Prediction of plant height in arabidopsis thaliana using DNA methylation data

Yaodong Hu, Gota Morota, Guilherme J.M. Rosa, Daniel Gianola

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

Prediction of complex traits using molecular genetic information is an active area in quantitative genetics research. In the postgenomic era, many types of -omic (e.g., transcriptomic, epigenomic, methylomic, and proteomic) data are becoming increasingly available. Therefore, evaluating the utility of this massive amount of information in prediction of complex traits is of interest. DNA methylation, the covalent change of a DNA molecule without affecting its underlying sequence, is one quantifiable form of epigenetic modification. We used methylation information for predicting plant height (PH) in Arabidopsis thaliana nonparametrically, using reproducing kernel Hilbert spaces (RKHS) regression. Also, we used different criteria for selecting smaller sets of probes, to assess how representative probes could be used in prediction instead of using all probes, which may lessen computational burden and lower experimental costs. Methylation information was used for describing epigenetic similarities between individuals through a kernel matrix, and the performance of predicting PH using this similarity matrix was reasonably good. The predictive correlation reached 0.53 and the same value was attained when only preselected probes were used for prediction. We created a kernel that mimics the genomic relationship matrix in genomic best linear unbiased prediction (G-BLUP) and estimated that, in this particular data set, epigenetic variation accounted for 65% of the phenotypic variance. Our results suggest that methylation information can be useful in whole-genome prediction of complex traits and that it may help to enhance understanding of complex traits when epigenetics is under examination.

Original languageEnglish (US)
Pages (from-to)779-793
Number of pages15
JournalGenetics
Volume201
Issue number2
DOIs
StatePublished - Oct 2015

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DNA Methylation
Arabidopsis
Epigenomics
Methylation
Genetic Research
Proteomics
Molecular Biology
Genome
Costs and Cost Analysis
DNA

Keywords

  • DNA methylation
  • Epigenetics
  • GenPred
  • MeDIP-Chip
  • Phenotypic prediction
  • RKHS regression
  • Shared data resource

ASJC Scopus subject areas

  • Genetics

Cite this

Prediction of plant height in arabidopsis thaliana using DNA methylation data. / Hu, Yaodong; Morota, Gota; Rosa, Guilherme J.M.; Gianola, Daniel.

In: Genetics, Vol. 201, No. 2, 10.2015, p. 779-793.

Research output: Contribution to journalArticle

Hu, Yaodong ; Morota, Gota ; Rosa, Guilherme J.M. ; Gianola, Daniel. / Prediction of plant height in arabidopsis thaliana using DNA methylation data. In: Genetics. 2015 ; Vol. 201, No. 2. pp. 779-793.
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