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

Alpaca production traits (such as fiber diameter and fleece weight) are determined by genes which reside on the chromosomes located inside the nucleus of the cells which comprise an alpaca’s body. There are 74 chromosomes per alpaca cell. There are two sex chromosomes (“X” and “Y”) and 72 non-sex chromosomes (called autosomes). Each alpaca chromosome contains numerous genes.

Historical methods of genetic selection of alpacas focused on visual appraisal of animals and/or pedigrees. Several years ago, the alpaca industry started using statistical genetics tools to calculate estimated breeding values (EBVs) of animals for traits of economic importance. Despite their tremendous value, EBVs are estimates of an animal’s ability to pass its genetic superiority on to its offspring and do not always precisely capture an animal’s true genetic value.

In recent years, the livestock industry began performing genetic selection based on knowledge of a portion of an animal’s actual genetic makeup. This technology is known as genomic selection, and it makes use of a tool known as a DNA microarray. The DNA microarray can be used to analyze specific DNA sequences scattered through an animal’s chromosomes. These specific DNA sequences, known as single nucleotide polymorphisms (or SNPs), enable a more precise identification of an animal’s genetic superiority. The genomic technology is used to supplement EBVs, and its use in other species has led to more rapid genetic improvement. In alpacas, genomics can is also very likely to be useful to help manage inbreeding.

In this study we collected DNA samples from 96 alpacas, samples were submitted to a commercial DNA testing laboratory for analysis with the 76K SNP alpaca custom array, and genotyping results were analyzed in a laboratory directed by Dr. Gustavo Gutierrez in Peru.

Results revealed that there is a high number of molecular markers (48,776 SNPs) that were polymorphic and suitable for genomic analysis of US alpacas. The use of the 76K SNP alpaca custom array allowed not only estimation of genomic relationships but also of genomic inbreeding coefficients. This information is quite important for genetic improvement programs to know the inbreeding status within alpaca herds and to scratch selection strategies to avoid inbreeding depression.

Despite of the high current cost of SNP genotyping service, the use of SNP information for estimating genomic relationships and inbreeding are highly valuable for managing alpaca herds. There is a need, however, to explore cheaper ways to get SNP genotypes by using new approaches such as genotyping by sequencing (GBS) at lower sequencing coverage.