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Targeted Proteomics Approach for Precision Plant Breeding

Chawade, Aakash LU ; Alexandersson, Erik; Bengtsson, Therese; Andreasson, Erik and Levander, Fredrik LU (2016) In Journal of Proteome Research 15(2). p.638-642
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... (More)
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. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Proteome Research
volume
15
issue
2
pages
9 pages
publisher
The American Chemical Society
external identifiers
  • scopus:84957677420
  • wos:000369771700027
ISSN
1535-3893
DOI
10.1021/acs.jproteome.5b01061
language
English
LU publication?
yes
id
93a9632f-c25e-43cc-81c9-d1752236543c
date added to LUP
2017-03-14 14:02:58
date last changed
2017-09-18 11:39:20
@article{93a9632f-c25e-43cc-81c9-d1752236543c,
  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.},
  author       = {Chawade, Aakash and Alexandersson, Erik and Bengtsson, Therese and Andreasson, Erik and Levander, Fredrik},
  issn         = {1535-3893},
  language     = {eng},
  month        = {02},
  number       = {2},
  pages        = {638--642},
  publisher    = {The American Chemical Society},
  series       = {Journal of Proteome Research},
  title        = {Targeted Proteomics Approach for Precision Plant Breeding},
  url          = {http://dx.doi.org/10.1021/acs.jproteome.5b01061},
  volume       = {15},
  year         = {2016},
}