Departament of Animal Science, Federal University of Santa Maria (UFSM), Santa Maria, 97105-900, Rio Grande do Sul, Brazil.
Departament of Animal Science, Federal University of Santa Maria (UFSM), Santa Maria, 97105-900, Rio Grande do Sul, Brazil.
J Dairy Sci. 2024 Oct;107(10):8130-8140. doi: 10.3168/jds.2023-24608. Epub 2024 May 31.
Missing pedigrees may produce bias in genomic evaluations. Thus, strategies to deal with this problem have been proposed as using unknown parent groups (UPG) or truncated pedigrees. The aim of this study was to investigate the impact of modeling missing pedigrees under single-step genomic best linear unbiased prediction (ssGBLUP) evaluations for productive and reproductive traits in dairy buffalo using different approaches: (1) traditional BLUP without UPG (BLUP), (2) traditional BLUP including UPG (BLUP/UPG), (3) ssGBLUP without UPG (ssGBLUP), (4) ssGBLUP including UPG in the A and A matrices (ssGBLUP/A_UPG), (5) ssGBLUP including UPG in all elements of the H matrix (ssGBLUP/H_UPG), (6) BLUP with pedigree truncation for the last 3 generations (BLUP/truncated), and (7) ssGBLUP with pedigree truncation for the last 3 generations (ssGBLUP/truncated). Unknown parent groups were not used in the scenarios with truncated pedigree. A total of 3,717, 4,126, and 3,823 records of the first lactation for accumulated 305-d milk yield (MY), age at first calving (AFC), and lactation length (LL), respectively, were used. Accuracies ranged from 0.27 for LL (BLUP) to 0.46 for MY (BLUP), bias ranged from -0.62 for MY (ssGBLUP) to 0.0002 for AFC (BLUP/truncated), and dispersion ranged from 0.88 for MY (BLUP/A_UPG) to 1.13 for LL (BLUP). Genetic trend showed genetic gains for all traits across 20 years of selection, and the impact of including genomic information, UPG, or pedigree truncation under GEBV accuracies ranged among the evaluated traits. Overall, methods using UPG, truncation pedigree, and genomic information exhibited potential to improve GEBV accuracies, bias, and dispersion for all traits compared with other methods. Truncated scenarios promoted high genetic gains. In small populations with few genotyped animals, combining truncated pedigree or UPG with genomic information is a feasible approach to deal with missing pedigrees.
缺失系谱可能会导致基因组评估产生偏差。因此，已经提出了一些处理此问题的策略，例如使用未知亲本组（UPG）或截断系谱。本研究的目的是使用不同的方法，通过单步基因组最佳线性无偏预测（ssGBLUP）评估，研究在奶牛中对生产和繁殖性状进行缺失系谱建模的影响：（1）没有 UPG 的传统 BLUP（BLUP），（2）包括 UPG 的传统 BLUP（BLUP/UPG），（3）没有 UPG 的 ssGBLUP（ssGBLUP），（4）在 A 和 A 矩阵中包括 UPG 的 ssGBLUP（ssGBLUP/A_UPG），（5）在 H 矩阵的所有元素中包括 UPG 的 ssGBLUP（ssGBLUP/H_UPG），（6）对最后 3 代进行系谱截断的 BLUP（BLUP/truncated），以及（7）对最后 3 代进行系谱截断的 ssGBLUP（ssGBLUP/truncated）。在具有截断系谱的情况下，不使用未知亲本组。使用了第一胎的累积 305 天产奶量（MY）、初配年龄（AFC）和泌乳期长度（LL）的第一个泌乳期的 3717、4126 和 3823 条记录。准确性范围从 0.27（BLUP）到 0.46（BLUP）的 MY，偏差范围从-0.62（ssGBLUP）到 0.0002（BLUP/truncated）的 AFC，分散度范围从 0.88（BLUP/A_UPG）到 1.13（BLUP）的 LL。遗传趋势显示，在 20 年的选择过程中，所有性状都有遗传增益，在 GEBV 准确性方面，包括基因组信息、UPG 或系谱截断的影响在评估的性状之间存在差异。总体而言，与其他方法相比，使用 UPG、截断系谱和基因组信息的方法有潜力提高所有性状的 GEBV 准确性、偏差和分散度。截断场景促进了高遗传增益。在具有少量基因分型动物的小群体中，结合截断系谱或 UPG 与基因组信息是处理缺失系谱的一种可行方法。
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