Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Sundsvägen 10, Alnarp, Sweden.
Present address: Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
BMC Plant Biol. 2020 Mar 18;20(1):120. doi: 10.1186/s12870-020-2305-x.
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.
马铃薯是世界上第三大消费作物。产量、产品质量和抗病原体等特性的培育是主要重点。确定这些特性和其他重要特性的分子特征对于未来的培育工作非常重要。在这项研究中，通过性状分析和 RNA-seq 研究了来自一个杂交品种 SW93-1015 和一个品种 Desiree 的后代群体，以了解分子水平上分离性状的情况，并鉴定与这些性状表达相关的转录本。在受控环境下具有预测田间表现价值的转录标记对于植物育种将具有重要价值。
在北欧气候条件下的田间和受控气候环境中，对来自 SW93-1015 和 Desiree 的 34 个后代系进行了 17 种不同性状的表型分析。通过对 RNA-seq 读取进行从头组装，构建了一个包含所有 34 个后代系和父母的主转录组。从 34 个系在受控环境中获得的基因表达数据通过不同的相似性指数（包括 Pearson 和 Spearman 以及计算基因表达和性状之间高值和低值共同出现的 DUO）与性状相关联。我们的研究将转录本与产量、生长速度、高产块茎、晚疫病和块茎枯萎病、块茎变绿和早期开花等性状联系起来。我们发现了一些与晚疫病抗性相关的转录本和编码受体的转录本与 Dickeya solani 易感性相关。UBX 结构域蛋白的转录本水平与产量呈负相关，GLABRA2 表达调节剂与生长速度呈负相关。
在我们的研究中，我们根据表达将 17 个马铃薯性状与 100 多个转录本联系起来，代表了已知和新的关联。这种方法可用于将转录组与性状联系起来。我们探讨了通过不同方法将来自受控、最佳环境的转录本表达水平与具有不同方法的后代群体中的性状联系起来的可能性，首次在转录组数据上应用了 DUO。我们在另一个后代群体中验证了五个假定转录本标记的表达模式。
