Blanchability, the ease of seed coat removal after roasting, is a critical post-harvest trait in groundnut (Arachis hypogaea L.) that directly influences processing efficiency and product quality. Despite its economic value, limited genetic understanding restricts breeding efforts for customized blanchability in groundnut. Here, we integrate whole-genome resequencing of 184 diverse groundnut genotypes with multi-season phenotyping to dissect the haplotype-level genomic architecture of blanchability. Genome-wide association studies identify 26 significant single-nucleotide polymorphism-trait associations across multiple chromosomes, six of which are further validated using KASP markers, with two successfully validating the expected allelic effects across breeding lines and genotypes. Haplo-pheno analyses identify distinct subspecies-specific signatures for the major associations on chromosomes Ah01, Ah05, Ah06, and Ah17. Superior high-blanchability haplotypes (Ah01HapBL4, Ah05HapBL3, Ah06HapBL5, Ah06HapBL10, and Ah17HapBL6) are predominantly found in the fastigiata subspecies from South Asia and South America. In contrast, the low-blanchability haplotypes (Ah01HapBL2, Ah05HapBL6, Ah06HapBL3, Ah17HapBL2) are enriched in the hypogaea subspecies, mainly from Africa. These contrasting haplotypes offer the flexibility to achieve either high or low blanchability tailored to specific end-use applications. The availability of diagnostic markers and donor genotypes harboring multiple favorable haplotypes provides immediate tools for haplotype-based breeding. Collectively, this study introduces blanchability as a novel, customizable breeding target and establishes a translational framework to enhance the processing quality and industrial value of groundnut through haplotype-based breeding.

Blanchability is the ability of seeds to shed their seed coat (testa) and is a trait of economic importance in the food processing industry, yet remains underexplored in breeding programs. In this study, blanchability was evaluated in 184 groundnut accessions from the ICRISAT minicore collection to identify associated genomic regions, candidate genes, and molecular markers. Significant variability was observed over two seasons, with values ranging from 3.98 to 70.08%. Ten genotypes, including ICG10890, ICG9507, ICG13982, and ICG297, showed high blanchability, with ICG297 emerging as a promising donor based on cluster analysis of blanchability and agronomic traits. Genome-wide associations study (GWAS) using the 58 K 'Axiom_Arachis' SNP array revealed 58 significant SNP-trait associations, highlighting important genes such as isocitrate dehydrogenase and ubiquitin ligase, which influence seed coat structure and cell wall integrity thereby affecting blanchability. Further, nine SNPs were selected via allele mining, among these four SNPs, on chromosomes A01 (snpAH00551, AhBL01), A06 (snpAH00554, AhBL02), B04 (snpAH00558, AhBL03), and B07 (snpAH00559, AhBL04), effectively distinguishing between high and low blanchability genotypes. These validated SNPs present valuable tools for genomics-assisted breeding. Overall, the finding contributes towards better understanding of the genetic basis of blanchability in groundnut, providing key genomic resources for improving processing-related traits.

Plumbagin is an important naphthoquinone with potent anticancer properties besides multitudinous uses in healthcare. It is produced in a limited number of species and families but mostly in the roots of Plumbaginaceae family members. The biosynthetic pathway and the genes that regulate plumbagin synthesis are not completely known, but details of these are being revealed. Several species, including Plumbago, Drosera, and others, are being uprooted for the extraction of plumbagin by pharmaceutical industries, leading to the destruction of natural habitats. The pharmaceutical industry is therefore facing an acute shortage of plant material. This necessitates enhancing the accumulation of plumbagin using suspensions and hairy roots to meet market demands. Many factors, such as the aggregate size of the inoculum, stability of the culture, and the sequential effects of elicitors, immobilization, and permeabilization, have been demonstrated to act synergistically and markedly augment plumbagin accumulation. Hairy root cultures can be used for the large-scale production, growth, and plumbagin accumulation, and the exploration of their efficacy is now imperative. The secretion of compounds into the spent medium and their in situ adsorption via resin has remarkable potential, but this has not been thoroughly exploited. Improvements in the quality of biomass, selection of cell lines, and production of plumbagin in bioreactors have thus far been sporadic, and these parameters need to be further exploited. In this review, we report the advances made relating to the importance of stable cell line selection for the accumulation of compounds in long-term cultures, hairy root cultures for the accumulation of plumbagin, and its semicontinuous production via total cell recycling in different types of bioreactors. Such advances might pave the way for industrial exploitation. The steps in the biosynthetic pathway that are currently understood might also aid us in isolating the relevant genes in order to examine the effects of their overexpression or heterologous downregulation or to edit the genome using CRISPR-Cas9 technology in order to enhance the accumulation of plumbagin. Its potential as an anticancer molecule and its mode of action have been amply demonstrated, but plumbagin has not been exploited in clinics due to its insolubility in water and its highly lipophilic nature. Plumbagin-loaded nanoemulsions, plumbagin–silver, or albumin nanoparticle formulations can overcome these problems relating to its solubility and are currently being tried to improve its bioavailability and antiproliferative activities, as discussed in the current paper.

