Background: Genomicinformationcanbeusedtopredictnotonlycontinuousbutalsocategorical(e.g.binomial) traits. Several traits of interest in human medicine and agriculture present a discrete distribution of phenotypes (e.g. disease status). Root vigor in sugar beet (B. vulgaris) is an example of binomial trait of agronomic importance. In this paper, a panel of 192 SNPs (single nucleotide polymorphisms) was used to genotype 124 sugar beet individual plants from 18 lines, and to classify them as showing “high” or “low” root vigor. Results: AthresholdmodelwasusedtofittherelationshipbetweenbinomialrootvigorandSNPgenotypes,through the matrix of genomic relationships between individuals in a genomic BLUP (G-BLUP) approach. From a 5-fold cross-validation scheme, 500 testing subsets were generated. The estimated average cross-validation error rate was 0.000731 (0.073%). Only 9 out of 12326 test observations (500 replicates for an average test set size of 24.65) were misclassified. Conclusions: Theestimatedpredictionaccuracywasquitehigh.Suchaccuratepredictionsmayberelatedtothe high estimated heritability for root vigor (0.783) and to the few genes with large effect underlying the trait. Despite the sparse SNP panel, there was sufficient within-scaffold LD where SNPs with large effect on root vigor were located to allow for genome-enabled predictions to work.
Genome-enabled predictions for binomial traits in sugar beet populations
STEVANATO, PIERGIORGIO;BROCCANELLO, CHIARA;SACCOMANI, MASSIMO
2014
Abstract
Background: Genomicinformationcanbeusedtopredictnotonlycontinuousbutalsocategorical(e.g.binomial) traits. Several traits of interest in human medicine and agriculture present a discrete distribution of phenotypes (e.g. disease status). Root vigor in sugar beet (B. vulgaris) is an example of binomial trait of agronomic importance. In this paper, a panel of 192 SNPs (single nucleotide polymorphisms) was used to genotype 124 sugar beet individual plants from 18 lines, and to classify them as showing “high” or “low” root vigor. Results: AthresholdmodelwasusedtofittherelationshipbetweenbinomialrootvigorandSNPgenotypes,through the matrix of genomic relationships between individuals in a genomic BLUP (G-BLUP) approach. From a 5-fold cross-validation scheme, 500 testing subsets were generated. The estimated average cross-validation error rate was 0.000731 (0.073%). Only 9 out of 12326 test observations (500 replicates for an average test set size of 24.65) were misclassified. Conclusions: Theestimatedpredictionaccuracywasquitehigh.Suchaccuratepredictionsmayberelatedtothe high estimated heritability for root vigor (0.783) and to the few genes with large effect underlying the trait. Despite the sparse SNP panel, there was sufficient within-scaffold LD where SNPs with large effect on root vigor were located to allow for genome-enabled predictions to work.File | Dimensione | Formato | |
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