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

Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha; Weighill, Deborah A.; Climer, Sharlee; Jacobson, Daniel A.; Andreasson, Erik

doi:10.1186/s12870-020-2305-x

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

Journal Article · 18 March 2020 · BMC Plant Biology

DOI: https://doi.org/10.1186/s12870-020-2305-x · OSTI ID:1615993

^[1]; Kushwaha, Sandeep ^[2]; Subedi, Aastha ^[3];

^[4]; Climer, Sharlee ^[5];

^[4]; Andreasson, Erik ^[3]

Swedish Univ. of Agricultural Sciences, Alnarp (Sweden); Harvard Univ., Boston, MA (United States)
Swedish Univ. of Agricultural Sciences, Alnarp, Uppsala (Sweden)
Swedish Univ. of Agricultural Sciences, Alnarp (Sweden)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
Univ. of Missouri-St. Louis, St. Louis, MO (United States)

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.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); Swedish Foundation for Environmental Strategic research (Mistra Biotech); Swedish Research Council Formas; National Institutes of Health (NIH); Knight Alzheimer’s Disease Research Center (ADRC)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1615993

Journal Information:: BMC Plant Biology, Journal Name: BMC Plant Biology Journal Issue: 1 Vol. 20; ISSN 1471-2229

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44 Massa, Alicia N.; Childs, Kevin L.; Lin, Haining PLoS ONE, Vol. 6, Issue 10 https://doi.org/10.1371/journal.pone.0026801	journal	October 2011
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Construction of Reference Chromosome-Scale Pseudomolecules for Potato: Integrating the Potato Genome with Genetic and Physical Maps Sharma, Sanjeev Kumar; Bolser, Daniel; de Boer, Jan G3: Genes\|Genomes\|Genetics, Vol. 3, Issue 11 https://doi.org/10.1534/g3.113.007153	journal	September 2013
Comparison of Maize ( Zea mays L.) F ₁ -Hybrid and Parental Inbred Line Primary Root Transcriptomes Suggests Organ-Specific Patterns of Nonadditive Gene Expression and Conserved Expression Trends Hoecker, Nadine; Keller, Barbara; Muthreich, Nils Genetics, Vol. 179, Issue 3 https://doi.org/10.1534/genetics.108.088278	journal	June 2008
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Additional file 10 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999037 The current record is supplemented by this text	text	January 2020
Additional file 10 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999037.v1 The current record is supplemented by this text	text	January 2020
Additional file 11 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999043 The current record is supplemented by this dataset	dataset	January 2020
Additional file 11 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999043.v1 The current record is supplemented by this dataset	dataset	January 2020
Additional file 1 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999049 The current record is supplemented by this dataset	dataset	January 2020
Additional file 1 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999049.v1 The current record is supplemented by this dataset	dataset	January 2020
Additional file 2 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999052 The current record is supplemented by this dataset	dataset	January 2020
Additional file 2 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999052.v1 The current record is supplemented by this dataset	dataset	January 2020
Additional file 3 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999058 The current record is supplemented by this dataset	dataset	January 2020
Additional file 3 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999058.v1 The current record is supplemented by this dataset	dataset	January 2020
Additional file 4 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999064 The current record is supplemented by this text	text	January 2020
Additional file 4 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999064.v1 The current record is supplemented by this text	text	January 2020
Additional file 5 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999073 The current record is supplemented by this dataset	dataset	January 2020
Additional file 5 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999073.v1 The current record is supplemented by this dataset	dataset	January 2020
Additional file 6 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999085 The current record is supplemented by this dataset	dataset	January 2020
Additional file 6 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999085.v1 The current record is supplemented by this dataset	dataset	January 2020
Additional file 7 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999094 The current record is supplemented by this image	image	January 2020
Additional file 7 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999094.v1 The current record is supplemented by this image	image	January 2020
Additional file 8 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999100 The current record is supplemented by this image	image	January 2020
Additional file 8 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999100.v1 The current record is supplemented by this image	image	January 2020
Additional file 9 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999109 The current record is supplemented by this dataset	dataset	January 2020
Additional file 9 of Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.11999109.v1 The current record is supplemented by this dataset	dataset	January 2020
Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.c.4898421 The current record is supplemented by this collection	collection	January 2020
Linking crop traits to transcriptome differences in a progeny population of tetraploid potato Alexandersson, Erik; Kushwaha, Sandeep; Subedi, Aastha https://doi.org/10.6084/m9.figshare.c.4898421.v1 The current record is supplemented by this collection	collection	January 2020

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

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