Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India.
Sci Rep. 2020 Jan 24;10(1):1152. doi: 10.1038/s41598-020-58167-4.
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 log fold change (FC) and down-regulation with ≤ -2 log 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.
马铃薯作物需要大量的氮（N）才能产生高产的块茎。过量施用 N 会导致环境污染并增加生产成本。因此，了解基因和调控元件对于加强对这种作物氮代谢的研究至关重要。在这项研究中，我们分析了在受控条件下生长的马铃薯组织（茎、根和匍匐茎）的转录组（RNA-seq），这些组织是在不同的氮供应下即低氮（0.2 毫摩尔 N）和高氮（4 毫摩尔 N）条件下在气培培养中收集的。使用 Illumina NextSeq500 生成了高质量的数据，每个样本的范围在 3.25 到 4.93Gb 之间，这导致了 83.60-86.50%的读取与参考马铃薯基因组的映射。基于统计学意义（p≤0.05）和上调≥2 倍对数倍变化（FC）和下调≤-2 倍 FC 值，在组织中观察到差异表达基因（DEGs）。在茎中，总共有 19730 个 DEGs，其中 761 个上调和 280 个下调的显著 DEGs被鉴定出来。在根中，总共有 20736 个 DEGs，其中 572 个（上调）和 292 个（下调）是显著的 DEGs。在匍匐茎中，总共有 21494 个 DEGs，其中 688 个和 230 个分别上调和下调。Venn 图分析显示了组织特异性和共同基因。通过 GO 术语对 DEGs 进行了功能分配，其中分子功能域在所有组织中都占主导地位。此外，DEGs 被分为 24 个 KEGG 途径，其中在茎、根和匍匐茎中分别注释了 5385、5572 和 5594 个 DEGs。RT-qPCR 分析验证了 RNA-seq 数据中选定基因的表达。我们鉴定了一些潜在的 DEGs，它们对马铃薯中的氮缺乏有反应，如在茎中：谷氧还蛋白、Myb 样 DNA 结合蛋白、WRKY 转录因子 16 和开花素 T；在根中：高亲和力硝酸盐转运蛋白、蛋白磷酸酶 2c、谷氧还蛋白家族蛋白、苹果酸合酶、CLE7、2-酮戊二酸依赖性加双氧酶和转录因子；在匍匐茎中：葡萄糖-6-磷酸/磷酸转运蛋白 2、BTB/POZ 结构域蛋白、F-box 家族蛋白和水通道蛋白 TIP1;3，以及许多功能未知的基因。我们的研究表明，这些潜在的基因在氮胁迫耐受中起着非常关键的作用，这可能有助于加强对马铃薯氮代谢的研究。
