Combining gene expression, metabolomics, and conventional breeding to increase the nitrogen use efficiency of Burley tobacco
High rates of nitrogen fertilization are required currently for cultivation of Burley tobacco to achieve the desired leaf yields and qualities. However, Maryland type tobaccos are grown using a nitrogen fertilization rate that is ~60-70 % lower than that used typically for Burley. Increased nitrogen use efficiency (NUE) can help increase productivity, reduce environmental impact and potentially limit undesired nitrogen containing constituents. The objective of this study was to understand the NUE potential of Maryland tobacco by identifying possible gene targets that differentiate nitrogen utilization of Maryland tobacco from Burley tobacco. Maryland and Burley tobacco plants were grown in the greenhouse using either 100 ppm nitrogen or 25 ppm nitrogen and were fed continuously in an ebb and flow system. Gene expression was analyzed at a whole genome level by RNA-seq. Metabolite profiling was performed using multiple approaches. Twenty-seven diagnostic metabolites were found that discriminate between the Maryland and Burley phenotypes. Correlation analysis was used to determine which genes had expression levels that correlated with 27 metabolites. Whole genome SNP analysis of breeding populations coupled with the gene expression correlations revealed genomic loci with concentrated numbers of differentially expressed genes. This study not only revealed possible gene targets that could be modified to improve nitrogen utilization in Burley tobacco, but also identified genetic loci that could be used for selecting nitrogen use efficient lines from breeding programs in the future.