Potato (Solanum tuberosum L.) is a globally vital food crop and a significant industrial source of starch. Potato starch is primarily composed of amylopectin (about 70–80%) and a smaller proportion of amylose (20–30%). The starch composition critically influences both nutritional profile (glycemic index, resistant starch content) and industrial properties (freeze–thaw stability, film-forming, adhesive properties etc.). Enhancing the quality and improving the composition of starch has been a prime focus of biotechnological research in potato. The Starch Synthases (SSs), Granule Bound Starch Synthase I (GBSSI), and Starch Branching Enzymes (SBEs) are among the key enzymes of starch biosynthesis and represent major targets for modifying its functional characteristics. Conventional breeding efforts in tetraploid potato plants were not very successful in improving starch quality and composition, due to the complex patterns of inheritance of this highly heterozygous crop. This has led the potato biologists to embark on the use of transgenic and recently introduced genome editing approaches for starch modification in potato. This review discusses advances in transgenic and modern genetic engineering strategies, including gene silencing, overexpression, and genome editing, for modifying starch in potatoes. Particular attention has been given to key enzymes in starch biosynthesis pathways, and their genetic manipulation to improve their functionality in food and industrial applications.

Sesbania bispinosa (Jacq.) W. Wight (Fabaceae), also known as Dhaincha, is a popular nitrogen-fixing green manure crop to improve soil fertility. Between July and September during the years 2022 to 2024, symptoms of wilting with necrotic lesions and rotting at the collar region were observed on dhaincha plants grown in the experimental fields of the ICAR-Central Potato Research Institute Regional Station, Meerut, Uttar Pradesh, India. The causing agent was isolated on potato dextrose agar (PDA), exhibiting fluffy white mycelium with dark brown scattered sclerotia. Pathogenicity assays successfully reproduced identical wilting symptoms, thereby fulfilling Koch’s postulates. Molecular identification using rDNA-ITS sequencing (GenBank Accession No. PX251733 and PX251734) and tef-1α gene sequencing (GenBank Accession No. PX250990) confirmed Agroathelia rolfsii as the causal agent. To the best of our knowledge, this is the first report of collar and stem rot disease of Sesbania bispinosa caused by Agroathelia rolfsii in India. These findings provide important insights into the expanded host range and will aid in designing effective crop rotation strategies within diverse cropping systems.

Micronutrient deficiencies, commonly referred to as hidden hunger, affect nearly two billion people worldwide and pose a major challenge to global nutritional security. Potato, the most widely consumed non-grain staple crop, offers strong potential for biofortification due to its high yield, short crop duration, wide adaptability, and consumer acceptance. In the present study, a panel of 288 highly diverse tetraploid potato accessions was evaluated for tuber micronutrient concentrations, including iron (Fe), zinc (Zn), copper (Cu), and manganese (Mn), over two years. Substantial phenotypic variation was observed for all micronutrients across the panel. Genotyping was performed using genotyping-by-sequencing (GBS), and sequence reads were aligned to the Solanum tuberosum reference genome, achieving a mapping rate of 94.0-98.1% with a mean error rate of 0.03%. A total of 132,766,447 SNPs were initially identified, from which 23,522 (75% threshold) and 5,470 (90% threshold) high-quality SNPs were retained for downstream analysis. Genome-wide association analysis using the GWASpoly package identified 16 significant marker-trait associations (MTAs) across additive and dominance models for micronutrient traits. Notably, a major locus associated with Mn content explained up to 20% of the phenotypic variance, indicating a relatively large-effect region. Several MTAs were co-localized with putative candidate genes encoding metal transporters, transcription factors, and regulatory proteins involved in nutrient homeostasis. These findings provide insights into the genetic architecture of tuber micronutrient accumulation and support the development of nutrient-enriched potato cultivars through molecular breeding approaches.

The growing resistance to synthetic insecticides and Bt toxins, alongside persistent crop losses despite heavy pesticide application, highlights the urgent need for safer, sustainable and efficient pest management strategies. This review presents genome editing as a precise and versatile approach to reduce pest impact by altering fertility, feeding patterns or vulnerability, while protecting beneficial organisms. Among the genome editing tools, CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) is one of the most promising genome editing techniques in insects. It facilitates targeted functional studies, integration with RNAi and dual-expression systems and gene drive applications. Deployment is envisioned in two phases, initial laboratory modification followed by regulated field release, with a strong emphasis on biosafety through terminator genes, marked individuals for gene flow monitoring, optimized dosages, stringent screening and long-term ecological surveillance, along with transparency and adherence to international safety protocols. Significant challenges encompass delivery efficiency, identification of edits, off-target mutations, dose-related efficacy and sterility, unstable transmission and resistance development. Innovations such as base and prime editing minimize unintended mutations by circumventing double-stranded breaks (DSBs), while paratransgenic strategies targeting gut symbionts offer supplementary avenues; plant-mediated insect gene editing emerges as a promising frontier. Overall, carefully regulated trials aligned with policy frameworks and stakeholder involvement are vital to assess effectiveness in natural environments and achieve targeted, dependable and ecologically responsible pest control.

Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas)-based genome editing technology has come out as very precise and effective tool for targeted modification in the gene of interest and offers unprecedented potentials in crop improvement. However, in the present regulatory framework for commercialization of genome edited crops, in many countries including India, the edited lines must be transgene-free. In India, only site directed nuclease (SDN) I and SDN II category of genome edited events which are transgene-free are permitted for commercialization. Potato is a vegetatively propagated crop, having autotetraploid genome and is highly heterozygous in nature. Removal of the transgene from potato genome of edited lines through genetic segregation, either by crossing or selfing, is not the appropriate method as the elite background of the genome gets disturbed due to heterozygous nature of the crop. Every individual seed of potato, i.e. true potato seed (TPS) behaves like a different individual than the parental line and is unable to maintain the genetic identity. In this review article, we have discussed several strategies that can be enacted for generation of transgene-free genome edited lines in potato. This article will provide deeper insight and enhance understandings about the optimum use of CRISPR as non-GMO technology in the genetic enhancement of potato and to adopt the best strategies in editing this important tuberous, clonally propagated crop.

Potato is an important vegetatively propagated, starch-rich tuber crop. High amylose potatoes containing more resistant starch offer healthier food alternatives. However, the resistant starch content is low in most cultivated potato varieties. In this study, targeted mutation of the starch branching enzyme2 (SBE2.1 & SBE2.2 isoforms) had been done in the commercially significant potato cultivar, Kufri Chipsona-I using Clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9 (CRISPR-Cas9 system) to develop high-amylose potato lines. SBE2 is one of the key enzymes involved in amylopectin biosynthesis, a starch component. Two isoforms, SBE2.1 & SBE2.2, were mutated using CRISPR-Cas9-mediated genome editing. After Agrobacterium-mediated genetic transformation, fifty transformed lines were generated on herbicide Basta selection medium, out of which 70% were found positive for bar and Cas9 genes. Overall, six mutant lines, viz. K301, K302, K303, K304, K305, K306, derived from distinct events, exhibited deletions and substitutions in the target exons. The CRISPR-Cas9 edited K304 potato line exhibited both insertion–deletion (indel) and substitution mutations in three out of the four selected targets across both genes, and was therefore identified as the most efficiently edited line. The harvested tubers from SBE2.1 & SBE2.2 mutant K304 line showed the highest amylose (95.91%) and resistant starch content (8.69 g/100 g). Evaluation of starch using X-ray crystallography (XRD) illustrated an altered crystallinity index (CI%) in all six mutant events in comparison to the wild study. Furthermore, 1H-NMR study demonstrated a substantial decline in branch chain elongation in amylopectin, and thus a low degree of branching in a range of 1.15%–3.66% was reported in mutant lines, relative to the wild type (5.46%). The present study demonstrated the efficacy of CRISPR-Cas9-mediated mutagenesis of starch biosynthetic genes to develop high-amylose potato lines with elevated resistant starch content for improved health benefits.

Potato (Solanum tuberosum L.) is a perennial food crop that helps to ensure global food and nutrition security. This study developed an in vitro callus and shoot induction protocol for the potato cultivar Kufri Sangam and assessed the frequency of callus and shoot regeneration. This study found that supplementing the Murashige and Skoog (MS) medium with 0.5 mgL−1 6-Benzylaminopurine (BAP) and 5 mgL−1 1-Naphthaleneacetic acid (NAA) resulted in 100

Food and nutritional security are the top priorities in Indian agriculture. Exponential population growth coupled with climate change effects has become a serious challenge for sustainable agriculture. Genome editing has revolutionized the agricultural sector because of its ability to create precise, stable and predictable modifications in the genome and therefore, offers great opportunities for crop improvement in India. However, for harvesting the real benefits of this technology in agriculture sector, there is a strong need of creating awareness among the end users and development of suitable policies for regularization of genome edited products. Many regulatory agencies around the world have been modernizing their regulatory approaches to be more risk proportionate and to reflect a more science-based approach. In this article, recent research initiatives and developments undertaken by different Indian institutes/organizations for the genetic improvement of agricultural and horticultural crops via genome editing technologies are summarized. Furthermore, to benefit from this potential technology in our country, regulatory policies must be clear, science-based and proportionate. Therefore, in the present review, the regulatory policies related to the genome editing of crop products in India are discussed in detail. This review will sensitize researchers and stakeholders to the application of genome editing techniques in crop improvement and various biosafety committees involved in the development and regulation of genome edited crops.

