title: Gene expression profiles predictive of cold-induced sweetening in potato.
abstract: Cold storage (2-4 °C) used in potato production to suppress diseases and sprouting during storage can result in cold-induced sweetening (CIS), where reducing sugars accumulate in tuber tissue leading to undesirable browning, production of bitter flavors, and increased levels of acrylamide with frying. Potato exhibits genetic and environmental variation in resistance to CIS. The current study profiles gene expression in post-harvest tubers before cold storage using transcriptome sequencing and identifies genes whose expression is predictive for CIS. A distance matrix for potato clones based on glucose levels after cold storage was constructed and compared to distance matrices constructed using RNA-seq gene expression data. Congruence between glucose and gene expression distance matrices was tested for each gene. Correlation between glucose and gene expression was also tested. Seventy-three genes were found that had significant p values in the congruence and correlation tests. Twelve genes from the list of 73 genes also had a high correlation between glucose and gene expression as measured by Nanostring nCounter. The gene annotations indicated functions in protein degradation, nematode resistance, auxin transport, and gibberellin response. These 12 genes were used to build models for prediction of CIS using multiple linear regression. Nine linear models were constructed that used different combinations of the 12 genes. An F-box protein, cellulose synthase, and a putative Lax auxin transporter gene were most frequently used. The findings of this study demonstrate the utility of gene expression profiles in predictive diagnostics for severity of CIS.
authors.affiliation: Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, 850 Lincoln Rd., Fredericton, N. B, E3B 4Z7, Canada. Jonathan.neilson@agr.gc.ca.
authors.forename: Jonathan
authors.identifier: http://orcid.org/0000-0002-0664-120X
authors.initials: J
authors.lastname: Neilson
authors.affiliation: Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, 850 Lincoln Rd., Fredericton, N. B, E3B 4Z7, Canada.
authors.forename: M
authors.initials: M
authors.lastname: Lagüe
authors.affiliation: The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch, New Zealand.
authors.forename: S
authors.initials: S
authors.lastname: Thomson
authors.affiliation: Station de Recherche du Comite Nord, Sipre-Responsable Scientifique Creation Varietale, 18 La Chaussée, 76110, Bretteville du Grand Caux, France.
authors.forename: F
authors.initials: F
authors.lastname: Aurousseau
authors.affiliation: Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, 850 Lincoln Rd., Fredericton, N. B, E3B 4Z7, Canada.
authors.forename: A M
authors.initials: AM
authors.lastname: Murphy
authors.affiliation: Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, 850 Lincoln Rd., Fredericton, N. B, E3B 4Z7, Canada.
authors.forename: B
authors.initials: B
authors.lastname: Bizimungu
authors.affiliation: Station de Recherche du Comite Nord, Sipre-Responsable Scientifique Creation Varietale, 18 La Chaussée, 76110, Bretteville du Grand Caux, France.
authors.forename: V
authors.initials: V
authors.lastname: Deveaux
authors.affiliation: Station de Recherche du Comite Nord, Sipre-Responsable Scientifique Creation Varietale, 18 La Chaussée, 76110, Bretteville du Grand Caux, France.
authors.forename: Y
authors.initials: Y
authors.lastname: Bègue
authors.affiliation: The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch, New Zealand.
authors.forename: J M E
authors.initials: JME
authors.lastname: Jacobs
authors.affiliation: Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, 850 Lincoln Rd., Fredericton, N. B, E3B 4Z7, Canada.
authors.forename: H H
authors.initials: HH
authors.lastname: Tai
mesh_terms: D058639:Cold-Shock Response; D018506:Gene Expression Regulation, Plant; D005947:Glucose / Q000235:genetics / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D011198:Solanum tuberosum / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism
chemical_list: D010940:Plant Proteins; D005947:Glucose
keywords: Biomarker; Cold-induced sweetening; Potato; Tuber