Procedures for genetic traceability of animal products and parentage testing mainly focus on microsatellites or SNPs panels. Nevertheless, current availability of high-throughput sequencing technologies must be considered as an appealing alternative. This research focused on the evaluation of low-coverage whole-genome sequencing for traceability and paternity testing purposes, within a context of evidential statistics. Analyses were performed on a simulation basis and assumed individuals with 30 100-Mb/100-cM chromosome pairs and ~1,000,000 polymorphic SNPs per chromosome. Ten independent populations were simulated under recombination and mutation with effective populations size 100 (generations 1–1000), 10,000 (generation 1001) and 25,000 (generation 1002), and this last generation was retained for analytical purposes. Appropriate both traceability and paternity tests were developed and evaluated on different high-throughput sequencing scenarios accounting for genome coverage depth (0.01×, 0.05×, 0.1× and 0.5×), length of base-pair reads (100, 1000 and 10,000 bp), and sequencing error rate (0%, 1% and 10%). Assuming true sequencing error rates and genotypic frequencies, 0.05× genome coverage depth guaranteed 100% sensitivity and specificity for traceability and paternity tests (n = 1000). Same results were obtained when sequencing error rate was arbitrarily set to 0, or the maximum value assumed during simulation (i.e., 1%). In a similar way, uncertainly about genotypic frecuencies did not impair sensitivity under 0.05× genome coverage, although it reduced specificity for paternity tests up to 85.2%. These results highlighted low-coverage whole-genome sequencing as a promising tool for the livestock and food industry with both technological and (maybe) economic advantages.

动物产品的遗传可追溯性和亲子鉴定程序主要集中在微卫星或 SNP 面板上。尽管如此，目前高通量测序技术的可用性必须被视为一种有吸引力的替代方案。这项研究的重点是在证据统计的背景下评估低覆盖率的全基因组测序，以实现可追溯性和亲子鉴定。分析是在模拟基础上进行的，假设个体具有 30 100-Mb/100-cM 染色体对和每条染色体约 1,000,000 个多态性 SNP。在重组和突变下模拟了 10 个独立种群，有效种群大小为 100（第 1-1000 代）、10,000（第 1001 代）和 25,000（第 1002 代），最后一代被保留用于分析目的。在考虑基因组覆盖深度（0.01×、0.05×、0.1×和0.5×）、碱基对读数长度（100、1000 和 10,000 bp）的不同高通量测序场景中开发和评估了适当的可追溯性和亲子鉴定测试和测序错误率（0%、1% 和 10%）。假设真正的测序错误率和基因型频率，0.05 倍的基因组覆盖深度保证了可追溯性和亲子鉴定的 100% 灵敏度和特异性（n  = 1000）。当测序错误率任意设置为 0 或模拟过程中假定的最大值（即1%）时，获得了相同的结果。以类似的方式，在 0.05 倍基因组覆盖率下，基因型频率的不确定性不会损害灵敏度，尽管它将亲子鉴定的特异性降低了 85.2%。这些结果突出了低覆盖率的全基因组测序作为具有技术和（可能）经济优势的畜牧业和食品工业的有前途的工具。