Explore the vast range of titles available.

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 2 fold change (FC) and down-regulation with ≤ −2 log 2 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.

CRISPR/Cas9 has been successfully deployed to edit N transporter gene to enhance NUE by introgression of NRT1.1B-indica allele into japonica rice (Li et al.,2018). [...]CRISPR/Cas9 has been mostly applied to mutate negative regulators, instead of overexpression of positive regulators. [...]knowledge about genes and regulatory elements such as TFs and microRNAs (miRNAs) are important to improve NUE. [...]the underlying molecular and physiological mechanisms and genetic factors remain elusive in potato for root system architecture, carbon-nitrogen economy and N metabolism (uptake, transport, utilization and remobilization). [...]genes like ferric chelate reductase, protein phosphatase 2 C, glutaredoxin, GDSL esterase/lipase, cytochrome P450 hydroxylase and TFs also appear important in roots. [...]carbohydrate metabolism genes like glucose-6-phosphate/phosphate translocator 2 and glucose-1-phosphate adenylyltransferase, and amino acid synthesis genes such as 2-oxoglutaratedependent dioxygenase, malate synthase and branched-chainamino-acid aminotransferase play crucial roles in potato tuberization.

Nitrogen is an important nutrient for plant growth and tuber quality of potato. Since potato crop requires high dose of N, improving nitrogen use efficiency (NUE) of plant is an inevitable approach to minimize N fertilization. The aim of this study was to identify and characterize microRNAs (miRNAs) by small RNA sequencing in potato plants grown in aeroponic under two contrasting N (high and low) regimes. A total of 119 conserved miRNAs belonging to 41 miRNAs families, and 1002 putative novel miRNAs were identified. From total, 52 and 54 conserved miRNAs, and 404 and 628 putative novel miRNAs were differentially expressed in roots and shoots, respectively under low N stress. Of total 34,135 predicted targets, the gene ontology (GO) analysis indicated that maximum targets belong to biological process followed by molecular function and cellular component. Eexpression levels of the selected miRNAs and targets were validated by real time-quantitative polymerase chain reaction (RT-qPCR) analysis. Two predicted targets of potential miRNAs (miR397 and miR398) were validated by 5' RLM-RACE (RNA ligase mediated rapid amplification of cDNA ends). In general, predicted targets are associated with stress-related, kinase, transporters and transcription factors such as universal stress protein, heat shock protein, salt-tolerance protein, calmodulin binding protein, serine-threonine protein kinsae, Cdk10/11- cyclin dependent kinase, amino acid transporter, nitrate transporter, sugar transporter, transcription factor, F-box family protein, and zinc finger protein etc. Our study highlights that miR397 and miR398 play crucial role in potato during low N stress management. Moreover, study provides insights to modulate miRNAs and their predicted targets to develop N-use efficient potato using transgenic/genome-editing tools in future.

Nitrogen (N) is a crucial nutrient for the growth and development of potatoes. However, excessive use of nitrogen fertilizers can have detrimental effects on human health, aquatic ecosystems, and the environment. Therefore, understanding the genes involved in nitrogen metabolism is essential for developing future strategies to improve nitrogen use efficiency (NUE) in plants. This study aimed to identify genes associated with high tuber yield in two contrasting potato varieties Kufri Jyoti (N inefficient) and Kufri Pukhraj (N efficient) grown under low and high nitrogen regimes using an aeroponics system. Both varieties were grown in aeroponics with two nitrogen doses (low N: 0.5 mM N; high N: 5 mM N) using a completely randomized design (CRD) with three replications over two years. The phenotypic results confirmed that Kufri Pukhraj was more nitrogen use efficient compared to Kufri Jyoti, particularly under low nitrogen conditions. Additionally, transcriptome analysis produced high-quality data ( ≥ Q20), ranging from 4.35 to 5.46 Gb per sample. Statistically significant genes ( p ≤  0.05) were identified based on the reference potato genome. Differentially expressed genes (DEGs) were categorized as either up-regulated or down-regulated in leaf and tuber tissues. Transcriptome profiling of both tuber and leaf tissues revealed genes associated with traits contributing to high tuber yield under both high and low nitrogen conditions. The DEGs were further characterized through gene ontology (GO) annotation and KEGG pathway analysis. Selected genes were validated through real-time quantitative polymerase chain reaction (RT-qPCR) analysis. In summary, several genes were identified as being involved in high tuber yield component traits in potatoes under different nitrogen conditions. These included glutaredoxin, transcription factors (BTB/POZ, AP2/ERF, and MYB), nitrate transporter, aquaporin TIP1;3, glutamine synthetase, aminotransferase, GDSL esterase/lipase, sucrose synthase, UDP-glycosyltransferases, osmotin, xyloglucan endotransglucosylase/hydrolase, and laccases. Additionally, we identified overexpressed genes including cysteine protease inhibitor 1, miraculin, sterol desaturase, and pectinesterase in Kufri Pukhraj under low N stress. Our study highlights these genes’ roles in enhancing tuber yield in potatoes cultivated under both high and low nitrogen in aeroponics.

