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

Abstract

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 transcriptsmore » 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 UBX-domain 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.« less

Authors:
ORCiD logo [1];  [2];  [3]; ORCiD logo [4];  [5]; ORCiD logo [4];  [3]
  1. Swedish Univ. of Agricultural Sciences, Alnarp (Sweden); Harvard Univ., Boston, MA (United States)
  2. Swedish Univ. of Agricultural Sciences, Alnarp, Uppsala (Sweden)
  3. Swedish Univ. of Agricultural Sciences, Alnarp (Sweden)
  4. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
  5. Univ. of Missouri-St. Louis, St. Louis, MO (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); Swedish Foundation for Environmental Strategic research (Mistra Biotech); Swedish Research Council Formas; National Institutes of Health (NIH); Knight Alzheimer’s Disease Research Center (ADRC)
OSTI Identifier:
1615993
Grant/Contract Number:  
AC05-00OR22725; RF1 AG053303; GM100364
Resource Type:
Accepted Manuscript
Journal Name:
BMC Plant Biology
Additional Journal Information:
Journal Volume: 20; Journal Issue: 1; Journal ID: ISSN 1471-2229
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Alexandersson, Erik, Kushwaha, Sandeep, Subedi, Aastha, Weighill, Deborah A., Climer, Sharlee, Jacobson, Daniel A., and Andreasson, Erik. Linking crop traits to transcriptome differences in a progeny population of tetraploid potato. United States: N. p., 2020. Web. doi:10.1186/s12870-020-2305-x.
Alexandersson, Erik, Kushwaha, Sandeep, Subedi, Aastha, Weighill, Deborah A., Climer, Sharlee, Jacobson, Daniel A., & Andreasson, Erik. Linking crop traits to transcriptome differences in a progeny population of tetraploid potato. United States. doi:https://doi.org/10.1186/s12870-020-2305-x
Alexandersson, Erik, Kushwaha, Sandeep, Subedi, Aastha, Weighill, Deborah A., Climer, Sharlee, Jacobson, Daniel A., and Andreasson, Erik. Wed . "Linking crop traits to transcriptome differences in a progeny population of tetraploid potato". United States. doi:https://doi.org/10.1186/s12870-020-2305-x. https://www.osti.gov/servlets/purl/1615993.
@article{osti_1615993,
title = {Linking crop traits to transcriptome differences in a progeny population of tetraploid potato},
author = {Alexandersson, Erik and Kushwaha, Sandeep and Subedi, Aastha and Weighill, Deborah A. and Climer, Sharlee and Jacobson, Daniel A. and Andreasson, Erik},
abstractNote = {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 UBX-domain 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.},
doi = {10.1186/s12870-020-2305-x},
journal = {BMC Plant Biology},
number = 1,
volume = 20,
place = {United States},
year = {2020},
month = {3}
}

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