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.

Indian mustard (Brassica juncea) is a crucial oilseed crop in India, enhancing the nation's oilseed production. A primary agricultural goal is to develop high-yielding, disease-resistant varieties with superior nutritional quality. To address this, a novel recombinant inbred lines (RIL) population was developed by crossing an exotic East European genotype, 'Heera' with the high-yielding Indian mustard variety 'DRMRIJ-31' using a single seed descent method. Our study presents the comprehensive characterisation of this RIL population for yield components and oil quality traits. Over the 2 years (2021-2022 and 2022-2023), we meticulously phenotyped 320 individuals from this RIL population, focusing on yield component traits. The RIL population showed a high level of variability for traits such as plant height (175-236 cm), days to 50% flowering (48-72 DAS), days to maturity (145-164), number of primary branches (5-9), thousand seed weight (1.6-6.2 g), seed coat colour and yield (957-3039 kg/ha). Concurrently, we conducted biochemical analysis, measuring total antioxidants (11.3-110.2 mg/g), phenol (57.6-274.3 mu g/g), flavonoids (29.2-1591.6 mu g/g) and glucosinolates (21.2-140.3 mu mol/g) and erucic acid content (0.5%34%) to gain insights into the nutritional and anti-nutritional components of this RIL population. This multi-faceted characterisation provides a holistic understanding of the RIL population, offering valuable insights for future breeding programmes and crop improvement strategies.

Indian mustard (Brassica juncea L. Czern & Coss.) is a highly economically important oilseed crop of India. An accurate estimation of genetic diversity inherent in breeding material is a pre-requisite for the success of any hybrid breeding programme, as it leads to identification of genetically divergent parents for exploiting high heterotic levels. In the present study, 200 genome-wide spanned simple sequence repeat (SSR) markers were used for estimation of genetic diversity and identification of genetically divergent parental combinations in a panel of 28 parental lines of Indian mustard comprising of 21 cytoplasmic male sterile (CMS) 'A' lines and 7 restrorer 'R' lines. A total of 179 SSR markers resulted in positive amplification with 155 (81.57 %) SSRs producing polymorphic amplicons and 24 (13.41 %) SSRs resulted into monomorphic products. Allele number varied from 2 to 6 with a mean value of 3.27 alleles per SSR marker. PIC values ranged from 0.23 to 0.7 with a mean value of 0.38 per SSR marker. Gene diversity values were in the range of 0.27-0.75 with average value of 0.47, inferring the presence of a moderate level of genetic diversity in the plant material. Neighbor-Joining dendrogram could not exactly differentiate 'A' and 'R' lines into different groups. This study led to identification of few genetically diverse A and R lines, suitable for making crosses for heterotic hybrid development in Indian mustard. On the basis of Euclidean distances, various cross-combinations viz. MJA10 & MJR3/EC597313, MJA 14 & MJR3/EC597313, and MH 12-12/EC597313S & MJR9 were designated as genetically diverse genotypes. These cross-combinations may be used in hybrid breeding program to exploit heterosis in Indian mustard improvement.

Background High temperature stress is an important abiotic factor, which affects tuberization and ultimately causes heavy yield reduction in potato. Objectives Identification and characterization of genes associated with tuberization under high temperature stress is essential for future management through biotechnology. Methodology Two contrasting potato varieties Kufri Anand (profuse tuber-bearing) versus Kufri Frysona (very less/scanty tuber-bearing, control) were cultivated in aeroponics under high temperature stress, and transcriptomes were analyzed. Results Potato cv. Kufri Anand was found superior over control (Kufri Frysona) for tuber yield and its component traits along with root morphology under aeroponics. Transcriptomes of tuber and leaf tissues were analyzed. Statistically significant ( p < 0.05) differentially expressed genes (DEGs) were categorised into up-regulated (> 2 log 2 fold change, FC) and down-regulated (< -2 log2 FC) genes. DEGs were annotated by gene ontology and KEGG pathways. A few selected up-regulated genes of both tissues were identified, and phylogeny tree and motif analysis were analysed based on 36 peptide sequences representing 15 selected DEGs in this study. Further, gene expression markers were developed and validated by real time qPCR analysis for the identification of high temperature tolerant genotypes. Conclusion A few key genes associated in tuberization under high temperature conditions were heat shock proteins (e.g. 18.5 kDa class I heat shock protein), sugar metabolism (e.g. glucosyltransferase), transcription factor (e.g. WRKY), and phytohormones (e.g. auxin-induced beta-glucosidase). Our study provides an overview of key genes involved in tuberization under high temperature stress in potato cv. Kufri Anand under aeroponics.

