows us to deeply interrogate 18 regions. These regions intersect with genes and known regions associated with reproduction and environmental stress (e.g., immunity and heat stress) suggesting that the genome of the zebu × taurine admixed cattle has been uniquely selected to maximize hybrid fitness both in terms of reproduction and survivability.

Technical Abstract: The East African Shorthorn Zebu (EASZ) cattle are ancient hybrid between Asian zebu × African taurine cattle preferred by local farmers due to their adaptability to the African environment. The genetic controls of these adaptabilities are not clearly understood yet. Here, we genotyped 92 EASZ samples from Kenya (KEASZ) with more than 770,000 SNPs and sequenced the genome of a pool of 10 KEASZ. We observe an even admixed autosomal zebu × taurine genomic structure in the population. A total of 101 and 165 candidate regions of positive selection, based on genome-wide SNP analyses (meta-SS, Rsb, iHS, and AF) and pooled heterozygosity (Hp) full genome sequence analysis, are identified, in which 35 regions are shared between them. A total of 142 functional variants, one novel, have been detected within these regions, in which 30 and 26 were classified as of zebu and African taurine origins, respectively. High density genome-wide SNP analysis of zebu × taurine admixed cattle populations from Uganda and Nigeria show that 25 of these regions are shared between KEASZ and Uganda cattle, and seven regions are shared across the KEASZ, Uganda, and Nigeria cattle. The identification of common candidate regions allows us to finemap 18 regions. These regions intersect with genes and QTL associated with reproduction and environmental stress (e.g., immunity and heat stress) suggesting that the genome of the zebu × taurine admixed cattle has been uniquely selected to maximize hybrid fitness both in terms of reproduction and survivability.