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To date, several transcriptomic studies during fruit development have been reported, however no comprehensive integrated study on expression diversity, alternative splicing and metabolomic profiling was reported in Capsicum. This study analyzed RNA-seq data and untargeted metabolomic profiling from early green (EG), mature green (MG) and breaker (Br) fruit stages from two Capsicum species i.e. C. annuum (Cann) and C. frutescens (Cfrut) from Northeast India. A total of 117416 and 96802 alternatively spliced events (AltSpli-events) were identified from Cann and Cfrut, respectively. Among AltSpli-events, intron retention (IR; 32.2% Cann and 25.75% Cfrut) followed by alternative acceptor (AA; 15.4% Cann and 18.9% Cfrut) were the most abundant in Capsicum. Around, 7600 genes expressed in at least one fruit stages of Cann and Cfrut, were AltSpli. The study identified spliced variants of genes including transcription factors (TFs) involved in fruit development/ripening (Aux/IAA 16-like, ETR, SGR1, ARF, CaGLK2, ETR, CaAGL1, MADS-RIN, FUL1, SEPALLATA1), carotenoid (PDS, CA1, Ccs, CCD4, NCED3, xanthoxin dehydrogenase, CaERF82, CabHLH100, CaMYB3R-1, SGR1, CaWRKY28, CaWRKY48, CaWRKY54) and capsaicinoids biosynthesis (CaMYB48, CHS, CaWRKY51), which were significantly differentially spliced (DS) between consecutive Capsicum fruit stages. Also, this study observed that differentially expressed isoforms (DEiso) from 38 genes with differentially spliced events (DSE) were significantly enriched in various metabolic pathways such as starch and sucrose metabolism, amino-acid metabolism, cysteine cutin suberin and wax biosynthesis, and carotenoid biosynthesis. Furthermore, the metabolomic profiling revealed that metabolites from aforementioned pathways such as carbohydrates (mainly sugars such as D-fructose, D-galactose, maltose and sucrose), organic acids (carboxylic acids) and peptide groups significantly altered during fruit development. Taken together, our findings could help in alternative splicing-based targeted studies of candidate genes involved in fruit development and ripening in Capsicum crop.

Single-base cytosine methylation analysis across fruits of Capsicum annuum, C. chinense and C. frutescens showed global average methylation ranging from 82.8-89.1%, 77.6-83.9%, and 22.4-25% at CG, CHG and CHH contexts, respectively. High gene-body methylation at CG and CHG was observed across Capsicum species. The C. annuum showed the highest proportion (>80%) of mCs at different genomic regions compared to C. chinense and C. frutescens. Cytosine methylation for transposable-elements were lower in C. frutescens compared to C. annuum and C. chinense. A total of 510,165 CG, 583112 CHG and 277,897 CHH DMRs were identified across three Capsicum species. The differentially methylated regions (DMRs) distribution analysis revealed C. frutescens as more hypo-methylated compared to C. annuum and C. chinense, and also the presence of more intergenic DMRs in Capsicum genome. At CG and CHG context, gene expression and promoter methylation showed inverse correlations. Furthermore, the observed correlation between methylation and expression of genes suggested the potential role of methylation in Capsicum fruit development/ripening.

Plant growth and development are largely regulated by non-coding RNAs (ncRNA); thus ncRNA based markers would be rewarding in molecular breeding. In the present study, for the first time we developed total 623 ncRNA based SSRs including 119 microRNASSRs (miRNASSRs) and 504 long non-coding RNASSRs (lncRNASSRs) distributed across 12 Capsicum chromosomes. Out of 623 ncRNASSRs, 120 (including 60 each miRNASSRs and lncRNASSRs) were used for genotyping of 96 Capsicum accessions belonging to C. annuum, C. chinense and C. frutescens; and 75% SSRs were polymorphic. Model-based and distance-based cluster analyses identified three species specific clusters, i.e. cluster-I (C. annuum), cluster-II (C. frutescens) and cluster-III (C. chinense); therefore, these SSRs may have a potential role to play in interspecific Capsicum breeding. Tissue specific expression of SSR containing ncRNAs and versatile functions of their targets suggested the usefulness of SSRs for mapping of genes/QTLs and breeding of wide range of traits in Capsicum.

The molecular mechanism of the underlying genes involved in the process of fruit ripening in Capsicum (family Solanaceae) is not clearly known. In the present study, we identified orthologs of 32 fruit development/ripening genes of tomato in Capsicum, and validated their expression in fruit development stages in C. annuum, C. frutescens, and C. chinense. In silico expression analysis using transcriptome data identified a total of 12 out of 32 genes showing differential expression during different stages of fruit development in Capsicum. Real time expression identified gene LOC107847473 (ortholog of MADS-RIN) had substantially higher expression (>500 folds) in breaker and mature fruits, which suggested the non-climacteric ripening behaviour of Capsicum. However, differential expression of Ehtylene receptor 2-like (LOC107873245) gene during fruit maturity supported the climacteric behaviour of only C. frutescens (hot pepper). Furthermore, development of 49 gene based simple sequence repeat (SSR) markers would help in selection of identified genes in Capsicum breeding.

