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A novel genomic selection method combining GBLUP and LASSO.

Hengde Li1, Jingwei Wang, Zhenmin Bao

  • 1Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China, hengde.li@cafs.ac.cn.

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Genomic selection models were enhanced by incorporating quantitative trait locus (QTL) information. The elastic net method (ENGBLUP) demonstrated superior prediction accuracy and persistence for genetic traits in breeding.

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Area of Science:

  • Quantitative genetics
  • Animal and plant breeding
  • Statistical genomics

Background:

  • Genomic selection accurately estimates genetic merit using genome-wide SNPs.
  • Genomic Best Linear Unbiased Prediction (GBLUP) is a standard method for genomic selection.
  • Integrating quantitative trait locus (QTL) information can potentially improve prediction accuracy.

Purpose of the Study:

  • To extend GBLUP by incorporating QTL information derived from SNPs using LASSO methods.
  • To evaluate the performance of different LASSO-based GBLUP models in genomic prediction.
  • To assess the prediction accuracy and generational persistence of the proposed models.

Main Methods:

  • Developed GBLUP variants: standard LASSO (SLGBLUP), adaptive LASSO (ALGBLUP), and elastic net (ENGBLUP).
  • QTLs were identified using LASSO methods and fitted as fixed effects.
  • Remaining SNPs were fitted using a realized genetic relationship matrix.
  • Simulations were conducted under various scenarios to assess prediction accuracy and persistence.

Main Results:

  • SLGBLUP showed the lowest prediction accuracy.
  • ALGBLUP and ENGBLUP achieved prediction accuracies comparable to or higher than GBLUP, except with a large number of QTLs.
  • ENGBLUP exhibited the strongest persistence of prediction accuracy across generations.

Conclusions:

  • ENGBLUP offers a robust and computationally efficient approach for genomic selection.
  • Integrating QTL information via elastic net enhances genomic prediction models.
  • The developed methods provide improved tools for plant and animal breeding programs.