Utilizing Long-Read Sequencing Technology to Develop a Sex and Fiber-Color Specific Skin Transcriptome Atlas for Alpaca

Principal investigator:

Felipe Avila, PhD
Veterinary Genetics Laboratory
University of California, Davis
January 1, 2024 – December 31, 2025
$32,724

Since the sequencing of the alpaca genome around 15 years ago, major advancements have been made in the field of camelid genetics. However, the bulk of alpaca genomics research has revolved around the discovery of DNA mutations potentially associated with economically important traits and diseases. While mutations in coding DNA (i.e., DNA that makes protein) may lead to different phenotypes and disorders, the impact of changes in non-coding DNA (i.e., DNA that does not encode proteins) remains largely unknown. It is known that the vast majority of the alpaca genome comprises non-coding DNA, and that some of which may act as “on/off switches” to regulate gene expression in a tissue-specific manner. The most important phenotypic trait in alpacas is arguably fiber color, due to its economic impact on the textile industry; however, the genetic mechanisms underlying color variation in alpacas are poorly understood. Therefore, the goal of this study is to leverage novel, cutting-edge long-range sequencing technologies to improve our understanding of which genes are transcribed specifically in the skin of the alpaca, and how these “on/off switches” may influence fiber color and the risk for skin disorders. The data generated in this study will enable, for the first time, the development of a comprehensive fiber-color and sex-specific skin transcriptome atlas in alpaca. This atlas will also serve as a resource to guide a better annotation of the alpaca reference genome. Most importantly, the database will be made available for all researchers to advance the field of camelid genomics.