Abstract
BackgroundPotato 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.ResultsA 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.ConclusionIn 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.
Highlights
Potato is the third most consumed crop in the world
Phenotyping correlations in the progeny population We phenotyped 34 lines for 17 plant traits in three trait categories (Table 1), namely Biotic Stress: P. infestans resistance in leaves (PIR), tuber blight caused by P. infestans (TBS), Dickeya response (DR, suseptibility), Lesions after Alternaria infection in leaves (LAI), Alternaria infection volume (AIV) in tubers, degree of Hypersensitive response (HR)-like lesions (HRL); Tuber: Number of tubers (NoT), Tuber greening in field (TGF), Visible tubers close to soil surface (VT), Yield per plant 2013 (YP13), Yield per plant 2014 (YP14); Leaf/ Shoot/Flower: Senescence level in the late season (SLS), Growth rate (GR), Height (H), Level of necrotic leaves in the late season (NLL), Leaf texture (LT), Flowering time (FT)
The progeny lines show clear difference in scoring values for most traits and scoring values of the parents are often different from the average values of the traits in the segregating progeny lines
Summary
Potato is the third most consumed crop in the world. Breeding for traits such as yield, product quality and pathogen resistance are main priorities. Next-generation sequencing (NGS) offers new possibilities to do high throughput transcriptome profiling of plant progeny populations and offers new ways to study transcript expression associated to phenotypic traits. Linking transcripts to phenotypes can be a way to develop new transcript markers and transcript profiles, socalled molecular signatures, associated to a certain trait. This has been shown in other crops where, e.g., transcripts important in leaf development were identified in a maize mapping population [3, 4]. A number of transcript and metabolite markers associated to the complex trait drought tolerance in potato was described [5]. These putative transcript markers provide the first step in revealing genes involved in complex traits of polygenic origin, which could possibly overcome part of the challenge in analysing polyploid species
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