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

Alexandersson, Erik and Kushwaha, Sandeep Kumar and Subedi, Aastha and Weighill, Deborah and Climer, Sharlee and Jacobson, Daniel and Andreasson, Erik (2020). Linking crop traits to transcriptome differences in a progeny population of tetraploid potato. BMC Plant Biology. 20 , 120
[Research article]

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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, Desiree, 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 Desiree 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.

Authors/Creators:Alexandersson, Erik and Kushwaha, Sandeep Kumar and Subedi, Aastha and Weighill, Deborah and Climer, Sharlee and Jacobson, Daniel and Andreasson, Erik
Title:Linking crop traits to transcriptome differences in a progeny population of tetraploid potato
Series Name/Journal:BMC Plant Biology
Year of publishing :2020
Volume:20
Article number:120
Number of Pages:14
Publisher:BMC
ISSN:1471-2229
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 401 Agricultural, Forestry and Fisheries > Agricultural Science
URN:NBN:urn:nbn:se:slu:epsilon-p-105153
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-105153
Additional ID:
Type of IDID
DOI10.1186/s12870-020-2305-x
Web of Science (WoS)000521248900001
ID Code:21936
Faculty:LTV - Fakulteten för landskapsarkitektur, trädgårds- och växtproduktionsvetenskap
Department:(LTJ, LTV) > Department of Plant Protection Biology
(LTJ, LTV) > Department of Plant Breeding (from 130101)
Deposited By: SLUpub Connector
Deposited On:03 Feb 2021 02:43
Metadata Last Modified:03 Feb 2021 06:01

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