Breeding SNP barcode for animal product traceability
Y. Da1, L. Ma1, N. Li2, X.X Hu2, H. Qu3, D.M. Shu3, H. Li4, X.Q. Zhang5, J.Q. Li5, X. Jiang6
1
Department of Animal Science, University of Minnesota, St. Paul, MN 55108, USA
State Key Laboratories of AgroBiotechnology, China Agricultural University, Beijing 100094,
P.R. China
3
Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou
510640, P.R. China
4
College of Animal Science and Technology, Northeastern Agricultural University, Harbin
150030, P.R. China
5
Department of Animal Science, South China Agricultural University, Guangzhou 510642, P.R.
China
6
Sichuan Animal Science Academy, Chengdu 610066, P.R. China
2
The traceability of animal products has important applications in food safety, disease control and
intellectual property of animal breeding and genetics. Tracing an animal product to the provider
may be necessary to identify the source of the product. Similarly, a distinct mark of an animal
product will help defend the provider’s reputation or intellectual property such as an animal
breed or line achieved through a significant investment. We propose a breeding approach to
establish a unique SNP “barcode” as a unique DNA profile of an animal product. This unique
SNP barcode consists of a set of homozygous SNP loci at specific chromosome locations. Let ‘1'
denote the homozygous genotype of allele ‘1', and ‘2' the homozygous genotype of allele ‘2'.
Then, ‘121' means homozygous genotypes of allele ‘1' at loci 1 and 3 and homozygous genotype
of allele ‘2' at locus 2. This type of unique SNP barcode can be achieved by mating parents with
the required homozygous genotypes. The total number of possible SNP barcodes is 2n, where n =
number of SNP loci. Since the number of SNPs is large on any known animal genome, the
availability of unique SNP barcodes is virtually unlimited. The approach of SNP barcode for
traceability is considerably easier to implement than methods based on parentage testing because
the barcode approach does not require the availability of DNA samples for the parents and even
does not require knowing the parental identities. Breeding an SNP barcode means the fixation of
one allele and elimination of the alternative allele at each SNP locus in the barcode. Therefore,
gene pool conservation and careful study of the potential function of each allele to be eliminated
should be considered. Exclusion probability of SNP barcode was derived as a measure of
statistical power and a likelihood ratio was recommended as a measure of statistical confidence
in testing the uniqueness of an SNP barcode.