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Using Genotyping Tools, Researchers Trace Cattle Domestication, Breed History

NEW YORK (GenomeWeb News) — Through a study of admixture patterns in domesticated cattle, researchers led by the University of Missouri's Jeremy Taylor have begun to untangle how different breeds are related.

As they reported in PLOS Genetics yesterday, the researchers compared SNPs in more than 1,500 cattle from 134 domesticated breeds to trace the origins of modern cattle in Africa, Asia, Europe, and the Americas. Taylor and his colleagues found, for instance, that Asian cattle are the product of the domestication of and admixture between several species, while African cattle arose through the introduction of domesticated taurines from the Middle East that mixed with wild African aurochs.

"In many ways, the history of cattle genetics mirrors human history," Jared Decker, an assistant professor at the University of Missouri and first author of the paper, said in a statement. "In the case of African cattle, anthropologists and geneticists used to suspect that domesticated African cattle were native to the continent, when in fact, they were brought by migrating peoples thousands of years ago. By better understanding the history of the animals we domesticate, we can better understand ourselves."

Further, Decker noted that cattle are economically important, and understanding the genetic history of various breeds could inform how farmers work to increase dairy and meat production.

The researchers genotyped 1,543 cattle samples from cattle breeds from around the world using the Illumina BovineSNP50 BeadChip. Then, drawing on principal component analysis, ancestry graphs determined through TreeMix, and ancestry models made using ADMIXTURE, the researchers examined the relationships among the 134 bovid breeds.

Overall, they uncovered that cattle mainly differ by the amount of Bos taurus taurus and B. t. indicus ancestry they contain; B. t. taurus was domesticated in the Fertile Crescent while B. t. indicus was domesticated in India. The second principal component split the African taurine populations from the Eurasian taurine, indicine, and Bali cattle.

They further noted that the modern cattle genomes appear to reflect the history of the animals' movements as migratory farmers brought cattle out of the Fertile Crescent and India. Using TreeMix, they uncovered evidence of cattle moving from India to Southeast Asia and China as well as to Africa, and from Africa to the Iberian Peninsula and Mediterranean Europe. Cattle also moved from India and Europe to the Americas.

African taurines are more diverged from European and Asian taurines than expected, the researchers reported. They suspected that part of the difference is due to introgression from wild African aurochs, now extinct, as well as admixture between the European and Asian cattle.

Others, they added, had previously hypothesized that the divergence could also be because of a third wave of domestication of cattle in Africa. Here, though, Taylor and his colleagues said that their phylogenetic trees and models did not support that theory as they indicate a single domestication origin for taurine with African cattle also intermixing with wild auroch, resulting in a 26 percent auroch ancestry and 74 percent Fertile Crescent ancestry.

Further, they suggested that the wild auroch introgression into cattle might have been driven by trypanosomiasis resistance in African aurochs, which persists in African taurines today, but is not seen in others.

Across the various continents, the researchers also found geographically driven gradients of ancestry. For instance, in Africa, taurine cattle in the western part of the continent have little or no indicine ancestry, but moving from west to east, as well as from southern to central Africa, the percent of indicine ancestry increases.

Likewise, Asian cattle vary in their taurine or indicine ancestry based on geography; cattle in Pakistan, India, southern China, and India are mostly B. t. indicus while cattle in the north and northeast are B. t. taurus, and in between are hybrids.

Previous work, Taylor and his colleagues said, placed American Criollo cattle breeds — a group that includes the Texas Longhorns — as a sister clade to Spanish cattle. However, from this work, they found that this placement was likely due to the previous finding of higher levels of indicine ancestry in Spanish and American cattle.

Further, though, they noted that Spanish and European cattle do not have as high levels of indicine ancestry as previously thought. "[I]ndicine ancestry in European taurine cattle is extremely rare," the researchers wrote.

Three Italian cattle breeds do have indicine ancestry, which the researchers said likely dated back to Romans capturing African taurines with some indicine ancestry.

American cattle also have indicine ancestry, but Taylor and his colleagues say that this introgression occurred after Spanish cattle arrived in the Americas and mixed with Brahman cattle from India, making the American Criollo breeds.

"Domestication, exportation, admixture, and breed formation have had tremendous impacts on the variation present within and between cattle breeds," the researchers said. "In Asia, Africa, North and South America, cattle breeders have crossbred Bos t. taurus and Bos t. indicus cattle to produce hybrids which were well suited to the environment and endemic production systems."

Having this understanding of how the various breeds were produced could inform modern agricultural practices as well.

"Now that we have this more complete genetic history of cattle worldwide, we can better understand the diversity of the species," Decker said. "By understanding the variations present, we can improve cattle for agricultural purposes, whether that is through breeding more disease-resistant animals or finding ways to increase dairy or beef production."