USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA.
J Anim Sci. 2023 Jan 3;101. doi: 10.1093/jas/skad166.
Genotyping pools of commercial cattle and individual seedstock animals may reveal hidden relationships between sectors enabling use of commercial data for genetic evaluation. However, commercial data capture may be compromised by inexact pool formation. We aimed to estimate the concordance between distances or genomic covariance among pooling allele frequencies (PAFs) of DNA pools comprised of 100 animals with 0% or 50% overlap of animals in common between pools. Cattle lung samples were collected from a commercial beef processing plant on a single day. Six pools of 100 animals each were constructed so that overlap between pools was 0% or 50%. Two pools of all 200 animals were constructed to estimate PAFs for all 200 animals. Frozen lung tissue (0.01 g) from each animal was weighed into a tube containing a pool; there were two pools of 200 animals each and six pools of 100 animals each. Every contribution of an individual animal was an independent measurement to insure independence of pooling errors. Lung samples were kept on dried ice during the pooling process to keep them from thawing. The eight pools were then assayed for approximately 100,000 single nucleotide polymorphisms (SNP). PAF for each SNP and pool was based on the relative intensity of the two dyes used to detect the alleles rather than genotype calls which are not tractable from pooling data. Euclidean distances and genomic relationships among the PAFs for the eight pools were estimated and distances were tested for concordance with pool overlap using permutation-based analysis of distance. Distances among pools were concordant with the planned overlap of animals shared between pools (P = 0.0024); pool overlap accounted for 70% of the variation and pooling error accounted for 30%. Pools containing 100 animals with no overlap were the most distant from one another and pools with 50% overlap were the least distant. This work shows that we can discern differences in distance between pairs of overlapping DNA pools sharing 0% and 50% of the animals. Genomic correlations among nonoverlapping pools indicated that nonoverlapping pool pairs did not share many related animals because genomic correlations were near zero for these pairs. On the other hand, one pair of nonoverlapping pools likely contained related animals between pools because the correlation was 0.21. Pools sharing 50% overlap ranged in genomic relationship between 0.21 and 0.39 (N = 12).
对商业牛群和个体种畜的基因分型池进行分析，可能揭示各领域之间隐藏的关系，从而使商业数据能够用于遗传评估。然而，由于池的形成不精确，商业数据的捕获可能会受到影响。我们的目标是估计由 100 头动物组成的 DNA 池的等位基因频率（PAF）的距离或基因组协方差之间的一致性，其中池之间有 0%或 50%的动物重叠。在一天内从一个商业牛肉加工厂收集牛肺样本。构建了 6 个 100 头动物的池，池之间的重叠率为 0%或 50%。构建了两个包含所有 200 头动物的池，以估计所有 200 头动物的 PAF。将每头动物的 0.01 克冷冻肺组织称重到含有一个池的管中；每个池中都有 200 头动物的两个池和 100 头动物的六个池。个体动物的每一个贡献都是一个独立的测量，以确保池错误的独立性。在池化过程中，将肺样本放在干冰上，以防止其解冻。然后对这 8 个池进行了大约 100,000 个单核苷酸多态性（SNP）的检测。每个 SNP 和池的 PAF 是基于用于检测等位基因的两种染料的相对强度，而不是从池化数据中可获得的基因型调用。估计了 8 个池的 PAF 之间的欧几里得距离和基因组关系，并使用基于距离的置换分析测试了距离与池重叠的一致性。池之间的距离与池之间共享动物的计划重叠一致（P = 0.0024）；池重叠占 70%，池化误差占 30%。没有重叠的包含 100 头动物的池彼此之间距离最远，而重叠 50%的池彼此之间距离最近。这项工作表明，我们可以分辨出共享 0%和 50%动物的重叠 DNA 池之间的距离差异。非重叠池之间的基因组相关性表明，非重叠池对之间没有共享许多相关动物，因为这些对之间的基因组相关性接近零。另一方面，一对非重叠池可能包含池之间的相关动物，因为相关性为 0.21。共享 50%重叠的池的基因组关系在 0.21 到 0.39 之间（N = 12）。
