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. 2014 Jul 22:15:87.
doi: 10.1186/1471-2156-15-87.

Genome-enabled predictions for binomial traits in sugar beet populations

Filippo Biscarini  1 , Piergiorgio Stevanato, Chiara Broccanello, Alessandra Stella, Massimo Saccomani
Affiliations

Genome-enabled predictions for binomial traits in sugar beet populations

Filippo Biscarini et al. BMC Genet. .

Abstract

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.

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Figures

Figure 1
Figure 1
Heatmap of genomic relationships between sugar beet individual plants. Plants have been groupd by line. Darker colors indicate stronger genomic relationships.
Figure 2
Figure 2
Box plots of estimated probability vs observed root vigor in the training (left) and validation/test (right) data. True high- and low-root-vigor individuals are in light yellow and dark red respectively. The dotted line is the classification threshold (P (Y = [ 0/1]|X) = 0.5).
Figure 3
Figure 3
Boxplot of the cross-validation test error rate for the original data ( h 2 = 0 . 783) and for lower heritabilities.
Figure 4
Figure 4
Snp effects for root vigor along the genome of B. vulgaris .
Figure 5
Figure 5
Linkage disequilibrium between all SNPs (left) and between SNPs on scaffolds 00184, 00349 and 00704 (right, from top to bottom).
See this image and copyright information in PMC

References

    1. Van Tassell CP, Smith TP, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenschild CD, Moore SS, Warren WC, Sonstegard TS. Snp discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Med. 2008;5(3):247–252. - PubMed
    1. Abraham G, Tye-Din JA, Bhalala OG, Kowalczyk A, Zobel J, Inouye M. Accurate and robust genomic prediction of celiac disease using statistical learning. PloS one. 2013;10(2):1004137. - PMC - PubMed
    1. Hayes B, Bowman P, Chamberlain A, Goddard M. Invited review: genomic selection in dairy cattle: Progress and challenges. J Dairy Sci. 2009;92(2):433–443. - PubMed
    1. Albrecht T, Wimmer V, Auinger H-J, Erbe M, Knaak C, Ouzunova M, Simianer H, Schön C-C. Genome-based prediction of testcross values in maize. Theor Appl Genet. 2011;123(2):339–350. - PubMed
    1. Kumar S, Bink MC, Volz RK, Bus VG, Chagné D. Towards genomic selection in apple (malus× domestica borkh.) breeding programmes: prospects, challenges and strategies. Tree Genet Genomes. 2012;8(1):1–14.

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