Late blight is a serious disease of potato worldwide. Our study aimed to unveil genes involved in late blight resistance in potato by RNA-seq analysis after artificial inoculation under controlled conditions. In this study, two potato somatic hybrids (P7 and Crd6) and three varieties such as Kufri Girdhari, Kufri Jyoti and Kufri Bahar (control) were used. Transcriptiome analysis revealed statistically significant ( p  < 0.05) differentially expressed genes (DEGs), which were analysed into up-regulated and down-regulated genes. Further, DEGs were functionally characterized by the Gene Ontology annotations and the Kyoto Encyclopedia of Genes and Genomes pathways. Overall, some of the up-regulated genes in resistant genotypes were disease resistance proteins such as CC-NBS-LRR resistance protein, ankyrin repeat family protein, cytochrome P450, leucine-rich repeat family protein/protein kinase family, and MYB transcription factor. Sequence diversity analysis based on 38 peptide sequences representing 18 genes showed distinct variation and the presence of three motifs in 15 amino acid sequences. Selected genes were also validated by real-time quantitative polymerase chain reaction analysis. Interestingly, gene expression markers were developed for late blight resistant genotypes. Our study elucidates genes involved in imparting late blight resistance in potato, which will be beneficial for its management strategies in the future.

Potato is one of the most important food crops in the world. Late blight, viruses, soil and tuber-borne diseases, insect-pests mainly aphids, whiteflies, and potato tuber moths are the major biotic stresses affecting potato production. Potato is an irrigated and highly fertilizer-responsive crop, and therefore, heat, drought, and nutrient stresses are the key abiotic stresses. The genus Solanum is a reservoir of genetic diversity, however, a little fraction of total diversity has been utilized in potato breeding. The conventional breeding has contributed significantly to the development of potato varieties. In recent years, a tremendous progress has been achieved in the sequencing technologies from short-reads to long-reads sequence data, genomes of Solanum species (i.e., pan-genomics), bioinformatics and multi-omics platforms such as genomics, transcriptomics, proteomics, metabolomics, ionomics, and phenomics. As such, genome editing has been extensively explored as a next-generation breeding tool. With the available high-throughput genotyping facilities and tetraploid allele calling softwares, genomic selection would be a reality in potato in the near future. This mini-review covers an update on germplasm, breeding, and genomics in potato improvement for biotic and abiotic stress tolerance.

We investigated genome-wide DNA methylation and transcriptome (RNA-seq) profiling for tuber shape variation in potato. Mother plant (M1, round) and tissue culture-derived clonal variant plant (M2, elongated) were used. Total number of DNA methylation sites at cytosine contexts (CpG, CHG and CHH) was higher in M2 than M1, where CHH was the highest followed by CHG and CpG. Differential methylation regions (DMRs) analysis in M1 (control) and M2 revealed maximum DMRs number on chromosome 5 in CHG context and hypo-methylation was higher than hyper-methylation. Further, transcriptome analysis revealed that a total of 20,747 genes were differentially expressed between M1 (control) and M2, of which 280 (over-expressed) and 612 (under-expressed) genes were statistically significant (p ≤ 0.05). The gene ontology (GO) annotation showed predominance of molecular function, whereas signal transduction and carbohydrate metabolism were major KEGG (Kyoto encyclopedia of genes and genomes) pathways. RNA-seq gene expression was validated for the ten selected genes by real-time quantitative polymerase chain reaction (RT-qPCR) analysis. Based on the comparative analysis, we observed a few candidate genes associated with tuber developmental processes such as phytohormones-related (e.g. SAUR family protein, abscisic acid environmental stress-inducible protein TAS14), sugar metabolism (e.g. UDP-glucosyltransferase, glycosyltransferase family GT8 protein), transcription factors (e.g. F-box family protein, MYB, WRKY, MADS-box), stress-responsive proteins (e.g. early-responsive to dehydration 3, cytochrome P450, proline-rich protein) and cell wall modifying genes (e.g. endo-1,4-beta-glucanase, glycine-rich cell wall structural protein 1.8, 3-ketoacyl-CoA synthase 10). Our study suggests that these candidate genes probably play key roles in tuber shape variation in potato.

