Chickens provide one of the world's most popular animal proteins, with billions of birds grown every year for eggs and meat. Interpreting the farm animal’s genome is vital for understanding how genes control traits, such as growth, feed efficiency, reproduction and disease resistance.

A team of UC Davis researchers created a comprehensive catalogue of genomic information for chickens, which was published May 3 in the journal, Science Advances. The data could be a valuable resource that may be applied for genetic improvements of economically important traits in poultry.

Comprising about 1.1 billion DNA base pairs, the chicken was the first livestock to have its genome sequenced nearly 20 years ago. Huaijun Zhou, professor with the Department of Animal Science and corresponding author of the paper, said his team decoded more than 1.5 million regulatory elements in the chicken genome. Regulatory elements are like switches that turn genes on, off or tune. They play a major role in the development and functioning of physiological processes of the chicken’s body by controlling which genes are expressed, when and to what extent.

A wealth of DNA information

Researchers analyzed and created a total of 377 datasets from 23 tissues in adult chickens. By combining these datasets, they built a robust catalogue of regulatory elements and described tissue-specific functionalities, creating one of the most comprehensive inventories of regulatory elements for any farm animal.

“This functional information across so many tissues will provide novel information that hasn’t been available before,” said Zhou, recipient of the 2023 National Academy of Sciences Prize in Food and Agriculture Sciences.

Zhou said this data may also translate into significant improvements for poultry producers. He expects the information to be used to identify potential genetic variants that influence growth rate, feed efficiency and disease resistance.

With this year’s devastating avian flu outbreak, which led to a spike in poultry product prices, understanding how genetic factors contribute to disease risks is important to the industry. Zhou said identifying how the regulatory elements function could potentially lead to strategies to prevent and treat diseases.

“Ultimately, this will enhance genome-based approaches to improve efficiency, sustainability, and biosecurity of poultry production,” he said.

Other co-authors listed are: Zhangyuan Pan (lead author), Ying Wang, Shenwen Gu, Liqi An, Michelle Halstead, Dailu Guan, Ye Bi, Shang Wu, Mary Delany, Xuechen Bai, Joana Damas and Harris Lewin from UC Davis; and researchers from Aarhus University, USDA ARS, Chinese Academy of Agricultural Sciences, China Agricultural University and other institutions.

This study was primarily supported by the USDA National Institute of Food and Agriculture, California Agricultural Experimental Station.