Gamarra David, Taniguchi Masaaki, Aldai Noelia, Arakawa Aisaku, Lopez-Oceja Andres, de Pancorbo Marian M
Biomics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain.
Animal Genome Unit, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba 305-0901, Japan.
Animals (Basel). 2020 Sep 5;10(9):1584. doi: 10.3390/ani10091584.
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 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 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 markers is proposed for a confident parentage analysis and high traceability.
皮雷奈卡牛是西班牙北部巴斯克地区受保护地理标志（PGI）牛肉质量标签下最重要的本土牛品种。短串联重复序列（STR）是用于阐明法医案件以及农业食品领域可追溯性的有力标记。本研究的主要目的是研究皮雷奈卡牛与该地区通常饲养的其他品种之间的系统发育关系，并提供用于亲子鉴定和可追溯性目的的最少STR标记数量。将国际动物遗传学会 - 联合国粮食及农业组织（ISAG - FAO）推荐的30个STR面板与其他商业STR面板进行了比较。30个STR面板显示联合匹配概率为1.89×10，双亲排除概率为0.99998。然而，商业STR面板在皮雷奈卡牛可靠的亲子鉴定分析中显示出有限的效率，至少需要一个21个STR的面板才能达到0.9999的排除概率。机器学习分析还表明，在选择皮雷奈卡个体中F值最高的标记进行赋值时，准确率达到95%。总体而言，本研究展示了皮雷奈卡牛的遗传特征及其与巴斯克地区通常饲养的其他品种的系统发育关系。最后，提出了一个具有最高F值标记的21个STR面板，用于可靠的亲子鉴定分析和高可追溯性。
