Identification of Genomic Structural Variation in Alpacas

Principal investigator:

Federico Ponce de Leon
University of Minnesota
Minneapolis, Minnesota

Alpacas, native to South America, are of increasing economic importance in the US. Due to their valuable fiber and gentle temperament, they are rapidly gaining popularity around the world. Alpacas come in a variety of colors and two fiber types: Huacaya with short fluffy fleece and Suri with draping locks of glossy silky fiber. The genes that control the variation in color as well as other production traits of interest are not well understood. Structural variation (SV) includes the loss, gain or change of orientation of genome fragments ranging from 50 bp to huge regions of millions of bp, encompassing several genes. Because of their size, SV contribute more than single nucleotide variation to animal diversity, evolution and disease. In this study, 49734 SVs were identified of which 9457 are located in protein coding sequences and 511 were selected as located on candidate gene regions considering the impact they may have on their resulting proteins. An example of the latter is an inversion in chromosome 19, involving the ASIP gene and observed in white and brown alpacas and not detected in black animals. Additional samples need to be analyzed to determine if this inversion is linked to white and/or brown color phenotypes and whether it occurs in other colors or pigmentation patterns. Genetic testing of this variant could be valuable for production purposes: breeding strategies can be planned to increase the likelihood of producing animals with the desired color, while also maintaining the diversity of color variants by crossing animals with different genotypes.

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