A comprehensive study on size and definition of the core group in the proven and young algorithm for single-step GBLUP.
A comprehensive study on size and definition of the core group in the proven and young algorithm for single-step GBLUP.
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DOI：
10.1186/s12711-022-00726-6
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发表时间：
2022-05-20
影响因子：
4.1
通讯作者：
Misztal, Ignacy
中科院分区：
文献类型：
--
作者：
Abdollahi-Arpanahi, Rostam;Lourenco, Daniela;Misztal, Ignacy
已证明的年轻算法 (APY) 已被建议作为递归计算大型基因组关系矩阵 (G) 的逆矩阵的稀疏表示的解决方案。在 APY 中，基因分型个体的子集用作核心，其余基因分型个体用作非核心。核心的大小和定义是APY应用的相关研究课题，特别是考虑到基因分型个体数量不断增加。本研究的目的是调查几个核心定义，包括最受欢迎的动物（MPA）（即对遗传库贡献较高的动物）、最不受欢迎的雄性动物（LPM）、最不受欢迎的雌性动物（LPF）、随机集（Rnd）、均匀分布在谱系路径上的动物（Ped）、无关个体（Unrel）、或基于科内选择（Fam）或基于基因内容矩阵分解（QR）。根据使用 APY 的单步基因组最佳线性无偏预测 (ssGBLUP) 的预测准确性，对六个核心大小的每个定义进行了评估。使用 G 的完全逆的 ssGBLUP 的预测精度作为基线。该数据集包含 357,000 头杜洛克猪，其中 111,000 头具有基因型记录，以及 220,000 头表型记录。当核心大小等于解释 G 变化 50% 的最大特征值数量时 (n = 160)，MPA 和 Ped 核心定义提供最高的平均预测精度 (~ 0.41−0.53)。随着核心大小增加到解释 G 变异 99% 的特征值数量 (n = 7320)，所有核心类型的预测精度几乎相同，并且对于所有核心定义，与 G 完全反转的 ssGBLUP 的基因组估计育种值 (GEBV) 的相关性均大于 0.99。代表所有代的核心，例如 Rnd、Ped、Fam 和 Unrel，在 GEBV 的层次聚类中分组在一起。对于小磁芯尺寸，磁芯的定义很重要；然而，当核心的大小达到等于解释 G 99% 变化的最大特征值数量的最佳值时，核心的定义就变得任意了。
The algorithm for proven and young (APY) has been suggested as a solution for recursively computing a sparse representation for the inverse of a large genomic relationship matrix (G). In APY, a subset of genotyped individuals is used as the core and the remaining genotyped individuals are used as noncore. Size and definition of the core are relevant research subjects for the application of APY, especially given the ever-increasing number of genotyped individuals. The aim of this study was to investigate several core definitions, including the most popular animals (MPA) (i.e., animals with high contributions to the genetic pool), the least popular males (LPM), the least popular females (LPF), a random set (Rnd), animals evenly distributed across genealogical paths (Ped), unrelated individuals (Unrel), or based on within-family selection (Fam), or on decomposition of the gene content matrix (QR). Each definition was evaluated for six core sizes based on prediction accuracy of single-step genomic best linear unbiased prediction (ssGBLUP) with APY. Prediction accuracy of ssGBLUP with the full inverse of G was used as the baseline. The dataset consisted of 357k pedigreed Duroc pigs with 111k pigs with genotypes and ~ 220k phenotypic records. When the core size was equal to the number of largest eigenvalues explaining 50% of the variation of G (n = 160), MPA and Ped core definitions delivered the highest average prediction accuracies (~ 0.41−0.53). As the core size increased to the number of eigenvalues explaining 99% of the variation in G (n = 7320), prediction accuracy was nearly identical for all core types and correlations with genomic estimated breeding values (GEBV) from ssGBLUP with the full inversion of G were greater than 0.99 for all core definitions. Cores that represent all generations, such as Rnd, Ped, Fam, and Unrel, were grouped together in the hierarchical clustering of GEBV. For small core sizes, the definition of the core matters; however, as the size of the core reaches an optimal value equal to the number of largest eigenvalues explaining 99% of the variation of G, the definition of the core becomes arbitrary.
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影响因子：
4.1
作者：
Fernando, Rohan L.;Cheng, Hao;Garrick, Dorian J.
通讯作者：
Garrick, Dorian J.
影响因子：
3.5
作者：
Aguilar, I.;Misztal, I.;Lawlor, T. J.
通讯作者：
Lawlor, T. J.
影响因子：
3.5
作者：
Masuda, Y.;Misztal, I.;Lawlor, T. J.
通讯作者：
Lawlor, T. J.
DOI：
10.1186/s12711-021-00683-6
发表时间：
2021-11-27
期刊：
Genetics, selection, evolution : GSE
影响因子：
--
作者：
Abdollahi-Arpanahi R;Lourenco D;Legarra A;Misztal I
通讯作者：
Misztal I
DOI：
10.1186/s12711-016-0261-6
发表时间：
2016-10-31
期刊：
Genetics, selection, evolution : GSE
影响因子：
--
作者：
Pocrnic I;Lourenco DA;Masuda Y;Misztal I
通讯作者：
Misztal I