title: Targeted Proteomics Approach for Precision Plant Breeding.
abstract: 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.
authors.affiliation: Department of Immunotechnology, Lund University , Lund, Scania, Sweden.
authors.forename: Aakash
authors.initials: A
authors.lastname: Chawade
authors.affiliation: Department of Plant Protection Biology, Swedish University of Agricultural Sciences , Alnarp, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Alexandersson
authors.affiliation: Department of Plant Protection Biology, Swedish University of Agricultural Sciences , Alnarp, Sweden.
authors.forename: Therese
authors.initials: T
authors.lastname: Bengtsson
authors.affiliation: Department of Plant Protection Biology, Swedish University of Agricultural Sciences , Alnarp, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Andreasson
authors.affiliation: Department of Immunotechnology, Lund University , Lund, Scania, Sweden.|Bioinformatics Infrastructure for Life Sciences (BILS), Lund University , Lund, Scania, Sweden.
authors.forename: Fredrik
authors.initials: F
authors.lastname: Levander
mesh_terms: D015415:Biomarkers / Q000378:metabolism; D060467:Disease Resistance / Q000235:genetics; D054884:Host-Pathogen Interactions; D013058:Mass Spectrometry; D015999:Multivariate Analysis; D010455:Peptides / Q000378:metabolism; D055750:Phytophthora infestans / Q000502:physiology; D000069600:Plant Breeding / Q000379:methods*; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism / Q000382:microbiology; D010940:Plant Proteins / Q000378:metabolism*; D035281:Plant Tubers / Q000235:genetics / Q000378:metabolism / Q000382:microbiology; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D011198:Solanum tuberosum / Q000235:genetics / Q000378:metabolism* / Q000382:microbiology
chemical_list: D015415:Biomarkers; D010455:Peptides; D010940:Plant Proteins; D020543:Proteome
keywords: MAS; PASS00692; SRM; Solanum tuberosum; breeding; marker assisted selection; potato; proteomics; secretome; selected reaction monitoring