Journal
G3-GENES GENOMES GENETICS
Volume 10, Issue 7, Pages 2265-2273Publisher
OXFORD UNIV PRESS INC
DOI: 10.1534/g3.120.401165
Keywords
genomic selection; wheat; plant breeding; training population optimization; haplotype prediction; quantitative trait loci; GenPred; Shared data resources
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Funding
- Minnesota Agricultural Experiment Station
- Minnesota Wheat Research & Promotion Council
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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 bothk-fold cross validation and stratified sampling optimization. After confirming population structure, the stratified sampling improved the predictive ability compared withk-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 andk-fold cross validation. These results emphasize the effectiveness of using haplotypes in genomic selection to increase genetic gain in self-fertilized crops.
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