The use of SNP markers for cattle breed identification

• Published in: Journal of applied genetics Vol. 65; no. 3; pp. 575 - 589
• Main Authors: Jasielczuk, Igor, Gurgul, Artur, Szmatoła, Tomasz, Radko, Anna, Majewska, Anna, Sosin, Ewa, Litwińczuk, Zygmunt, Rubiś, Dominika, Ząbek, Tomasz
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01-09-2024; Springer Nature B.V
• Subjects: Algorithms; Animal Genetics and Genomics; Animal Genetics • Original Paper; Animal husbandry; Animals; Biomedical and Life Sciences; Breeding; Cattle; Cattle - genetics; Genetic analysis; Genetic diversity; Genetic Markers; Genetic resources; Genetic structure; Genetics, Population; Genotype; Human Genetics; Life Sciences; Microbial Genetics and Genomics; Nucleotides; Oligonucleotide Array Sequence Analysis; Panels; Plant Genetics and Genomics; Poland; Polymorphism, Single Nucleotide - genetics; Population genetics; Population structure; Population studies; Resource conservation; Single-nucleotide polymorphism; Poland; Breed assignment; Population structure; Genetic diversity; Bos Taurus; Native breeds
• ISSN: 1234-1983; 2190-3883
• DOI: 10.1007/s13353-024-00857-0

A potential application of single nucleotide polymorphisms (SNPs) in animal husbandry and production is identification of the animal breed. In this study, using chosen marker selection methods and genotypic data obtained with the use of Illumina Bovine SNP50 BeadChip for individuals belonging to ten cattle breeds, the reduced panels containing the most informative SNP markers were developed. The suitability of selected SNP panels for the effective and reliable assignment of the studied individuals to the breed of origin was checked by three allocation algorithms implemented in GeneClass 2. The studied breeds set included both Polish-native breeds under the genetic resources conservation programs and highly productive breeds with a global range. For all of the tested marker selection methods (“delta” and two F
ST
-based variants), two separate methodological approaches of marker assortment were used and three marker panels were created with 96, 192, and 288 SNPs respectively, to determine the minimum number of markers required for effective differentiation of the studied breeds. Moreover, the usefulness of the most effective panels of markers to assess the population structure and genetic diversity of the analyzed breeds was examined. The conducted analyses showed the possibility of using SNP subsets from medium-density genotypic microarrays to distinguish breeds of cattle kept in Poland and to analyze their genetic structure.