期刊
BMC PLANT BIOLOGY
卷 20, 期 1, 页码 -出版社
BMC
DOI: 10.1186/s12870-020-2305-x
关键词
-
资金
- Swedish Foundation for Environmental Strategic research (Mistra Biotech)
- Swedish Research Council Formas [2015-442]
- Swedish farmer's foundation for agricultural research [0-15-20-557]
- Plant Breeding Platform, Swedish University of Agricultural Sciences
- Plant-Microbe Interfaces Scientific Focus Area in the Genomic Science Program
- Office of Biological and Environmental Research (BER) in the U.S. Department of Energy Office of Science
- Department of Energy, Laboratory Directed Research and Development at the Oak Ridge National Laboratory [8321]
- US DOE [DE-AC05-00OR22725]
- National Institutes of Health [RF1 AG053303, GM100364]
- Knight Alzheimer's Disease Research Center (ADRC) Pilot Grant
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.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据