Genetic Characterization of the Local Pirenaica Cattle for Parentage and Traceability Purposes

Abstract

Pirenaica is the most important autochthonous cattle breed within the Protected Geographic Indication (PGI) beef quality label in the Basque region, in northern Spain. The short tandem repeats (STRs) are powerful markers to elucidate forensic cases and traceability across the agri-food sector. The main objective of the present work was to study the phylogenetic relationships of Pirenaica cattle and other breeds typically raised in the region and provide the minimum number of STR markers for parentage and traceability purposes. The 30-STR panel recommended by the International Society of Animal Genetics-Food and Agriculture Organization of the United Nations (ISAG-FAO) was compared against other commercial STR panels. The 30-STR panel showed a combined matching probability of 1.89 × 10^-25 and a power of exclusion for duos of 0.99998. However, commercial STR panels showed a limited efficiency for a reliable parentage analysis in Pirenaica, and at least a 21-STR panel is needed to reach a power of exclusion of 0.9999. Machine-learning analysis also demonstrated a 95% accuracy in assignments selecting the markers with the highest F_ST in Pirenaica individuals. Overall, the present study shows the genetic characterization of Pirenaica and its phylogeny compared with other breeds typically raised in the Basque region. Finally, a 21-STR panel with the highest F_ST markers is proposed for a confident parentage analysis and high traceability.

Keywords: Blonde d´Aquitaine; Holstein-Friesian; Limousin; Salers; Terreña; assignment test; identity; microsatellite; multiplex PCR; structure.

Figure 1

Genetic variations and phylogenetic differentiation analyses among cattle breeds. (a) 3D-FCA, (b) NJ radiation tree (Scale measured in R_ST distance values), size of circles represents bootstraps percentage and (c) mean probabilities of individual cluster memberships using structure (K = 4).

Figure 2

Comparison of combined power of exclusions (CPE) between the panels of short tandem repeat markers. Short tandem repeats (STRs) considering one known parent, two known parents, sibling and identical are shown in blue (CPE₁), red (CPE₂), green (CPE_SI), and purple (CPE_I = 1 − CMP) cases, respectively. Little arrows (top) show the minimal number of markers for 99.99% of CPE. Boxes (below) show the markers included in recommended and commercial STR panels (grey, Stockmarks; garnet, ISAG core; blue, Bovine genotype 1.2 and 2.2). Numbers in brackets shows other panels used in literature.

Figure 3

Assignment accuracies (%), according to Monte-Carlo cross-validation and depicted as bar-plots. (a) Pirenaica and Terreña breeds’ assignments for balanced populations (10, 15 and 20 individuals) crossed by three levels of train STRs with the highest F_ST (red: 5-STR; green: 8-STR) and all loci (blue: 11-STR), (b) Pirenaica, Blonde d´Aquitaine and Limousin breeds’ assignments for balanced populations (25, 50 and 75 individuals) crossed by four levels of train STRs with the highest F_ST (red: 8-STR; green: 11-STR; turquoise: 12-STR) and all loci (fuchsia: 16-STR). (c) Pirenaica, Salers and Holstein-Friesian breeds’ assignments for balanced populations (5, 8 and 12 individuals) crossed by four levels of train STRs with the highest F_ST (red: 11-STR; green: 16-STR; turquoise: 21-STR) and all loci (fuchsia: 30-STR).