New genetic atlas reveals traces of 10,000 years of sheep breeding

Swati Mestri

Scientific Editor

Robert Egan

Senior Editor

For around 10,000 years, humans have selectively bred sheep for desirable traits. Generation after generation, we have chosen animals for their wool, size and reproductive characteristics and gradually left our mark on their DNA.

But how has this long history of breeding affected the genetic mechanisms that control when and where genes are active?

An international team of researchers, including scientists from Aarhus University, has now brought us closer to answering that question.

The team has developed the most comprehensive map to date of how genetic variation influences gene regulation in sheep. By studying 51 different tissues and cell types, the researchers identified hundreds of thousands of genetic regulatory effects.

The resulting atlas, called SheepGTEx, allows scientists to connect genetic variants with specific genes, biological mechanisms and the tissues in which they act.

And it has already revealed new insights into the history of sheep domestication.

By combining the atlas with DNA from 52 ancient sheep spanning approximately 10,000 years, the researchers found evidence that domestication and selective breeding have shaped not only the DNA sequences of sheep but also the genetic mechanisms that regulate gene activity.

One finding was particularly striking: Genetic variants that regulate genes in just one or a few tissues showed stronger signs of selection than variants that affect multiple tissues.

"What surprised me most was the relationship between tissue-specific gene regulation and the genetic signatures left by selection. Our findings suggest that domestication and breeding may have altered particular traits by changing gene regulation in specific tissues," says Lingzhao Fang, associate professor at the Center for Quantitative Genetics and Genomics (QGG) at Aarhus University.

The paper is published in the journal Nature Genetics.

Becoming common over millennia

The researchers found evidence that thousands of years of selective breeding have influenced genetic variants that regulate gene activity in tissues such as the skin and cervix. These patterns are consistent with human selection for traits related to wool, pigmentation and reproduction.

But why does it matter that these genetic changes are associated with particular tissues?

Because genes do not necessarily behave in the same way throughout the body. Genetic variants can influence how active a gene is in one tissue without having the same effect elsewhere.

One example involves THNSL2, a gene whose activity in the skin is influenced by genetic variation. The researchers found that a variant associated with higher THNSL2 activity in modern sheep generally became more common among European sheep between the Neolithic period and the Middle Ages, although its frequency fluctuated over time.

By combining ancient DNA with their findings from modern sheep, the researchers could infer how the genetic regulation of this gene may have changed over thousands of years.

The finding is particularly interesting because wool grows from hair follicles in the skin. It suggests a possible connection between changes in gene regulation during domestication and the evolution of wool-related traits, although the researchers have not established a direct effect on wool production.

"What makes this finding particularly interesting is that we can trace how a genetic variant associated with gene activity in the skin became more common over thousands of years. It gives us a glimpse of how domestication may have shaped not only the genes sheep carry but also how those genes are regulated," says Fang.

A genetic atlas covering the entire sheep body

These new insights into sheep domestication are the result of a major international research effort.

The team analyzed 6,761 RNA-sequencing samples from 2,816 sheep, covering 51 tissues and cell types. They investigated seven types of molecular regulation and mapped hundreds of thousands of genetic regulatory effects.

Together, these data provide a far more detailed picture of how genetic variation influences gene regulation across the sheep body than was previously available.

Until now, genetic studies could identify regions of the genome associated with particular traits, but often struggled to pinpoint the genes involved, the biological mechanisms at work or the tissues in which the variants exerted their effects.

SheepGTEx helps to bridge that gap.

The atlas has also revealed new insights into traits in modern sheep.

For example, the researchers identified a genetic association involving the regulation of a gene called FXYD1 in the anterior pituitary gland, a hormone-producing tissue that plays an important role in reproduction. The finding provides a possible clue to the biological mechanisms underlying differences in litter size.

It does not prove that FXYD1 determines how many lambs a sheep produces. However, it gives researchers a specific biological hypothesis that can now be tested experimentally.

The SheepGTEx map is the result of extensive collaboration between research groups around the world. Aarhus University played an important role in shaping the project's scientific strategy, coordinating international efforts and bringing together expertise in molecular genetics, quantitative genetics and animal breeding.

The atlas is publicly available, allowing researchers worldwide to explore new questions about sheep biology, evolution and genetic traits.

Future sheep breeding

Beyond shedding light on the past, SheepGTEx could also help shape the future of sheep breeding.

Modern breeding programs already use genetic markers to predict an animal's genetic potential. However, scientists do not always know which biological mechanisms underlie these markers.

With SheepGTEx, researchers can identify genetic variants that are more likely to have functional effects and investigate how they relate to economically important traits, including fertility and wool quality.

There is still work to be done before these findings can be used directly in breeding programs. The candidate variants need to be validated in independent sheep populations, their biological effects must be tested, and researchers need to establish whether incorporating this information actually improves the accuracy of genomic predictions.

Nevertheless, the atlas provides a valuable new starting point.

"We now have a much stronger foundation for identifying the genetic variants that deserve further investigation. In the longer term, our goal is to translate this knowledge into more precise breeding tools," says Fang.

Publication details

Mian Gong et al., A multi-tissue atlas of genetic regulatory effects in sheep, Nature Genetics (2026). DOI: 10.1038/s41588-026-02825-2

Journal information:
Nature Genetics

Provided by
Aarhus University

Citation: New genetic atlas reveals traces of 10,000 years of sheep breeding (2026, November 13) retrieved 13 November 2026 from https://phys.org/news/2026-11-genetic-atlas-reveals-years-sheep.html