The root is an important plant organ, which uptakes nutrients and water from the soil, and provides anchorage for the plant. Abiotic stresses like heat, drought, nutrients, salinity, and cold are the major problems of potato cultivation. Substantial research advances have been achieved in cereals and model plants on root system architecture (RSA), and so root ideotype (e.g., maize) have been developed for efficient nutrient capture to enhance nutrient use efficiency along with genes regulating root architecture in plants. However, limited work is available on potatoes, with a few illustrations on root morphology in drought and nitrogen stress. The role of root architecture in potatoes has been investigated to some extent under heat, drought, and nitrogen stresses. Hence, this mini-review aims to update knowledge and prospects of strengthening RSA research by applying multi-disciplinary physiological, biochemical, and molecular approaches to abiotic stress tolerance to potatoes with lessons learned from model plants, cereals, and other plants.

Late blight ( Phytophthora infestans ) is a serious disease of potatoes. The aim of this study was to screen wild potato species and identify differentially expressed genes (DEGs) associated with late blight resistance. Wild potato species such as PIN45 ( Solanum pinnatisectum ), CPH62 ( Solanum cardiophyllum ), JAM07 ( Solanum jamesii ), MCD24 ( Solanum microdontum ), PLD47 ( Solanum polyadenium ), and cv. Kufri Bahar (control) were tested by artificial inoculation of P. infestans under controlled conditions. Transcriptomes of the leaf tissues (96 h post-inoculation) were sequenced using the Illumina platform. Statistically significant ( p < 0.05) DEGs were analyzed in wild species by comparison with the control, and upregulated (>2 log 2 fold change, FC) and downregulated (<−2 log 2 FC) genes were identified. DEGs were functionally characterized with Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Selected genes were validated by real-time PCR analysis to confirm RNA-seq results. We identified some upregulated genes associated with late blight resistance in wild species such as cytochrome P450, proline-rich protein, MYB transcription factor MYB139, ankyrin repeat-containing protein, and LRR receptor-like serine/threonine-protein kinase in PIN45; glucosyltransferase, fructose-bisphosphate aldolase, and phytophthora-inhibited protease 1 in CPH62; steroid binding protein and cysteine proteinase 3 in JAM07; glycine-rich cell wall structural protein 1 and RING finger protein in MCD24; and cysteine proteinase 3 and major latex protein in PLD47. On the other hand, downregulated genes in these species were snakin-2 and WRKY transcription factor 3 in PIN45; lichenase and phenylalanine ammonia-lyase 1 in CPH62; metallothionein and LRR receptor-like serine/threonine-protein kinase in JAM07; UDP-glucoronosyl/UDP-glucosyl transferase family protein and steroid binding protein in MCD24; and cytoplasmic small heat shock protein class I and phosphatase PLD47. Our study identified highly resistant wild potato species and underlying genes such as disease resistance, stress response, phytohormones, and transcription factors (e.g., MYB, WRKY, AP2/ERF, and AN1) associated with late blight resistance in wild potato species.

India is the second largest producer of potatoes in the world. Seed is the single most important input in potato cultivation. High seed rate (2.5–3.0 tons/ha), low rate of multiplication, progressive viral degeneration, storage, and transportation are major issues of potato seed production in the country. Potato seed alone accounts for 40%-50% of the total potato production cost, and huge quantities of potentially edible food is put back into the soil as potato seed. The delayed penetration of new improved potato/seed varieties into farmers’ fields due to the slow multiplication rate and frequent seed replacement because of degeneration are associated issues. To circumvent these issues, continuous efforts are being made by potato researchers to develop innovative technologies for quick multiplication of initial healthy breeder’s seed of the released varieties in sufficient quantities to meet the demand in our country. A paradigm shift in potato seed production methods has taken place globally since the early 1900s. Major potato producers of the world have shifted from conventional to hi-tech seed production systems to improve the seed quality and enhance seed multiplication rate. New innovations can overcome many of the problems associated with potato seed production, particularly in tropical and sub-tropical countries. Recent advances in potato seed production systems in India and challenges ahead for seed production are described here.