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



We 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.



Results 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.
Department of Agricultural Biotechnology, Animal Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea.|Bahir Dar University, College of Agriculture and Environmental Sciences, PO Box 79, Bahir Dar, Ethiopia.
Mengistie
M
Taye
National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA.
Jaemin
J
Kim
Department of Agricultural Biotechnology, Animal Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea.
Sook Hee
SH
Yoon
Department of Agricultural Biotechnology, Animal Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea.
Wonseok
W
Lee
The University of Nottingham, School of Life Sciences, Nottingham, NG7 2RD, UK.|International Livestock Research Institute (ILRI), PO Box 5689, Addis Ababa, Ethiopia.
Olivier
O
Hanotte
International Livestock Research Institute (ILRI), PO Box 5689, Addis Ababa, Ethiopia.
Tadelle
T
Dessie
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, Midlothian, EH25 9RG, Scotland.
Stephen
S
Kemp
International Livestock Research Institute (ILRI), PO Box 30709-00100, Nairobi, Kenya.
Okeyo Ally
OA
Mwai
Department of Animal Sciences, University of Illinois, Urbana, IL, 61801, USA.
Kelsey
K
Caetano-Anolles
C&K genomics, Main Bldg. #514, SNU Research Park, Seoul, 151-919, Republic of Korea.
Seoae
S
Cho
National Institute of Animal Science, RDA, Wanju, Republic of Korea.
Sung Jong
SJ
Oh
The Animal Molecular Genetics & Breeding Center, Department of Animal Biotechnology, Chonbuk National University, Jeonju, 561-756, Korea.
Hak-Kyo
HK
Lee
Department of Agricultural Biotechnology, Animal Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea. heebal@snu.ac.kr.|C&K genomics, Main Bldg. #514, SNU Research Park, Seoul, 151-919, Republic of Korea. heebal@snu.ac.kr.|Institute for Biomedical Sciences, Shinshu University, Nagano, Japan. heebal@snu.ac.kr.
Heebal
H
Kim
D000818:Animals; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D063427:Food Quality; D023281:Genomics; D010802:Phylogeny; D010858:Pigmentation; D000069466:Red Meat
African cattle; Ankole cattle; Meat quality; Sanga cattle; XP-CLR; XP-EHH