Potato (Solanum tuberosum L.) plays a crucial role in meeting global food demands due to its extensive cultivation and high nutritional value. Despite their significance, potatoes are subjected to biotic and abiotic stresses that hamper their growth and productivity. Traditional breeding methods have been used to develop disease-resistant and pest-resistant potato varieties; however, progress is slow due to lengthy breeding cycles. Genome editing (GE) allows precise and efficient modification of genomic loci to create elite crop varieties with desired traits. Among various GE tools, the advent of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas) system represents a major advancement in genetic engineering. This tool allows precise mutagenesis, gene knockouts, multiplex GE, and gene expression manipulations, thereby significantly advancing crop research and the development of designer crops. In autopolyploid crops like potatoes, CRISPR/Cas-based GE technology has been employed to manage various important traits, such as disease resistance, by targeting the genes involved in viral replication, susceptibility factors, and by introducing resistance genes. The CRISPR/Cas tool has also enhanced the tolerance to abiotic stresses, such as drought and salinity, making the potato more resilient to changing environmental conditions. Additionally, this technology has improved tuber quality by manipulating amylose and amylopectin contents, and by reducing steroidal glycoalkaloid content and enzymatic browning. The present review article delves into CRISPR/Cas technology and highlights its potential to improve key traits in potatoes.

Transcriptome analysis in potato varieties revealed genes associated with tuber yield-related traits and developed gene expression markers. This study aimed to identify genes involved in high tuber yield and its component traits in test potato varieties (Kufri Frysona, Kufri Khyati, and Kufri Mohan) compared to control (Kufri Sutlej). The aeroponic evaluation showed significant differences in yield-related traits in the varieties. Total RNA sequencing was performed using tuber and leaf tissues on the Illumina platform. The high-quality reads (QV > 25) mapping with the reference potato genomes revealed statistically significant (P < 0.05) differentially expressed genes (DEGs) into two categories: up-regulated (> 2 Log2 fold change) and down-regulated (< -2 Log2 fold change). DEGs were characterized by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Collectively, we identified genes participating in sugar metabolism, stress response, transcription factors, phytohormones, kinase proteins, and other genes greatly affecting tuber yield and its related traits. A few selected genes were UDP-glucose glucosyltransferase, glutathion S-transferase, GDSL esterase/lipase, transcription factors (MYB, WRKY, bHLH63, and BURP), phytohormones (auxin-induced protein X10A, and GA20 oxidase), kinase proteins (Kunitz-type tuber invertase inhibitor, BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1) and laccase. Based on the selected 17 peptide sequences representing 13 genes, a phylogeny tree and motifs were analyzed. Real time–quantitative polymerase chain reaction (RT-qPCR) analysis was used to validate the RNA-seq results. RT-qPCR based gene expression markers were developed for the genes such as 101 kDa heat shock protein, catechol oxidase B chloroplastic, cysteine protease inhibitor 1, Kunitz-type tuber invertase inhibitor, and laccase to identify high yielding potato genotypes. Thus, our study paved the path for potential genes associated with tuber yield traits in potato under 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.

Following the identification of the self-compatibility gene (Sli) in diploid potatoes two decades ago, the breeding of inbred based diploid hybrid potatoes made its way. Tetraploid potatoes have a long history of cultivation through domestication and selection. Tetrasomic inheritance, heterozygosity and clonal propagation complicate genetic studies, resulting in a low genetic gain in potato breeding. Diploid hybrid TPS potato breeding, similar to the developments in hybrid maize, was pursued as an alternative to the genetic improvement of potatoes. However, several challenges, like self-incompatibility and high inbreeding depression associated with diploid potatoes, must be overcome to develop inbred lines in potatoes. Moreover, the inbred lines must retain good fertility and vigour for hybrid breeding. Good progress has been made by creating di-haploids of popular varieties, mapping self-incompatibility inhibitor gene, understanding the genetic basis of inbreeding depression, and identifying genomic regions for deleterious alleles and fertility. Further, the genome sequencing of diploid inbred lines has revealed the genetics of key traits associated with potato breeding. This article discussed these insights and summarized the progress of diploid hybrid TPS potato breeding. Recent advances in genetic and genomic research and genome editing technology have shown promise for this technology's success and far-reaching implications.