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. 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. 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.

中文翻译：

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将农作物性状与四倍体马铃薯后代中的转录组差异联系起来

马铃薯是世界第三大消费作物。诸如产量，产品质量和病原体抗性等特性的育种是首要任务。识别这些特征和其他重要特征的分子标记对将来的育种工作很重要。在这项研究中，通过性状分析和RNA-seq研究了繁殖系SW93-1015和栽培品种Désirée之间的杂交后代，以便在分子水平上理解分离性状并鉴定转录本。这些特征的表达相关性。具有可控性的田间表现预测价值的转录标记对于植物育种具有重要价值。在北欧气候条件和受控气候条件下，针对一个田地中的17种不同性状，对来自SW93-1015和Désirée的总共34个子代表型进行了表型分析。通过从头组装RNA-seq读物，用所有34个后代系和亲本构建了一个主转录组。在受控环境中从34个品系获得的基因表达数据通过不同的相似性指标与性状相关，包括Pearson和Spearman以及DUO，DUO计算基因表达和性状的高值和低值之间的共现。我们的研究将转录本与诸如产量，生长速率，高产块茎，晚疫病和块茎枯萎，块茎绿化和早开花等性状相关联。我们发现了几个与晚疫病抗性有关的转录本，以及编码受体的转录本与Dickeya solani的易感性有关。UBX结构域蛋白的转录水平与产量负相关，而GLABRA2表达调节剂与生长速度负相关。在我们的研究中，我们确定了100个转录本，这些转录本基于表达与马铃薯的17个性状的表达进行了推测性关联，分别代表着著名的和新颖的关联。该方法可用于将转录组与性状联系起来。我们探索了将转录本表达水平从可控的最佳环境与子代种群中的性状相关联的可能性，并通过不同的方法首次将DUO应用于转录组数据上。