Sparse kernel models provide optimization of training set design for genomic prediction in multiyear wheat breeding data

Marco Lopez-Cruz, Susanne Dreisigacker, Leonardo Crespo-Herrera, Alison R. Bentley, Ravi Singh, Jesse Poland, Sandesh Shrestha, Julio Huerta-Espino, Velu Govindan, Philomin Juliana, Suchismita Mondal, Paulino Pérez-Rodríguez*, Jose Crossa*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


The success of genomic selection (GS) in breeding schemes relies on its ability to provide accurate predictions of unobserved lines at early stages. Multigeneration data provides opportunities to increase the training data size and thus, the likelihood of extracting useful information from ancestors to improve prediction accuracy. The genomic best linear unbiased predictions (GBLUPs) are performed by borrowing information through kinship relationships between individuals. Multigeneration data usually becomes heterogeneous with complex family relationship patterns that are increasingly entangled with each generation. Under these conditions, historical data may not be optimal for model training as the accuracy could be compromised. The sparse selection index (SSI) is a method for training set (TRN) optimization, in which training individuals provide predictions to some but not all predicted subjects. We added an additional trimming process to the original SSI (trimmed SSI) to remove less important training individuals for prediction. Using a large multigeneration (8 yr) wheat (Triticum aestivum L.) grain yield dataset (n = 68,836), we found increases in accuracy as more years are included in the TRN, with improvements of ∼0.05 in the GBLUP accuracy when using 5 yr of historical data relative to when using only 1 yr. The SSI method showed a small gain over the GBLUP accuracy but with an important reduction on the TRN size. These reduced TRNs were formed with a similar number of subjects from each training generation. Our results suggest that the SSI provides a more stable ranking of genotypes than the GBLUP as the TRN becomes larger.

Original languageEnglish (US)
Article numbere20254
JournalPlant Genome
Issue number4
StatePublished - Dec 2022

ASJC Scopus subject areas

  • Genetics
  • Agronomy and Crop Science
  • Plant Science


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