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

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0467-1) contains supplementary material, which is available to authorized users.

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“…Nonetheless, 15 of 28 common genes were associated with heat tolerance and disease resistance (Table and Table ) in our study. The majority of selection signatures that we detected here are consistent with previous reports on selection signatures in Bangladesh zebu (Edea et al ), African indigenous cattle (Taye et al ), African Sanga cattle (Taye et al ), Limousin beef cattle (Gurgul et al ), Korean native cattle (Lee et al ) and dairy cattle (Alshawi et al ), etc. (Table ).…”

“…In our study, two candidate genes ( ATP8A1 , SHC3 ) were detected to be associated with feed intake. ATP8A1 is associated with feed intake, feed conversion ratio, residual feed intake and weight gain in Nellore (Santana et al ) and African Ankole cattle (Taye et al ). SHC3 is linked to the residual feed intake of beef cattle based on GWASs (Bolormaa et al ; Sharma et al ).…”

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