Blanchability, defined as the ease of seed coat removal after roasting, is a vital trait for enhancing processing efficiency and product quality in groundnut ( Arachis hypogaea L.). To enable a comprehensive haplotype-level genetic dissection of this trait, SNPs derived from whole-genome resequencing (WGRS) were used to perform genome-wide association study (GWAS) using multi-locus models (BLINK and FarmCPU) on a diverse groundnut mini-core collection phenotyped across two crop seasons. A total of 26 significant SNP-trait associations (STAs) were identified across multiple chromosomes, with major loci on chromosomes Ah05, Ah06, and Ah17, some of which were further validated using KASP (Kompetitive Allele-Specific PCR) markers. Candidate genes, such as those involved in cell wall biosynthesis (e.g., galactoside 2-alpha-L-fucosyltransferase-like protein, protein kinase superfamily members, and glycerophosphoryl diester phosphodiesterase 3 ), were found to be within linkage disequilibrium (LD) of the identified STAs, suggesting their plausible association with blanchability. Haplo-pheno analyses identified superior high-blanchability haplotypes; Ah05HapBL3 , Ah06HapBL5 , Ah06HapBL10 , and Ah17HapBL6, which were predominantly found in the fastigiata subspecies (including Valencia and Spanish bunch agronomic types) from South Asia and South America, while the low-blanchability haplotypes were from hypogaea subspecies (including Virginia runner and Virginia bunch agronomic types) from Africa. Overall, this study provides valuable insights for customizing blanchability through haplotype-based breeding of processing-grade cultivars thereby improving groundnut value chains to meet diverse industrial demands. ### Competing Interest Statement The authors have declared no competing interest. Bill & Melinda Gates Foundation, https://ror.org/0456r8d26, OPP1114827

Rice serves as a principal food class globally and the crop have been gradually impeded by environmental constraints such as drought, floods, salinity, heat, and cold. Plants adapt their physiological operations in response to external stimuli via signal transduction, thereby modulates gene expression and triggers a range of cellular responses. To feed the current population expansion, it is necessary to develop crops which are able to withstand climate change is highly desirable. OsDHSRP1 is an E3-ubiquitin ligase whose expression is highly stimulated by salinity, heat, and drought conditions, and it acts as a negative modulator by boosting ROS production. The genome-wide comprehensive and expression analysis of OsDHSRP1 in rice have still not been reported. In the current research, we are providing genome wide prediction, structural, evolutionary characterization, and expression analysis of OsDHSRP gene family of Oryza under diverse abiotic stresses. A total of 15 OsDHSRP genes were discovered in Oryza genome, which contains C3HC4 zinc finger conserved domain. The elucidation of Intron/Exon and motif patterns provide structural aspects of these genes. Cis-regulatory analysis and Transcription factor prediction studies revealed their roles and interaction with genes involved in multiple abiotic variables. Expression evaluation of OsDHSRP genes by q-RT PCR revealed that OsDHSRP1 exhibited strong expression trends in leaflets during cold stress followed by drought and salt stress conditions, suggests the role of OsDHSRP1 under diverse abiotic stress circumstances in Oryza. This study provides further insights into regulation of expression of OsDHSRP genes for developing climate resilient crops.

