Abstract
Despite only 8% of cattle being found in Europe, European breeds dominate current genetic resources. This adversely impacts cattle research in other important global cattle breeds, especially those from Africa for which genomic resources are particularly limited, despite their disproportionate importance to the continent’s economies. To mitigate this issue, we have generated assemblies of African breeds, which have been integrated with genomic data for 294 diverse cattle into a graph genome that incorporates global cattle diversity. We illustrate how this more representative reference assembly contains an extra 116.1 Mb (4.2%) of sequence absent from the current Hereford sequence and consequently inaccessible to current studies. We further demonstrate how using this graph genome increases read mapping rates, reduces allelic biases and improves the agreement of structural variant calling with independent optical mapping data. Consequently, we present an improved, more representative, reference assembly that will improve global cattle research.
Highlights
Despite only 8% of cattle being found in Europe, European breeds dominate current genetic resources
European breeds largely all originate from the same domestication event that occurred in the Middle East, at least one further domestication event occurred in South Asia giving rise to the humped indicine breeds (Bos taurus indicus)[6]
We address the current lack of reference genomes for African cattle breeds by generating assemblies for the N’Dama and Ankole breeds
Summary
Despite only 8% of cattle being found in Europe, European breeds dominate current genetic resources. Due to their use as draft animals and their ability to convert low-quality forage into energy-dense muscle and milk, they provide a significant source of nutrition and livelihood to over 6 billion people Since their domestication almost 10,000 years ago, hundreds of distinct cattle breeds have been established, displaying a diverse range of heritable phenotypes, from differences in production phenotypes such as milk yield, to environmental adaptation, disease tolerance and altered physical characteristics such as horn shape and skin pigmentation[2,3]. European breeds largely all originate from the same domestication event that occurred in the Middle East, at least one further domestication event occurred in South Asia giving rise to the humped indicine breeds (Bos taurus indicus)[6] These two Bos lineages have been estimated to have last had a common ancestor over 210,000 years ago[7] meaning the current Hereford reference genome poorly represents the indicus sub-species. This diversity is not reflected in the genomic resources currently available
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