Abstract
Potato crop requires high dose of nitrogen (N) to produce high tuber yield. Excessive application of N causes environmental pollution and increases cost of production. Hence, knowledge about genes and regulatory elements is essential to strengthen research on N metabolism in this crop. In this study, we analysed transcriptomes (RNA-seq) in potato tissues (shoot, root and stolon) collected from plants grown in aeroponic culture under controlled conditions with varied N supplies i.e. low N (0.2 milli molar N) and high N (4 milli molar N). High quality data ranging between 3.25 to 4.93 Gb per sample were generated using Illumina NextSeq500 that resulted in 83.60–86.50% mapping of the reads to the reference potato genome. Differentially expressed genes (DEGs) were observed in the tissues based on statistically significance (p ≤ 0.05) and up-regulation with ≥ 2 log2 fold change (FC) and down-regulation with ≤ −2 log2 FC values. In shoots, of total 19730 DEGs, 761 up-regulated and 280 down-regulated significant DEGs were identified. Of total 20736 DEGs in roots, 572 (up-regulated) and 292 (down-regulated) were significant DEGs. In stolons, of total 21494 DEG, 688 and 230 DEGs were significantly up-regulated and down-regulated, respectively. Venn diagram analysis showed tissue specific and common genes. The DEGs were functionally assigned with the GO terms, in which molecular function domain was predominant in all the tissues. Further, DEGs were classified into 24 KEGG pathways, in which 5385, 5572 and 5594 DEGs were annotated in shoots, roots and stolons, respectively. The RT-qPCR analysis validated gene expression of RNA-seq data for selected genes. We identified a few potential DEGs responsive to N deficiency in potato such as glutaredoxin, Myb-like DNA-binding protein, WRKY transcription factor 16 and FLOWERING LOCUS T in shoots; high-affinity nitrate transporter, protein phosphatase-2c, glutaredoxin family protein, malate synthase, CLE7, 2-oxoglutarate-dependent dioxygenase and transcription factor in roots; and glucose-6-phosphate/phosphate translocator 2, BTB/POZ domain-containing protein, F-box family protein and aquaporin TIP1;3 in stolons, and many genes of unknown function. Our study highlights that these potential genes play very crucial roles in N stress tolerance, which could be useful in augmenting research on N metabolism in potato.
Highlights
Potato crop requires high dose of nitrogen (N) to produce high tuber yield
Arabidopsis thaliana, and model crops rice and maize where rich source of genomics-based information is available on N metabolism research[3,7], knowledge about potential genes involved in N deficiency and sufficiency in potato is very limited
The key enzymes/genes involved in N metabolism pathways are nitrate transporter (NRT), ammonium transporter, nitrate reductase, nitrite reductase, glutamine synthetase, glutamate synthase, glutamate dehydrogenase, asparagine synthetase, aspartate aminotransferase, alanine aminotransferase; and many other genes/regulatory molecules alter N pathways and determine gene expression as well as phenotypes[3]
Summary
Potato crop requires high dose of nitrogen (N) to produce high tuber yield. Excessive application of N causes environmental pollution and increases cost of production. Arabidopsis thaliana, and model crops rice and maize where rich source of genomics-based information is available on N metabolism research[3,7], knowledge about potential genes involved in N deficiency and sufficiency in potato is very limited. RNA-sequencing technology has been proven to discover numerous genes/ factors involved in N gene networks in several crops for multiple traits such as role of N starvation in rice[8,9]; identifying nitrogen deficiency genes in cucumber[10]; effect of N limitation condition in maize[7], N use efficiency genes in Brassica juncea[11], N responsive regulatory elements in potato[12], N utilization genes in tea[13] and so on. The aim of this study was to discover genes/regulatory elements associated with N deficiency (low N) versus sufficient N (high N, control) in potato plants grown in aeroponic culture under controlled conditions by RNA-sequence-based transcriptomes analysis. Our results usher an insight on enrichment of genes in potato under N deficiency, which could be utilized for N metabolism related research in potato
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
