Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine.
Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine.
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DOI：
10.1186/s12864-020-07188-4
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发表时间：
2020-11-16
期刊：
影响因子：
4.4
通讯作者：
Wu HX
中科院分区：
文献类型：
--
作者：
Calleja-Rodriguez A;Pan J;Funda T;Chen Z;Baison J;Isik F;Abrahamsson S;Wu HX
基因组选择（GS）或基因组预测是一种很有前途的方法，可以通过缩短育种计划中的后代测试时间来获得更高的遗传收益。为了证明苏格兰松（Pinus sylvestris L.）的概念，对183个全同胞家族的694个个体进行了基因组预测研究，这些个体采用基因分型测序（GBS）进行了基因分型，并对生长和木材品质性状进行了表型分析。8719个snp被用来比较不同的基因组与家系预测模型。此外，通过分配不同比例的训练集和验证集以及多个SNP标记子集，使用四种预测效率方法来评估基因组育种价值估计的影响。基因组最佳线性无偏预测（GBLUP）和贝叶斯岭回归（BRR）结合期望最大化（EM） imputation算法的预测效率略高于系谱最佳线性无偏预测（PBLUP）和贝叶斯LASSO，但有一些例外。大约6000个SNP标记的子集足以提供与全套8719个标记相似的预测效率。此外，基因组模型的预测效率足以实现更高的选择响应，比传统的基于家系的选择高50-143%。虽然基因组模型和系谱模型的预测效率相似，但假设在苗期可以进行更早的选择，减少后代测试时间，从而将育种周期长度缩短约50%，基因组模型的相对选择响应翻了一番。在线版本包含补充材料，可在（doi:10.1186/s12864-020-07188-4）获得。
Genomic selection (GS) or genomic prediction is a promising approach for tree breeding to obtain higher genetic gains by shortening time of progeny testing in breeding programs. As proof-of-concept for Scots pine (Pinus sylvestris L.), a genomic prediction study was conducted with 694 individuals representing 183 full-sib families that were genotyped with genotyping-by-sequencing (GBS) and phenotyped for growth and wood quality traits. 8719 SNPs were used to compare different genomic with pedigree prediction models. Additionally, four prediction efficiency methods were used to evaluate the impact of genomic breeding value estimations by assigning diverse ratios of training and validation sets, as well as several subsets of SNP markers. Genomic Best Linear Unbiased Prediction (GBLUP) and Bayesian Ridge Regression (BRR) combined with expectation maximization (EM) imputation algorithm showed slightly higher prediction efficiencies than Pedigree Best Linear Unbiased Prediction (PBLUP) and Bayesian LASSO, with some exceptions. A subset of approximately 6000 SNP markers, was enough to provide similar prediction efficiencies as the full set of 8719 markers. Additionally, prediction efficiencies of genomic models were enough to achieve a higher selection response, that varied between 50-143% higher than the traditional pedigree-based selection. Although prediction efficiencies were similar for genomic and pedigree models, the relative selection response was doubled for genomic models by assuming that earlier selections can be done at the seedling stage, reducing the progeny testing time, thus shortening the breeding cycle length roughly by 50%. The online version contains supplementary material available at (doi:10.1186/s12864-020-07188-4).
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影响因子：
1.8
作者：
Almqvist, Curt
通讯作者：
Almqvist, Curt
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影响因子：
4.4
作者：
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通讯作者：
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影响因子：
3.8
作者：
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通讯作者：
Vigneron, Ph
影响因子：
4.5
作者：
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通讯作者：
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影响因子：
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作者：
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通讯作者：
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