Open AccessCan metabolic prediction be an alternative to genomic prediction in barley?
Author(s) -
Mathias Ruben Gemmer,
Chris Richter,
Yong Jiang,
Thomas Schmutzer,
Manish L. Raorane,
Björn H. Junker,
Klaus Pillen,
Andreas Maurer
Publication year - 2020
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0234052
Subject(s) - biology , snp , population , computational biology , bottleneck , selection (genetic algorithm) , hordeum vulgare , plant breeding , snp genotyping , sampling (signal processing) , genomic selection , crop , genotype , genetics , single nucleotide polymorphism , agronomy , computer science , poaceae , machine learning , gene , medicine , environmental health , filter (signal processing) , computer vision , embedded system
Like other crop species, barley, the fourth most important crop worldwide, suffers from the genetic bottleneck effect, where further improvements in performance through classical breeding methods become difficult. Therefore, indirect selection methods are of great interest. Here, genomic prediction (GP) based on 33,005 SNP markers and, alternatively, metabolic prediction (MP) based on 128 metabolites with sampling at two different time points in one year, were applied to predict multi-year agronomic traits in the nested association mapping (NAM) population HEB-25. We found prediction abilities of up to 0.93 for plant height with SNP markers and of up to 0.61 for flowering time with metabolites. Interestingly, prediction abilities in GP increased after reducing the number of incorporated SNP markers. The estimated effects of GP and MP were highly concordant, indicating MP as an interesting alternative to GP, being able to reflect a stable genotype-specific metabolite profile. In MP, sampling at an early developmental stage outperformed sampling at a later stage. The results confirm the value of GP for future breeding. With MP, an interesting alternative was also applied successfully. However, based on our results, usage of MP alone cannot be recommended in barley. Nevertheless, MP can assist in unravelling physiological pathways for the expression of agronomically important traits.