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

BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-016-0467-1) contains supplementary material, which is available to authorized users

Gir for the Giriama: The case for Zebu dairying in the tropics - a Review.

The aim of this review paper is to evaluate opportunities for selecting the most profitable cow for smallholder dairy production in hot and humid tropics. The inherent climatic characteristics of the tropics are discussed here as possible bottlenecks to productivity of dairy cattle. The traits relevant for dairy production cut across functionality of the animal, adaptation to the environment to the most important milk production traits. A contrast of performance in various traits between most common breeds utilized for dairy in the tropics has been highlighted. Body conformation, thermo-tolerance, parasitic resistance, feed efficiency, locomotion, fertility and milk production are discussed here as part of the unavoidable considerations when breeding for tropical dairy production. Notably, to sustain the production of milk, functional and survival traits account for the sustainability and profitability of the milk business. Longevity, a composite trait that enables achievement of higher milk average per cow per year should be targeted in an optimal milk breeding objective. Tropical highlands have benefitted from high milk producing Bos taurus breeds, however, dairy farmers from the coastal lowlands have been unable to replicate this success. It is proposed here that matching a dairy breed to the environment could be more sustainable than adjusting the environment to fit a particular breed. The development of Zebu cattle for dairy production has been attempted with varying levels of success. Very rarely are Zebu cattle developed for purebred dairy production. This review paper highlights the case of Brazilian-Gir cattle and recommends strategic use of proven Zebu genetics as an entry point for improving productivity of smallholder dairy farming in Coastal lowland tropics