Genome-enabled predictions for binomial traits in sugar beet populations

BMC Genetics

Massimo Saccomani¹  Alessandra Stella³  Chiara Broccanello¹  Piergiorgio Stevanato¹  Filippo Biscarini² 

[1] DAFNE, Università di Padova, 24105 Padova, Italy;Department of Bioinformatics, PTP, Via Einstein - Loc. Cascina Codazza, Lodi, Italy;IBBA-CNR, Via Einstein, 26900 Lodi, Italy

关键词: Sugar beet;    Root vigor;    Binomial traits;    Genomic predictions;   

Others  :  869584
DOI  :  10.1186/1471-2156-15-87

 received in 2014-04-07, accepted in 2014-07-04,  发布年份 2014

【 摘 要 】

Background

Genomic information can be used to predict not only continuous but also categorical (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

A threshold model was used to fit the relationship between binomial root vigor and SNP genotypes, 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

The estimated prediction accuracy was quite high. Such accurate predictions may be related to the 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.

【 授权许可】

   
2014 Biscarini et al.; licensee BioMed Central Ltd.

【 图 表 】

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