Ferulate 5-hydroxylase (F5H), a cytochrome P450-dependent monooxygenase, catalyzes the hydroxylation of coniferaldehyde, a crucial step in the formation of syringyl lignin monomer (S). However, evolutionary divergence, expression patterns under abiotic stress conditions (ABA, PEG and NaOH) and lignin content-related features of the F5H gene family in Sorghum bicolor have not been explored. This study envisaged mining of Sorghum genomic data leading to the identification of 61 SbF5H genes. Bioinformatics analysis revealed the phylogenetic evolutionary relations, gene structures, conserved motifs, physicochemical properties, and promoter cis-acting elements related to these genes and their encoded proteins. Based on the gene structural and phylogenetic features, these 61 SbF5Hs were grouped into 4 subclasses. The in silico expression analysis revealed higher accumulation of SbF5H1 transcripts in embryo and in root under stress conditions. Similarly, Other SbF5H genes have shown expression in stem and root, thus indicating SbF5H genes involvement in Sorghum lignin biosynthesis. By exploring into the functional aspects of the F5H gene, our study sought to shed light on its significance in influencing not only the chemical makeup of lignin but also the resultant plant phenotypes. This insight into the molecular mechanisms governing lignin biosynthesis can have implications for bioenergy production and crop improvement.

For most people across the planet, rice is also considered as most beneficial crops in terms of fulfilling every day's energy and nutritional needs. Worldwide food safety is seriously threatened since severe limitations on rice output caused by both abiotic and biotic variables. Even though rice features much more developed regeneration mechanism than other agricultural crops, majority of desi cultivars continue to stay as impervious to genetic alterations and regeneration. Therefore, among preliminary steps in the transgenic plant generation necessitates to improve tissue culture procedures to produce viable plants via embryogenic calli mediated regeneration. In this study, we reporting that enhanced rate of plant regeneration was observed from mature seed-derived embryogenic calli of the indica rice cultivar MTU1010 following partially desiccation procedure. We studied the effects of several plant growth regulators on the efficiency of inducing embryogenic callus and regeneration of whole plantlets. The MS-CIM medium with 2.0 mg-1 2,4, D showed the highest callus induction percentage. Maximum rate of shoot regeneration (92%) was observed from 48hr partially dehydrated calli, when enriched with high cytokinin (2 mg/l kinetin) and lower auxin (0.5 mg/l NAA) concentrations. Calli that had been moderately dehydrated showed significantly greater regeneration rates than undehydrated calli. Upon being transferred onto a rooting medium, the well-rooted plantlets were shifted to shaded glass house for hardening. Hence, this approach is rather simple to apply and can be employed in genetic modification studies alongside other biotechnological endeavours.

Stress-related NAC (NAM, ATAF1-2 and CUC2) genes, known as SNAC sub-family have been identified in four different species such as Arabidopsis thaliana, Oryza sativa, Sorghum bicolor and Zea mays using the tools of bioinformatics. These genes have been characterized by finding out their introns, exons, cis-regulatory elements, sub-cellular localization, highly conserved motifs, and motif signatures. Phylogenetic tree has been constructed using protein sequences, calculated synonymous to non-synonymous substitution rates (Ka/Ks) of SNAC paralogs and generated 3-dimensional protein models. Predicted SNAC homologs in maize genome have been studied by analysing the synteny of ZmSNAC genes with NAC genes in Arabidopsis thaliana, Oryza sativa and Sorghum bicolor. miRNA binding sites have been predicted and analysis of cis-regulatory elements in the promoter regions of SNAC genes in the four plant species has been performed. Identification of SNAC transcription factor homologues in the four plant species and their comparative analysis may provide a basis for further characterization of SNAC transcription factors in various other plant species. Available data have been mined for gene expression analysis under different abiotic stress conditions which displayed up- and down-regulations indicating apparent involvement of SNAC genes during abiotic stress responses.

