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A novel genomic selection method combining GBLUP and LASSO

文献类型： 外文期刊

作者： Li, Hengde 1 ; Wang, Jingwei 1 ; Bao, Zhenmin 2 ;

作者机构： 1.Chinese Acad Fishery Sci, Ctr Appl Aquat Genom, Beijing 100141, Peoples R China

2.Ocean Univ China, Coll Marine Life, Qingdao 266003, Peoples R China

3.Fujian Agr & Forestry Univ, Coll Anim Sci, Fuzhou 350002, Fujian, Peoples R China

关键词： Genomic selection;Genomic best linear unbiased prediction;Least absolute shrinkage selection operator;Quantitative trait loci

期刊名称：GENETICA （ 影响因子：1.082； 五年影响因子：1.489 ）

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收录情况： SCI

摘要： Genetic prediction of quantitative traits is a critical task in plant and animal breeding. Genomic selection is an accurate and efficient method of estimating genetic merits by using high-density genome-wide single nucleotide polymorphisms (SNP). In the framework of linear mixed models, we extended genomic best linear unbiased prediction (GBLUP) by including additional quantitative trait locus (QTL) information that was extracted from high-throughput SNPs by using least absolute shrinkage selection operator (LASSO). GBLUP was combined with three LASSO methods-standard LASSO (SLGBLUP), adaptive LASSO (ALGBLUP), and elastic net (ENGBLUP)-that were used for detecting QTLs, and these QTLs were fitted as fixed effects; the remaining SNPs were fitted using a realized genetic relationship matrix. Simulations performed under distinct scenarios revealed that (1) the prediction accuracy of SLGBLUP was the lowest; (2) the prediction accuracies of ALGBLUP and ENGBLUP were equivalent to or higher than that of GBLUP, except under scenarios in which the number of QTLs was large; and (3) the persistence of prediction accuracy over generations was strongest in the case of ENGBLUP. Building on the favorable computational characteristics of GBLUP, ENGBLUP enables robust modeling and efficient computation to be performed for genomic selection.

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