GCRF-BBR: A compendium of structural variation across African cattle breeds

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Cattle are a vital component of the economies of low and middle income countries across the globe. They are a source of meat and dairy products, provide leather and other by-products and are often used as working animals. Cattle can be grazed where crops are not easily grown, provide manure as effective fertiliser and can convert forage into high-protein food. Often cattle are the most valuable possession individuals in low and middle income countries own, but are susceptible to a range of infectious diseases, which not only inflict a heavy economic burden on these countries but can also often be transmissible to humans.Over two-thirds of the global cattle population are in low and middle income countries. Reducing the burden of cattle infectious diseases would consequently have major benefits to these areas. However for many diseases no vaccine or treatment is available. Where they are available, poor veterinary services generally mean the livestock keepers must pay for vaccines and treatments themselves. Consequently these diseases are major barriers to escaping poverty. Due to the co-evolution of pathogens and cattle there are various examples of cattle breeds that show natural tolerance or resistance to important infectious diseases. Although these breeds are often less productive, making them less attractive to LMIC farmers, if the mechanisms underlying their resistance could be identified and harnessed, then breeds of both higher productivity and tolerance could be developed. Likewise certain breeds have been shown to be better adapted to particular environmental conditions. With certain breeds better able to tolerate extreme temperatures and limited access to feed and water for example.Structural variants (SVs), large alterations in an animal's genome sequence, have been linked in livestock to adaptation to environments and natural tolerance to important diseases. Despite their potential value, little is currently known about the genome-wide location of SVs in cattle and almost nothing in African cattle breeds. Native African cattle are particularly well adapted to African environments and pathogens, with structural variants expected to underlie many such important traits. Knowledge of the location of structural variants in African cattle breeds will enable researchers to determine their functional consequences and develop better breeding programs. In this project we will develop a database of structural variants focused on African cattle breeds to enable studies of their role in shaping important phenotypes.