Genomic characterization of adaptation and ancient introgression in local European cattle

• Applicant: Maulik Upadhyay, Ph.D.
• Subject Area: Animal Breeding, Animal Nutrition, Animal Husbandry ; General Genetics and Functional Genome Biology
• Term: since 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 526367023

Globally, over 1000 cattle breeds are recognized. They contain a vast and precious pool of genetic diversity. This diversity is distributed in breeds of two different species (or subspecies): Asian zebu cattle (Bos indicus) and taurine cattle (Bos taurus) (here referred as indicine and taurine cattle, respectively). Their lineages split ~200,000 years ago and evolved in different environments: taurine cattle in temperate Europe and indicine cattle in tropical South Asia. Recent studies have identified ~5-10% of indicine ancestry in many southeastern European (SEE) taurine breeds along the route from Anatolia to the Alps. Indeed, a study of ancient cattle genomes representing different geographical regions and time periods also suggested introduction of zebu ancestry in the near Eastern taurine lineage around 4,100 years ago. It is not known, however, whether the source of zebu ancestry present in the SEE taurine cattle is the same as identified in ancient cattle genomes of the near Eastern taurine. Further, the contribution of this zebu component in the adaptive fitness of SEE taurine cattle is also not well-studied. Interestingly, SEE cattle breeds are adapted to a wide range of nutritional conditions and environments, from semiarid to alpine. Compared to commercial breeds such as Holstein-Friesian and Jersey, they have higher genetic diversity, fertility, and parasitic-disease resistance. Hence, they contain a valuable gene pool to be utilized in sustainable animal breeding in the face of climate change and production demands under stress. We hypothesized that a part of gene pool in these cattle breeds consists of indicine and African cattle ancestry providing adaptive advantage. However, the lack of whole genome data from these cattle breeds has been a major constraint in characterizing the zebu ancestry in detail. Therefore, as a first step, in this project, ancient cattle genome originated from Greece and Cyprus and genomes of modern cattle breeds of SEE, Italy and Spain will be sequenced. Next, by applying state-of-the art graph-genome based approaches on these genomes, this project aimed to characterize the genomic segments and allelic variants providing adaptation in these local European cattle. Further, this project, by analyzing over 750 newly sequenced and publicly available whole genome sequences (~650 modern and ~100 ancient cattle), will characterize in-depth the demographic processes, including introgression from zebu and African taurine, which have contributed to adaptive fitness of local European cattle. The results of this project will not only contribute significantly to the sustainable animal breeding practices but will also increase our understanding of how past processes such as climate changes, human migration and ancient animal husbandry practices have shaped the gene pool of modern European cattle breeds.

• DFG Programme: Research Grants