Targeted Proteomics Approach for Precision Plant Breeding

Selected
reaction monitoring (SRM) is a targeted mass spectrometry
technique that enables precise quantitation of hundreds of peptides
in a single run. This technique provides new opportunities for multiplexed
protein biomarker measurements. For precision plant breeding, DNA-based
markers have been used extensively, but the potential of protein biomarkers
has not been exploited. In this work, we developed an SRM marker panel
with assays for 104 potato (Solanum tuberosum) peptides
selected using univariate and multivariate statistics. Thereafter,
using random forest classification, the prediction markers were identified
for Phytopthora infestans resistance in leaves, P. infestans resistance in tubers, and plant yield in potato
leaf secretome samples. The results suggest that the marker panel
has the predictive potential for three traits, two of which have no
commercial DNA markers so far. Furthermore, the marker panel was also
tested and found to be applicable to potato clones not used during
the marker development. The proposed workflow is thus a proof-of-concept
for targeted proteomics as an efficient readout in accelerated breeding
for complex and agronomically important traits.