Myeloblastosis (MYB) genes are important transcriptional regulators of plant growth, development, and secondary metabolic biosynthesis pathways, such as capsaicinoid biosynthesis in Capsicum. Although MYB genes have been identified in Capsicum annuum, no comprehensive study has been conducted on other Capsicum species. We identified a total of 251 and 240 MYB encoding genes in Capsicum chinense MYBs (CcMYBs) and Capsicum baccatum MYBs (CbMYBs). The observation of twenty tandem and 41 segmental duplication events indicated expansion of the MYB gene family in the C. chinense genome. Five CcMYB genes, i.e., CcMYB101, CcMYB46, CcMYB6, CcPHR8, and CcRVE5, and two CaMYBs, i.e., CaMYB3 and CaHHO1, were found within the previously reported capsaicinoid biosynthesis quantitative trait loci. Based on phylogenetic analysis with tomato MYB proteins, the Capsicum MYBs were classified into 24 subgroups supported by conserved amino acid motifs and gene structures. Also, a total of 241 CcMYBs were homologous with 225 C. annuum, 213 C. baccatum, 125 potato, 79 tomato, and 23 Arabidopsis MYBs. Synteny analysis showed that all 251 CcMYBs were collinear with C. annuum, C. baccatum, tomato, potato, and Arabidopsis MYBs spanning over 717 conserved syntenic segments. Using transcriptome data from three fruit developmental stages, a total of 54 CcMYBs and 81 CaMYBs showed significant differential expression patterns. Furthermore, the expression of 24 CcMYBs from the transcriptome data was validated by quantitative real-time (qRT) PCR analysis. Eight out of the 24 CcMYBs validated by the qRT-PCR were highly expressed in fiery hot C. chinense than in the lowly pungent C. annuum. Furthermore, the co-expression analysis revealed several MYB genes clustered with genes from the capsaicinoid, anthocyanin, phenylpropanoid, carotenoid, and flavonoids biosynthesis pathways, and related to determining fruit shape and size. The homology modeling of 126 R2R3 CcMYBs showed high similarity with that of the Arabidopsis R2R3 MYB domain template, suggesting their potential functional similarity at the proteome level. Furthermore, we have identified simple sequence repeat (SSR) motifs in the CcMYB genes, which could be used in Capsicum breeding programs. The functional roles of the identified CcMYBs could be studied further so that they can be manipulated for Capsicum trait improvement.

Clubroot caused by Plasmodiophora brassicae is a severe disease of cruciferous crops that decreases crop quality and productivity. Several clubroot resistance-related quantitative trait loci and candidate genes have been identified. However, the underlying regulatory mechanism, the interrelationships among genes, and how genes are regulated remain unexplored. MicroRNAs (miRNAs) are attracting attention as regulators of gene expression, including during biotic stress responses. The main objective of this study was to understand how miRNAs regulate clubroot resistance-related genes in P. brassicae-infected Brassica rapa. Two Brassica miRNAs, Bra-miR1885a and Bra-miR1885b, were revealed to target TIR-NBS genes. In non-infected plants, both miRNAs were expressed at low levels to maintain the balance between plant development and basal immunity. However, their expression levels increased in P. brassicae-infected plants. Both miRNAs down-regulated the expression of the TIR-NBS genes Bra019412 and Bra019410, which are located at a clubroot resistance-related quantitative trait locus. The Bra-miR1885-mediated down-regulation of both genes was detected for up to 15 days post-inoculation in the clubroot-resistant line CR Shinki and in the clubroot-susceptible line 94SK. A qRT-PCR analysis revealed Bra019412 expression was negatively regulated by miR1885. Both Bra019412 and Bra019410 were more highly expressed in CR Shinki than in 94SK, the same expression pattern was detected in multiple clubroot-resistant and clubroot-susceptible inbred lines. A 5′ rapid amplification of cDNA ends analysis confirmed the cleavage of Bra019412 by Bra-miR1885b. Thus, miR1885s potentially regulate TIR-NBS gene expression during P. brassicae infections of B. rapa.

The indigenous communities across the globe especially in the rural areas consume locally available plants known as Traditional Food Plants (TFPs) for their nutritional and health-related needs. Recent research shows that many of the traditional food plants are highly nutritious as they contain health beneficial metabolites, vitamins, mineral elements and other nutrients. Excessive reliance on the mainstream staple crops has its own disadvantages. TFPs are nowadays considered important crops of the future and can act as supplementary foods for the burgeoning global population. They can also act as emergency foods in times of pandemics and other situations like COVID-19. The current situation necessitates locally available alternative nutritious TFPs for sustainable food production. To increase the cultivation or improve the traits in TFPs, it is essential to understand the molecular basis of the genes that regulate some important traits such as nutritional components and resilience to biotic and abiotic stresses. The integrated use of modern omics and gene editing technologies provide great opportunities to better understand the genetic and molecular basis of superior nutrient content, climate-resilient traits and adaptation to local agroclimatic zones. Recently, realising the importance and benefits of TFPs, scientists have shown interest in the prospection and sequencing of traditional food plants for their improvements, further cultivation and mainstreaming. Integrated omics such as genomics, transcriptomics, proteomics, metabolomics and ionomics are successfully used in plants and have provided a comprehensive understanding of gene-protein-metabolite networks. Combined use of omics and editing tools has led to successful editing of beneficial traits in few TFPs. This suggests that there is ample scope of integrated use of modern omics and editing tools/techniques for improvement of TFPs and their use for sustainable food production. In this article, we highlight the importance, scope and progress towards improvement of TFPs for valuable traits by integrated use of omics and gene editing techniques.

