Evaluation of an Alpaca DNA microarray (Genomic SNP Chip) for Potential Use by the North American Alpaca Industry

Evaluation of an Alpaca DNA microarray (Genomic SNP Chip) for Potential Use by the North American Alpaca Industry

Principal investigator:

Curtis R. Youngs, PhD
Iowa State University
Animal Science Department
September 1, 2021 – August 31, 2022
$18,092

Alpacas can sustainably convert low quality roughages to high quality product (eg fiber) to enhance human lives. Unfortunately, genetic improvement programs for alpacas are not as advanced as genetic improvement programs for species such as dairy cattle and sheep. In January 2020, the development of an alpaca-specific DNA microarray (genomic SNP chip) was announced. This DNA microarray provides opportunity to begin developing alpaca genetic improvement programs based on genotype (animals genetic make-up) rather than phenotype (how an animal appears or performs within a given environment). We propose to collect DNA samples from two alpaca herds maintained at three locations within the US which have extensive performance data, genetic evaluations (EPDs-expected progeny differences) and extended pedigree information. The sampling regimen will include trios (macho, hombre and aria) as well as genetic outliers and male replacement breeding stock. The DNA samples will be sent to a commercial DNA testing facility and results will be analyzed and interpreted. Data from this study will identify whether or not the SNP’s (single nucleotide polymorphisms) identified in alpacas in Peru, selected for fineness of fiber, are polymorphic in US alpacas. We will estimate allele frequencies of polymorphic SNPs to ascertain if the Peruvian SNP chip has utility in North American alpacas, or if an alternate alpaca SNP chip needs to be developed. These data will also enable estimation of genomic relationships among animals , which could subsequently be used to manage inbreeding.