Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef

BMC Genetics

Research Article

Seoae Cho¹  Wonseok Lee²  Sook Hee Yoon²  Mengistie Taye³  Heebal Kim⁴  Kelsey Caetano-Anolles⁵  Okeyo Ally Mwai⁶  Stephen Kemp⁷  Tadelle Dessie⁸  Jaemin Kim⁹  Sung Jong Oh^1,10  Hak-Kyo Lee^1,11  Olivier Hanotte^1,12 

[1] C&K genomics, Main Bldg. #514, SNU Research Park, 151-919, Seoul, Republic of Korea;Department of Agricultural Biotechnology, Animal Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, 151-921, Seoul, Korea;Department of Agricultural Biotechnology, Animal Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, 151-921, Seoul, Korea;Bahir Dar University, College of Agriculture and Environmental Sciences, PO Box 79, Bahir Dar, Ethiopia;Department of Agricultural Biotechnology, Animal Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, 151-921, Seoul, Korea;C&K genomics, Main Bldg. #514, SNU Research Park, 151-919, Seoul, Republic of Korea;Institute for Biomedical Sciences, Shinshu University, Nagano, Japan;Department of Animal Sciences, University of Illinois, 61801, Urbana, IL, USA;International Livestock Research Institute (ILRI), PO Box 30709-00100, Nairobi, Kenya;International Livestock Research Institute (ILRI), PO Box 30709-00100, Nairobi, Kenya;The Centre for Tropical Livestock Genetics and Health, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, EH25 9RG, Midlothian, Scotland;International Livestock Research Institute (ILRI), PO Box 5689, Addis Ababa, Ethiopia;National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, 20892, Bethesda, MD, USA;National Institute of Animal Science, RDA, Wanju, Republic of Korea;The Animal Molecular Genetics & Breeding Center, Department of Animal Biotechnology, Chonbuk National University, 561-756, Jeonju, Korea;The University of Nottingham, School of Life Sciences, NG7 2RD, Nottingham, UK;International Livestock Research Institute (ILRI), PO Box 5689, Addis Ababa, Ethiopia;

关键词: African cattle;    Ankole cattle;    Meat quality;    Sanga cattle;    XP-CLR;    XP-EHH;   

DOI  :  10.1186/s12863-016-0467-1

 received in 2016-07-06, accepted in 2016-12-20,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundAfrica is home to numerous cattle breeds whose diversity has been shaped by subtle combinations of human and natural selection. African Sanga cattle are an intermediate type of cattle resulting from interbreeding between Bos taurus and Bos indicus subspecies. Recently, research has asserted the potential of Sanga breeds for commercial beef production with better meat quality as compared to Bos indicus breeds. Here, we identified meat quality related gene regions that are positively selected in Ankole (Sanga) cattle breeds as compared to indicus (Boran, Ogaden, and Kenana) breeds using cross-population (XP-EHH and XP-CLR) statistical methods.ResultsWe identified 238 (XP-EHH) and 213 (XP-CLR) positively selected genes, of which 97 were detected from both statistics. Among the genes obtained, we primarily reported those involved in different biological process and pathways associated with meat quality traits. Genes (CAPZB, COL9A2, PDGFRA, MAP3K5, ZNF410, and PKM2) involved in muscle structure and metabolism affect meat tenderness. Genes (PLA2G2A, PARK2, ZNF410, MAP2K3, PLCD3, PLCD1, and ROCK1) related to intramuscular fat (IMF) are involved in adipose metabolism and adipogenesis. MB and SLC48A1 affect meat color. In addition, we identified genes (TIMP2, PKM2, PRKG1, MAP3K5, and ATP8A1) related to feeding efficiency. Among the enriched Gene Ontology Biological Process (GO BP) terms, actin cytoskeleton organization, actin filament-based process, and protein ubiquitination are associated with meat tenderness whereas cellular component organization, negative regulation of actin filament depolymerization and negative regulation of protein complex disassembly are involved in adipocyte regulation. The MAPK pathway is responsible for cell proliferation and plays an important role in hyperplastic growth, which has a positive effect on meat tenderness.ConclusionResults revealed several candidate genes positively selected in Ankole cattle in relation to meat quality characteristics. The genes identified are involved in muscle structure and metabolism, and adipose metabolism and adipogenesis. These genes help in the understanding of the biological mechanisms controlling beef quality characteristics in African Ankole cattle. These results provide a basis for further research on the genomic characteristics of Ankole and other Sanga cattle breeds for quality beef.

【 授权许可】

CC BY   
© The Author(s). 2017