TY  - THES
T1  - Comparison of omics technologies for hybrid prediction
A1  - Westhues,Matthias
Y1  - 2020/07/17
N2  - One of the great challenges for plant breeders is dealing with the vast number of putative candidates, which cannot be tested exhaustively in multi-environment field trials. Using pedigree records helped breeders narrowing down the number of candidates substantially. With pedigree information, only a subset of candidates need to be subjected to exhaustive tests of their phenotype whereas the phenotype of the majority of untested relatives is inferred from their common pedigree. A caveat of pedigree information is its inability to capture Mendelian sampling and to accurately reflect relationships among individuals. This shortcoming was mitigated with the advent of marker assays covering regions harboring causal quantitative trait loci. Today, the prediction of untested candidates using information from genomic markers, called genomic prediction, is a routine procedure in larger plant breeding companies.
Genomic prediction has revolutionized the prediction of traits with complex genetic architecture but, just as pedigree, cannot properly capture physiological epistasis, referring to complex interactions among genes and endophenotypes, such as RNA, proteins and metabolites. Given their intermediate position in the genotype-phenotype cascade, endophenotypes are expected to represent some of the information missing from the genome, thereby potentially improving predictive abilities.
In a first study we explored the ability of several predictor types to forecast genetic values for complex agronomic traits recorded on maize hybrids.
Pedigree and genomic information were included as the benchmark for evaluating the merit of metabolites and gene expression data in genetic value prediction.
Metabolites, sampled from maize plants grown in field trials, were poor predictors for all traits. Conversely, root-metabolites, grown under controlled conditions, were moderate to competitive predictors for the traits fat as well as dry matter yield. Gene expression data outperformed other individual predictors for the prediction of genetic values for protein and the economically most relevant trait dry matter yield. A genome-wide association study suggested that gene expression data integrated SNP interactions. This might explain the superior performance of this predictor type in the prediction of protein and dry matter yield. 
Small RNAs were probed for their potential as predictors, given their involvement in transcriptional, post-transcriptional and post-translational regulation. Regardless of the trait, small RNAs could not outperform other predictors. Combinations of predictors did not considerably improve the predictive ability of the best single predictor for any trait but improved the stability of their performance across traits. By assigning different weights to each predictor, we evaluated each predictors  optimal contribution for attaining maximum predictive ability. This approach revealed that pedigree, genomic information and gene expression data contribute equally when maximizing predictive ability for grain dry matter content. When attempting to maximize predictive ability for grain yield, pedigree information was superfluous. 
For genotypes having only genomic information, gene expression data were imputed by using genotypes having both, genomic as well as gene expression data. Previously, this single-step prediction framework was only used for qualitative predictors. Our study revealed that this framework can be employed for improving the cost-effectiveness of quantitative endophenotypes in hybrid prediction.
We hope that these studies will further promote exploring endophenotypes as additional predictor types in breeding.
KW  - Genetik
KW  - Mais
KW  - SNP
KW  - Prognose
KW  -  Hybride
CY  - Hohenheim
PB  - Kommunikations-, Informations- und Medienzentrum der Universität Hohenheim
AD  - Garbenstr. 15, 70593 Stuttgart
UR  - http://opus.uni-hohenheim.de/volltexte/2020/1707
ER  -