Caffeic acid O-methyltransferases (COMTs) are essential enzymes for producing natural products in plants, specifically involved in the phenylalanine metabolic pathway and the monolignol biosynthetic pathway. These enzymes are responsible for the methylation of caffeic acid compounds, which are the building blocks for many plant-derived compounds with various biological activities. The investigation of the evolutionary divergence, expression patterns under diverse abiotic stress conditions, and lignin content-related features of the COMT gene family in Sorghum has not been explored. In this study, forty-eight SbCOMTs were identified in S.bicolor. Based on the examination of evolutionary relationships, 48 SbCOMTs were classified into two distinct categories. The gene characterization and the conserved motif patterns in each group were similar, demonstrating the reliability of the phylogenetic categorization. Chromosomes 5 and 7 have been found as the hotspot of SbCOMTs with 10 and 7 genes respectively. Phylogenetic analysis revealed the conservation of Sorghum COMT genes among Zea mays and Oryza sativa. Investigation of regulatory elements specifies the significant roles that COMT genes play in the monolignol biosynthetic pathway of S. bicolor. Analysis of miRNA, transcription factor binding, and gene expression analysis provides insights to further engineer lignin biosynthetic pathway for better biofuel yield. We found that two SbCOMTs (SbCOMT26& 36) were highly expressed and their relative contents were similar to the variation drift of lignin content under abiotic stress conditions in S. bicolor. These results provide a clue for further study on the roles of SbCOMTs in the development of Sorghum and could favourably be foundations for the cultivation of Sorghum with higher biomass and yield with enhanced abiotic stress tolerance.

As a consequence of global climate change, acute water deficit conditions, soil salinity, and high temperature have been on the rise in their magnitude and frequency, which have been found to impact plant growth and development negatively. However, recent evidence suggests that many fruit plants that face moderate abiotic stresses can result in beneficial effects on the postharvest storage characters of the fruits. Salinity, drought, and high temperature conditions stimulate the synthesis of abscisic acid (ABA), and secondary metabolites, which are vital for fruit quality. The secondary metabolites like phenolic acids and anthocyanins that accumulate under abiotic stress conditions have antioxidant activity, and therefore, such fruits have health benefits too. It has been noticed that fruits accumulate more sugar and anthocyanins owing to upregulation of phenylpropanoid pathway enzymes. The novel information that has been generated thus far indicates that the growth environment during fruit development influences the quality components of the fruits. But the quality depends on the trade-offs between productivity, plant defense, and the frequency, duration, and intensity of stress. In this review, we capture the current knowledge of the irrigation practices for optimizing fruit production in arid and semiarid regions and enhancement in the quality of fruit with the application of exogenous ABA and identify gaps that exist in our understanding of fruit quality under abiotic stress conditions.

Malnutrition is a major challenge globally, and groundnut is a highly nutritious self-pollinated legume crop blessed with ample genomic resources, including the routine deployment of genomic-assisted breeding. This study aimed to identify genomic regions and candidate genes for high iron (Fe) and zinc (Zn) content, utilizing a biparental mapping population (ICGV 00440 × ICGV 06040;). Genetic mapping and quantitative trait locus (QTL) analysis (474 mapped single-nucleotide polymorphism loci; 1536.33 cM) using 2 seasons of phenotypic data together with genotypic data identified 5 major main-effect QTLs for Fe content. These QTLs exhibited log-of-odds (LOD) scores ranging from 6.5 to 7.4, explaining phenotypic variation (PVE) ranging from 22% (qFe-Ah01) to 30.0% (qFe-Ah14). Likewise, four major main effect QTLs were identified for Zn content, with LOD score ranging from 4.4 to 6.8 and PVE ranging from 21.8% (qZn-Ah01) to 32.8% (qZn-Ah08). Interestingly, three co-localized major and main effect QTLs (qFe-Ah01, qZn-Ah03, and qFe-Ah11) were identified for both Fe and Zn contents. These genomic regions harbored key candidate genes, including zinc/iron permease transporter, bZIP transcription factor, and vacuolar iron transporter which likely play pivotal roles in the accumulation of Fe and Zn contents in seeds. The findings of this study hold potential for fine mapping and diagnostic marker development for high Fe and Zn contents in groundnut.

