Transcriptome analysis of potato shoots, roots and stolons under nitrogen stress

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.

Transcriptome analysis reveals Nitrogen deficiency induced alterations in leaf and root of three cultivars of potato (Solanum tuberosum L.)

“…In these three varieties of our results, the different biochemical and gene expression profiles in response to nitrogen deficiency were consistent with previous reports [ 30 – 32 ]. Jozefowicz et al [ 30 ] found that there are proteomic differences between two potato cultivars in response to N deficiency.…”

“…These DEGs were differentially expressed among cultivars, the difference in promoter or copy number might be the two key reasons for the differential response and regulation of in three cultivars of potato. Tiwari et al reported that most of the StNRT family members were down-regulated in roots under low N conditions [ 32 ], which was consisted with our results. The NRTs , NR and NiR are crucial for the acquiring N and its conversion to ammonia ( Fig 8 ) [ 40 ].…”

“…Interestingly, Jozefowicz et al found that the GDH was up-regulated in both the N-deficiency tolerant and sensitive potato cultivars under N-deficiency conditions, while GS was up-regulated only in the N tolerant potato cultivar by N deficiency [ 30 ]. Tiwari’s report concluded that many potential genes play very crucial roles in N stress tolerance [ 32 ]. The difference is that this study used three potato varieties with different resistance to N deficiency for transcriptome studies.…”

Prospects of Improving Nitrogen Use Efficiency in Potato: Lessons From Transgenics to Genome Editing Strategies in Plants

“…Recently, we have reviewed application of integrated genomics, physiology and breeding approaches for improving NUE (Tiwari et al, 2018 ) and traits phenotyping under aeroponic in potato (Tiwari et al, 2020d ). Further, recent studies provide information about the genes and miRNAs associated with N stress in potato (Tiwari et al, 2020a , b , c ; Zhang et al, 2020 ). Potato is highly amenable to tissue culture and therefore transgenics protocols are well established.…”

“…We summarize here potential candidate genes for improving NUE in potato based on the recent research (Tiwari et al, 2020a , b , c ; Zhang et al, 2020 ). Our studies indicate that in potato roots, high-affinity nitrate transporters are the key candidate genes for manipulation in N uptake and transport.…”