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

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 FST 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 FST markers is proposed for a confident parentage analysis and high traceability.

A Statistical Method to Enhance the Analysis of the Differences Among High-Resolution Melting (HRM) Curves of PCR-Amplified DNA Fragments.

Consistent differences among melting curves of PCR-amplified DNA fragments are treated by normalizing the relative fluorescence units (RFU) and performing a clustering analysis, but statistically significant differences among curves are not usually determined. In the present study, an analysis based on functional data analysis (FDA) was implemented to evaluate the existence of statistically significant differences between normalized RFU curves obtained from PCR-HRM (high-resolution melting) analysis by using ANOVA for functional data. The effectiveness of the FDA method was analyzed with data from a set of samples of eight animal species of interest in food analysis, as well as mixtures of DNA from these species, analyzed by PCR-HRM to differentiate them. The statistical method described in this study has been demonstrated to be a robust and precise tool to discriminate among melting curves derived from HRM analysis. This method has advantages over the current comparison methods. PRACTICAL APPLICATION: As long as food fraud and mislabeling exist, new techniques for species identification are needed. High-resolution melting (HRM) has been shown to be a rapid, reliable and inexpensive species identification method. In the present study, functional data analysis (FDA) was applied to HRM curves of DNA from eight animal species used for food, as well as to mixtures of these species in different proportions. FDA has advantages over the usual methods, providing a deeper statistical analysis and facilitating the data interpretation as shown by the HRM analysis for a clearer comparison among individual species and mixtures of species.

Distinct correlations between lipogenic gene expression and fatty acid composition of subcutaneous fat among cattle breeds.

BACKGROUND: The fatty acid (FA) composition of adipose tissue influences the nutritional quality of meat products. The unsaturation level of FAs is determined by fatty acid desaturases such as stearoyl-CoA desaturases (SCDs), which are under control of the transcription factor sterol regulatory element-binding protein (SREBP). Differences in SCD genotype may thus confer variations in lipid metabolism and FA content among cattle breeds. This study investigated correlations between FA composition and lipogenic gene expression levels in the subcutaneous adipose tissue of beef cattle breeds of different gender from the Basque region of northern Spain. Pirenaica is the most important beef cattle breed in northern Spain, while Salers cattle and Holstein-Friesian cull cows are also an integral part of the regional beef supply. RESULTS: Pirenaica heifers showed higher monounsaturated FA (MUFA) and conjugated linoleic acid (CLA) contents in subcutaneous adipose tissue than other breeds (P < 0.001). Alternatively, Salers bulls produced the highest oleic acid content, followed by Pirenaica heifers (P < 0.001). There was substantial variability in SCD gene expression among breeds, consistent with these differences in MUFA and CLA content. Correlations between SCD1 expression and most FA desaturation indexes (DIs) were positive in Salers (P < 0.05) and Pirenaica bulls, while, in general, SCD5 expression showed few significant correlations with DIs. There was a significant linear correlation between SCD1 and SRBEP1 in all breeds, suggesting strong regulation of SCD1 expression by SRBEP1. Pirenaica heifers showed a stronger correlation between SCD1 and SREBP1 than Pirenaica bulls. We also observed a opposite relationship between SCD1 and SCD5 expression levels and opposite associations of isoform expression levels with the ∆9 desaturation indexes. CONCLUSIONS: These results suggest that the relationships between FA composition and lipogenic gene expression are influenced by breed and sex. The opposite relationship between SCD isoforms suggests a compensatory regulation of total SCD activity, while opposite relationships between SCD isoforms and desaturation indexes, specially 9c-14:1 DI, previously reported as an indicator of SCD activity, may reflect distinct activities of SCD1 and SCD5 in regulation of FA content. These findings may be useful for beef/dairy breeding and feeding programs to supply nutritionally favorable products.

New Q lineage found in bovine (Bos taurus) of Iberian Peninsula.

The northern Iberian Peninsula is home to a variety of autochthonous cattle breeds, such as the Terreña and Pirenaica. With the objective of characterizing the matrilineal lineages of these breeds, a study of mitochondrial DNA was performed. The D-loop of 155 individuals was analyzed and most of the individuals were carriers of the T3 haplogroup, while haplogroups T and T1 were much less frequent. A Pirenaica individual belonging to the Q haplogroup was found. To verify the presence of the Q haplogroup individual, the entire mitochondrial DNA was sequenced and compared with two descendants. The individuals were assigned to the Q1 sub-haplogroup. These findings extend the geographic distribution of the Q haplogroup to the south west of the European continent. This new Q1 lineage has seven polymorphisms in the coding region, so this lineage is probably as old as the Q lineages described to date.