Data mining nitrogen-responsive gene expression for source-sink relations and indicators of n status in potato


Parenteau, M.T., Gu, H., Zebarth, B.J., Cambouris, A.N., Lafond, J., Nelson, A., Nyiraneza, J., Davidson, C., Lagüe, M., Galvez, J.H., Strömvik, M.V., Tai, H.H. (2020). Data mining nitrogen-responsive gene expression for source-sink relations and indicators of n status in potato. Agronomy, [online] 10(10 October),

Plain language summary

Potato is dependent on N fertilizer to reach profitable yields. However, overapplication of fertilizer leads to environmental pollution. One way to reduce fertilizer overuse is to only apply fertilizer when the plant needs it. In this way, the plant will take up the fertilizer rather than leaving it in the soil resulting run-offs to groundwater. The question is how to determine when a plant is need of nitrogen fertilizer. The study examines application of gene expression to monitoring the need for fertilizer by the potato plant or the crop N status. Gene expression happens when a gene is put into action. Genes in leaves put into action by nitrogen fertilizer application were identified. These genes were then associated with yield. From this study a set of genes whose expression predicted yield was identified. These genes had biological functions that provided insight on the role of tuberization and amino acid biosynthesis in leaves that affects the amount of tuber production. These genes also have potential use in monitoring crop N status.


Potato tuber yields depend on nitrogen (N) supply, which affects source-sink relations. Transcriptome sequencing of the foliar source using a single field trial identified gene expression responsive to 180 kg N ha-1. The expression of N-responsive genes was further analyzed in the next stage using a NanoString nCounter over an expanded number of foliar samples from seven field trials with varying N rates, sites, and cultivars. Least absolute shrinkage and selection operator (LASSO) regression models of gene expression predictive of yield, total plant N uptake, and tuber-specific gravity (proxy for dry matter) were built. Genes in the LASSO model for yield were associated with source-sink partitioning. A key gene regulating tuberization and senescence, StSP6A Flowering locus T, was found in the LASSO model predicting tuber yield, but not the other models. An aminotransferase involved in photorespiratory N assimilation and amino acid biosynthesis was found in all LASSO models. Other genes functioning in amino acid biosynthesis and integration of sulfur (S) and N metabolism were also found in the yield prediction model. The study provides insights on N responses in foliage of potato plants that affect source-sink partitioning. Additionally, N-responsive genes predictive of yield are candidate indicators of N status.