Improving prediction accuracy using multi-allelic haplotype prediction and training population optimization in wheat

Ahmad H. Sallam, Emily Conley, Dzianis Prakapenka, Yang Da, James A. Anderson

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


The use of haplotypes may improve the accuracy of genomic prediction over single SNPs because haplotypes can better capture linkage disequilibrium and genomic similarity in different lines and may capture local high-order allelic interactions. Additionally, prediction accuracy could be improved by portraying population structure in the calibration set. A set of 383 advanced lines and cultivars that represent the diversity of the University of Minnesota wheat breeding program was phenotyped for yield, test weight, and protein content and genotyped using the Illumina 90K SNP Assay. Population structure was confirmed using single SNPs. Haplotype blocks of 5, 10, 15, and 20 adjacent markers were constructed for all chromosomes. A multi-allelic haplotype prediction algorithm was implemented and compared with single SNPs using both k-fold cross validation and stratified sampling optimization. After confirming population structure, the stratified sampling improved the predictive ability compared with k-fold cross validation for yield and protein content, but reduced the predictive ability for test weight. In all cases, haplotype predictions outperformed single SNPs. Haplotypes of 15 adjacent markers showed the best improvement in accuracy for all traits; however, this was more pronounced in yield and protein content. The combined use of haplotypes of 15 adjacent markers and training population optimization significantly improved the predictive ability for yield and protein content by 14.3 (four percentage points) and 16.8% (seven percentage points), respectively, compared with using single SNPs and k-fold cross validation. These results emphasize the effectiveness of using haplotypes in genomic selection to increase genetic gain in self-fertilized crops.

Original languageEnglish (US)
Pages (from-to)2265-2273
Number of pages9
JournalG3: Genes, Genomes, Genetics
Issue number7
StatePublished - Jul 7 2020

Bibliographical note

Funding Information:
We thank Susan Reynolds for excellent technical assistance. This research was funded by the Minnesota Agricultural Experiment Station and the Minnesota Wheat Research & Promotion Council.

Publisher Copyright:
Copyright © 2020 Sallam et al.


  • GenPred
  • Genomic selection wheat
  • Haplotype prediction
  • Plant breeding training population optimization
  • Quantitative trait loci
  • Shared data resources

PubMed: MeSH publication types

  • Research Support, Non-U.S. Gov't
  • Journal Article


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