Understanding the genetic foundations of desirable traits in alpacas, such as fiber quality, coat color, and the prevention of inherited disorders, is vital for the continued success of breeding programs. In a study led by Dr. F. Abel Ponce de León and his colleagues, researchers are exploring a relatively uncharted area of alpaca genetics: structural genomic variation (SV). These large-scale DNA alterations, which can involve insertions, deletions, inversions, or duplications, often have a greater impact on phenotype than single-nucleotide changes. Utilizing long-read DNA sequencing technologies and advanced bioinformatics, the team has identified nearly 50,000 SVs across alpacas of varying coat colors. Among these, one particularly compelling inversion involving the ASIP gene—a key player in pigment production—may offer new insights into the genetic basis of coat color variation. This blog post provides an overview of these findings and their potential implications for genetic testing and selective breeding in South American camelids.