Background: Lignins are phenylpropanoid polymers with complex composition and structures and crucial components in plant cell walls. Lignins are biosynthesized from oxidative polymerization of 4-hydroxycinnamyl alcohols, but differ in the degree of methoxylation. Objective: This review makes an endeavour to identify the gaps in our understanding of lignin modulation and gain insights into their relevance to abiotic stress tolerance. Methods: Critical review of the recent literature to understand the regulation of lignin, the major biopolymer involved in a multitude of functions. Results: Lignin contributes to the growth of tissues, and organs that give mechanical protection or lodging resistance and also responds to multiple biotic and abiotic stresses. The quantity and quality of accumulation of lignin is dependent on the type of plant species and abiotic stress. In this review, we briefly discuss the biosynthesis, modulation of lignin by diverse transcription factors and its role in salt, drought and temperature stress tolerance. Conclusion: We need to explore many areas to gain comprehensive knowledge about the secondary cell wall deposition of monolignols, and their transport, leading to lignin accumulation which imparts biotic and abiotic stress tolerance to plants.

Seed size is not only a yield-related trait but also an important measure to determine the commercial value of groundnut in the international market. For instance, small size is preferred in oil production, whereas large-sized seeds are preferred in confectioneries. In order to identify the genomic regions associated with 100-seed weight (HSW) and shelling percentage (SHP), the recombinant inbred line (RIL) population (Chico × ICGV 02251) of 352 individuals was phenotyped for three seasons and genotyped with an Axiom_Arachis array containing 58K SNPs. A genetic map with 4199 SNP loci was constructed, spanning a map distance of 2708.36 cM. QTL analysis identified six QTLs for SHP, with three consistent QTLs on chromosomes A05, A08, and B10. Similarly, for HSW, seven QTLs located on chromosomes A01, A02, A04, A10, B05, B06, and B09 were identified. BIG SEED locus and spermidine synthase candidate genes associated with seed weight were identified in the QTL region on chromosome B09. Laccase, fibre protein, lipid transfer protein, senescence-associated protein, and disease-resistant NBS-LRR proteins were identified in the QTL regions associated with shelling percentage. The associated markers for major-effect QTLs for both traits successfully distinguished between the small- and large-seeded RILs. QTLs identified for HSW and SHP can be used for developing potential selectable markers to improve the cultivars with desired seed size and shelling percentage to meet the demands of confectionery industries.

In addition to the challenge of meeting global demand for food production, there are increasing concerns about food safety and the need to protect consumer health from the negative effects of foodborne allergies. Certain bio-molecules (usually proteins) present in food can act as allergens that trigger unusual immunological reactions, with potentially life-threatening consequences. The relentless working lifestyles of the modern era often incorporate poor eating habits that include readymade prepackaged and processed foods, which contain additives such as peanuts, tree nuts, wheat, and soy-based products, rather than traditional home cooking. Of the predominant allergenic foods (soybean, wheat, fish, peanut, shellfish, tree nuts, eggs, and milk), peanuts (Arachis hypogaea) are the best characterized source of allergens, followed by tree nuts (Juglans regia, Prunus amygdalus, Corylus avellana, Carya illinoinensis, Anacardium occidentale, Pistacia vera, Bertholletia excels), wheat (Triticum aestivum), soybeans (Glycine max), and kidney beans (Phaseolus vulgaris). The prevalence of food allergies has risen significantly in recent years including chance of accidental exposure to such foods. In contrast, the standards of detection, diagnosis, and cure have not kept pace and unfortunately are often suboptimal. In this review, we mainly focus on the prevalence of allergies associated with peanut, tree nuts, wheat, soybean, and kidney bean, highlighting their physiological properties and functions as well as considering research directions for tailoring allergen gene expression. In particular, we discuss how recent advances in molecular breeding, genetic engineering, and genome editing can be used to develop potential low allergen food crops that protect consumer health.

