Targeted Proteomics Approach for Precision Plant Breeding

Chawade, Aakash; Alexandersson, Erik; Bengtsson, Tommy; Andréasson, Erik; Levander, Fredrik

doi:10.1021/acs.jproteome.5b01061

Cited by 48 publications

(39 citation statements)

References 33 publications

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“…Certain novel techniques, e.g. genomic selection and site directed mutagenesis, hold a great promise to enhance the efficiency of potato breeding (Nicolia et al 2015) as well as analyses with RNAseq, proteomics, and effector screening (Ali et al 2014;Chawade et al 2016;Lenman et al 2016). Diploid and F 1 hybrid breeding in potato (for example www.solynta.com) also shows great potential to overcome some of the limitations of traditional crossing with tetraploid material and speed up the development of new hybrid cultivars, thus further increasing the potential economic output.…”

Section: Gross Return On Investments In Plant Breedingmentioning

confidence: 99%

Overview and Breeding Strategies of Table Potato Production in Sweden and the Fennoscandian Region

et al. 2016

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Recent reductions in the public commitment to potato breeding in Sweden, Norway and Finland call for an evaluation of the current situation regarding the commercial basis for, and structure of, potato breeding in these countries. We here review the extent of cultivation, processing and consumption of table potato in Sweden, as well as provide an overview of the potato breeding tools and programmes in the three countries. We then discuss various strategies to provide long-term stability and increase the impact of public potato breeding, based on the similar overall conditions for potato cultivation across the Fennoscandian region. The conclusions are twofold; first, an increased long-term funding of the public potato breeding programmes is necessary to maintain a minimum level of material, and second, a coordination of the breeding activities in the Fennoscandian region would be of great benefit to all involved stakeholders and allow an enhancement of the current national breeding programmes. In addition, we propose a minimum first field year population size for potato breeding.

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Section: Gross Return On Investments In Plant Breedingmentioning

confidence: 99%

Overview and Breeding Strategies of Table Potato Production in Sweden and the Fennoscandian Region

et al. 2016

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“…Low levels of the Rpi-ABPT gene transcripts were detected in some, but not all resistant lines, and this transcript did therefore not pass the threshold to be included in the association analyses (see Methods and Material; data not shown). The regulated genes also associates to the study of secreted peptides in this population, where all peptides used to predict resistance were less abundant in the resistant combination even without any disease [11]. This data also adds to the discussion about cost and trade-offs of resistance [16].…”

Section: Identified Trait-associated Transcriptsmentioning

confidence: 65%

“…In this progeny population, tuber blight resistance was not linked to foliar blight resistance [11,21], and there were only two transcripts, which correlated with P. infestans resistance in both leaves and tubers. The two transcripts, actin-depolymerizing factor 2 (DMG400027752) and FGFR1 oncogene partner (DMG400032551), are involved in cellular organisation were positively correlated to resistance.…”

Section: Identified Trait-associated Transcriptsmentioning

confidence: 97%

“…Field trials were conducted in Borgeby (55°45′5.8″ N 13°2′13.5″E), Sweden and phenotypes were recorded in 2013 and 2014. Field growth conditions and managements have previously been described in Chawade et al [11]. Table 1 contain information about number of plants or tubers that were investigated in each phenotype study, and under what conditions it was carried out.…”

Section: Plant Growth Phenotyping Sample Collection and Preparationmentioning

confidence: 99%

“…Late blight resistance (caused by Phytophthora infestans) has previously been studied in this population, and the receptor resistance (R-) gene behind the resistance has been cloned [10]. From a previous quantitative proteomics study of this population based on selective reaction monitoring (SRM), we concluded that even in the absence of the pathogen, the resistance gene was affecting the abundance of a number of selected secreted proteins [11]. Here, we found transcriptome effects of this R-gene again without any pathogens present.…”

Section: Introductionmentioning

confidence: 99%

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Linking crop traits to transcriptome differences in a progeny population of tetraploid potato

et al. 2020

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Background: Potato is the third most consumed crop in the world. Breeding for traits such as yield, product quality and pathogen resistance are main priorities. Identifying molecular signatures of these and other important traits is important in future breeding efforts. In this study, a progeny population from a cross between a breeding line, SW93-1015, and a cultivar, Désirée, was studied by trait analysis and RNA-seq in order to develop understanding of segregating traits at the molecular level and identify transcripts with expressional correlation to these traits. Transcript markers with predictive value for field performance applicable under controlled environments would be of great value for plant breeding.Results: A total of 34 progeny lines from SW93-1015 and Désirée were phenotyped for 17 different traits in a field in Nordic climate conditions and controlled climate settings. A master transcriptome was constructed with all 34 progeny lines and the parents through a de novo assembly of RNA-seq reads. Gene expression data obtained in a controlled environment from the 34 lines was correlated to traits by different similarity indices, including Pearson and Spearman, as well as DUO, which calculates the co-occurrence between high and low values for gene expression and trait. Our study linked transcripts to traits such as yield, growth rate, high laying tubers, late and tuber blight, tuber greening and early flowering. We found several transcripts associated to late blight resistance and transcripts encoding receptors were associated to Dickeya solani susceptibility. Transcript levels of a UBXdomain protein was negatively associated to yield and a GLABRA2 expression modulator was negatively associated to growth rate. Conclusion: In our study, we identify 100's of transcripts, putatively linked based on expression with 17 traits of potato, representing both well-known and novel associations. This approach can be used to link the transcriptome to traits. We explore the possibility of associating the level of transcript expression from controlled, optimal environments to traits in a progeny population with different methods introducing the application of DUO for the first time on transcriptome data. We verify the expression pattern for five of the putative transcript markers in another progeny population.

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