Targeted Proteomics Approach for Precision Plant Breeding

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Targeted Proteomics Approach for Precision Plant Breeding. / Chawade, Aakash; Alexandersson, Erik; Bengtsson, Therese; Andreasson, Erik; Levander, Fredrik.

In: Journal of Proteome Research, Vol. 15, No. 2, 05.02.2016, p. 638-642.

Research output: Contribution to journalArticle

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Chawade, A, Alexandersson, E, Bengtsson, T, Andreasson, E & Levander, F 2016, 'Targeted Proteomics Approach for Precision Plant Breeding', Journal of Proteome Research, vol. 15, no. 2, pp. 638-642. https://doi.org/10.1021/acs.jproteome.5b01061

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Chawade, Aakash ; Alexandersson, Erik ; Bengtsson, Therese ; Andreasson, Erik ; Levander, Fredrik. / Targeted Proteomics Approach for Precision Plant Breeding. In: Journal of Proteome Research. 2016 ; Vol. 15, No. 2. pp. 638-642.

RIS

TY - JOUR

T1 - Targeted Proteomics Approach for Precision Plant Breeding

AU - Chawade, Aakash

AU - Alexandersson, Erik

AU - Bengtsson, Therese

AU - Andreasson, Erik

AU - Levander, Fredrik

PY - 2016/2/5

Y1 - 2016/2/5

N2 - 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.

AB - 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.

U2 - 10.1021/acs.jproteome.5b01061

DO - 10.1021/acs.jproteome.5b01061

M3 - Article

VL - 15

SP - 638

EP - 642

JO - Journal of Proteome Research

T2 - Journal of Proteome Research

JF - Journal of Proteome Research

SN - 1535-3893

IS - 2

ER -