Seed weight in groundnut (Arachis hypogaea L.) has direct impact on yield as well as market price because of preference for bold seeds by consumers and industry, thereby making seed-size improvement as one of the most important objectives of groundnut breeding programs globally. Marker-based early generation selection can accelerate the process of breeding for developing large-seeded varieties. In this context, we deployed the quantitative trait locus-sequencing (QTL-seq) approach on a biparental mapping population (Chico × ICGV 02251) to identify candidate genes and develop markers for seed weight in groundnut. A total of 289.4-389.4 million reads sequencing data were generated from three libraries (ICGV 02251 and two extreme bulks) achieving 93.9-95.1% genome coverage and 8.34-9.29× average read depth. The analysis of sequencing data using QTL-seq pipeline identified five genomic regions (three on chromosome B06 and one each on chromosomes B08 and B09) for seed weight. Detailed analysis of above associated genomic regions detected 182 single-nucleotide polymorphisms (SNPs) in genic and intergenic regions, and 11 of these SNPs were nonsynonymous in the genomic regions of 10 candidate genes including Ulp proteases and BIG SEED locus genes. Kompetitive allele specific polymerase chain reaction (KASP) markers for 14 SNPs were developed, and four of these markers (snpAH0031, snpAH0033, snpAH0037, and snpAH0038) were successfully validated for deployment in breeding for large-seeded groundnut varieties.

Systematic genome-wide analysis of Sorghum bicolor revealed the identification of a total of 48 homologous genes comprising 21 proline-rich proteins (PRPs) and 27 hybrid proline-rich proteins (HyPRPs). Comprehensive scrutiny of these gene homologs was conducted for gene structure, phylogenetic investigations, chromosome mapping, and subcellular localization of proteins. Promoter analysis uncovered the regions rich with phosphorous- (BIHD), ammonium-, sulfur-responsive (SURE), and iron starvation-responsive (IRO2) along with biotic, abiotic, and development-specific cis-elements. Further, PRPs exhibit more methylation and acetylation sites in comparison with HyPRPs. miRNAs have been predicted which might play a role in cleavage and translation inhibition. Several of the SbPRP genes were stimulated in a tissue-specific manner under drought, salt, heat, and cold stresses. Additionally, exposure of plants to abscisic acid (ABA) and zinc (Zn) also triggered PRP genes in a tissue-dependent way. Among them, SbPRP17 has been found upregulated markedly in all tissues irrespective of the stress imposed. The expressions of SbHyPRPs, especially SbHyPRP2, SbHyPRP6, and SbHyPRP17 were activated under all stresses in all three tissues. On the other hand, SbHyPRP8 (root only) and SbHyPRP12 (all three tissues) were highly responsive to cold stress and ABA while SbHyPRP26 was induced by drought and Zn in the stem. Taken together, this study indicates the critical roles that SbPRPs and SbHyPRPs play during diverse abiotic stress conditions and notably the plausible roles that these genes play upon exposure to zinc, the crucial micronutrient in plants.

Pre-harvest aflatoxin contamination (PAC) in groundnut is a serious quality concern globally, and drought stress before harvest further exacerbate its intensity, leading to the deterioration of produce quality. Understanding the host–pathogen interaction and identifying the candidate genes responsible for resistance to PAC will provide insights into the defense mechanism of the groundnut. In this context, about 971.63 million reads have been generated from 16 RNA samples under controlled and Aspergillus flavus infected conditions, from one susceptible and seven resistant genotypes. The RNA-seq analysis identified 45,336 genome-wide transcripts under control and infected conditions. This study identified 57 transcription factor (TF) families with major contributions from 6570 genes coding for bHLH (719), MYB-related (479), NAC (437), FAR1 family protein (320), and a few other families. In the host (groundnut), defense-related genes such as senescence-associated proteins, resveratrol synthase, seed linoleate, pathogenesis-related proteins, peroxidases, glutathione-S-transferases, chalcone synthase, ABA-responsive gene, and chitinases were found to be differentially expressed among resistant genotypes as compared to susceptible genotypes. This study also indicated the vital role of ABA-responsive ABR17, which co-regulates the genes of ABA responsive elements during drought stress, while providing resistance against A. flavus infection. It belongs to the PR-10 class and is also present in several plant–pathogen interactions.