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

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Fältnamn	Indikatorer	Metadata
000		04576naa a2200361 4500
001		oai:slubar.slu.se:105153
003		SwePub
008		240410s2020 \| \|\|\|\|\|\|\|\|\|\|\|000 \|\|eng\|
024	7	a https://res.slu.se/id/publ/1051532 URI
024	7	a https://doi.org/10.1186/s12870-020-2305-x2 DOI
040		a (SwePub)slu
041		a engb eng
042		9 SwePub
072	7	a ref2 swepub-contenttype
072	7	a art2 swepub-publicationtype
100	1	a Alexandersson, Eriku Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Växtskyddsbiologi,Department of Plant Protection Biology4 aut0 (Swepub:slu)47478
245	1 0	a Linking crop traits to transcriptome differences in a progeny population of tetraploid potato
264		c 2020-03-18
264	1	b Springer Science and Business Media LLC,c 2020
264	1	b BioMed Central,c 2024
520		a 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.
650	7	a LANTBRUKSVETENSKAPERx Lantbruksvetenskap, skogsbruk och fiskex Jordbruksvetenskap0 (SwePub)401012 hsv//swe
650	7	a AGRICULTURAL SCIENCESx Agriculture, Forestry and Fisheriesx Agricultural Science0 (SwePub)401012 hsv//eng
700	1	a Kushwaha, Sandeep Kumaru Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för växtförädling,Department of Plant Breeding,National Institute of Animal Biotechnology4 aut0 (Swepub:slu)104885
700	1	a Subedi, Aasthau Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Växtskyddsbiologi,Department of Plant Protection Biology4 aut
700	1	a Andreasson, Eriku Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Växtskyddsbiologi,Department of Plant Protection Biology4 aut0 (Swepub:slu)48766
710	2	a Sveriges lantbruksuniversitetb Växtskyddsbiologi4 org
710	2	a Sveriges lantbruksuniversitet
773	0	t BMC Plant Biologyd : Springer Science and Business Media LLCg 20q 20x 1471-2229
856	4	u https://pub.epsilon.slu.se/id/eprint/21936/contentsx primaryx Raw objectx freey FULLTEXT
856	4	u https://bmcplantbiol.biomedcentral.com/track/pdf/10.1186/s12870-020-2305-x
856	4 8	u https://res.slu.se/id/publ/105153
856	4 8	u https://doi.org/10.1186/s12870-020-2305-x

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Av författaren/redakt...: Alexandersson, E ...; Kushwaha, Sandee ...; Subedi, Aastha; Andreasson, Erik

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