Whole-Genome Resequencing Reveals Selection Signatures of Abigar Cattle for Local Adaptation
Wondossen Ayalew,
Xiaoyun Wu,
Getinet Mekuriaw Tarekegn,
Tesfaye Sisay Tessema,
Rakan Naboulsi,
Renaud Van Damme,
Erik Bongcam-Rudloff,
Zewdu Edea,
Solomon Enquahone,
Ping Yan
Affiliations
Wondossen Ayalew
Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
Xiaoyun Wu
Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
Getinet Mekuriaw Tarekegn
Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia
Tesfaye Sisay Tessema
Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia
Rakan Naboulsi
Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institute, Tomtebodavägen 18A, 17177 Stockholm, Sweden
Renaud Van Damme
Department of Animal Breeding and Genetics, Bioinformatics Section, Swedish University of Agricultural Sciences, P.O. Box 7023, S-750 07 Uppsala, Sweden
Erik Bongcam-Rudloff
Department of Animal Breeding and Genetics, Bioinformatics Section, Swedish University of Agricultural Sciences, P.O. Box 7023, S-750 07 Uppsala, Sweden
Zewdu Edea
Ethiopian Bio and Emerging Technology Institute, Addis Ababa P.O. Box 5954, Ethiopia
Solomon Enquahone
Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia
Ping Yan
Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
Over time, indigenous cattle breeds have developed disease resistance, heat tolerance, and adaptability to harsh environments. Deciphering the genetic mechanisms underlying adaptive traits is crucial for their improvement and sustainable utilization. For the first time, we performed whole-genome sequencing to unveil the genomic diversity, population structure, and selection signatures of Abigar cattle living in a tropical environment. The population structure analysis revealed that Abigar cattle exhibit high nucleotide diversity and heterozygosity, with low runs of homozygosity and linkage disequilibrium, suggesting a genetic landscape less constrained by inbreeding and enriched by diversity. Using nucleotide diversity (Pi) and population differentiation (FST) selection scan methods, we identified 83 shared genes that are likely associated with tropical adaption. The functional annotation analysis revealed that some of these genes are potentially linked to heat tolerance (HOXC13, DNAJC18, and RXFP2), immune response (IRAK3, MZB1, and STING1), and oxidative stress response (SLC23A1). Given the wider spreading impacts of climate change on cattle production, understanding the genetic mechanisms of adaptation of local breeds becomes crucial to better respond to climate and environmental changes. In this context, our finding establishes a foundation for further research into the mechanisms underpinning cattle adaptation to tropical environments.