Farmers often emphasize more on physical changes of color rather than physiological maturity for proper harvesting time of Khasi mandarin (Citrus reticulata Blanco). The study aimed to characterize...

Humans are directly or indirectly dependent on plant foods for their nutritional health. Hence it is important to characterize the macro and micro nutrients and mineral-elements of commonly consumed dietary vegetables like Capsicum (Chilli). In the present study global metabolites, total ascorbic acid, phenols, flavonoids, capsaicinoids, mineral-elements and antioxidant activities were determined on different developmental stages of Capsicum fruits (immature, breaker and mature) belonging to three Capsicum species namely Capsicum chinense, C. frutescens, and C. annuum. The results obtained from the present study showed the maturity dependent increase in the sugar and fatty acid metabolites, capsaicinoids, ascorbic acid and phenol content, and antioxidant activities. Similarly, essential mineral-elements also increased during the fruit maturation in C. chinense, however, contrasting results was observed in C. annuum. In addition to that some health beneficial compounds such as antibacterial and antifungal metabolites exclusively observed in matured C. chinense. These interesting observations have opened the possibility to understand and manipulate biosynthesis of macro/micronutrients and mineral elements in order to improve nutritional quality of Capsicum (Chilli) species.

Nutritional deficiency is found to be a major threat to human health, especially in low-income countries. Thus it is essential to improve nutritional qualities of important food crops. Foxtail millet is second largest cultivated millet and 2–5 times nutritionally richer than major cereal crops. During the present study, we identified genetic determinants of ten nutritional elements including potassium, nickel, calcium, boron, magnesium, phosphorus, sulphur, zinc, manganese and iron for the first time in foxtail millet. For this purpose, genome-wide association studies (GWAS) were conducted using 93 diverse accessions and 10 K SNPs (distributed across all the nine foxtail millet chromosomes). Altogether, 74 marker-trait associations (MTAs) were identified to be associated with above mentioned ten elements, out of which ten (10) MTAs (associated with B, Mg, Zn and Fe) showed high confidence [-log(p) > 5.78]. Identified desirable SNP alleles and favourable haplotypes may prove useful in foxtail breeding. Also, significant pyramiding effect suggested that associated elements can be substantially enhanced through combining more than one MTA. Candidate genes residing within or near the association signal may be selected for functional characterization. Superior genotypes identified may prove as a potential donor in foxtail millet breeding assisted through the molecular marker.

Capsicum belonging to the family Solanaceae is one of the most widely consumed crops in the world as a vegetable, spice and a raw salad and is distinctly valuable for its spicy pungent flavour. Proteomic investigation of crop plants is an essential step towards deciphering the functional basis of traits in an organism and to deepen our understanding on the regulation of various developmental patterns, biotic, and abiotic stress response and tolerance mechanisms. The differential proteome expression profiling of tissues during different developmental stages and under different conditions may indicate the specific proteome dynamics involved in the developmental programs and under stress conditions. Although substantial progress in proteomics of other Solanaceae plants has been made in the past two decades, a comprehensive review on Capsicum proteomics is still lacking. This review provides updated information on the advancement of Capsicum proteomic study in cytoplasmic male sterility, during fruit development and ripening, and under different biotic and abiotic stresses. Although limited information is available on the post translational protein modifications in Capsicum, a brief outline is given at the end detailing various post translational modifications. This proteomic update on Capsicum will be useful for future studies aimed at Capsicum improvement programs.

The Portulaca oleracea L. commonly known as Purslane is distributed all over the world and easily grows in diverse soil conditions. It has been traditionally used as a nutritious and ethnomedicinal food across the globe. Various studies have shown that the plant is a rich source of various important phytochemicals such as flavonoids, alkaloids, terpenoids, proteins, carbohydrates, and vitamins such as A, C, E, and B, carotenoids and minerals such as phosphorus, calcium, magnesium and zinc. It is particularly very important because of the presence of very high concentration of omega-3- fatty acids especially α-linolenic acid, gamma- linolenic acid and linoleic acid, which are not generally synthesized in terrestrial plants. Various parts of Purslane are known for ethnomedicinal and pharmacological uses because of its anti-inflammatory, antidiabetic, skeletal muscle relaxant, antitumor, hepatoprotective, anticancer, antioxidant, anti-insomnia, analgesic, gastroprotective, neuroprotective, wound healing and antiseptic activities. Due to multiple benefits of Purslane, it has become an important wonder crop and various scientists across the globe have shown much interest in it as a healthy food for the future. In this review, we provide an update on the phytochemical and nutritional composition of Purslane, its usage as nutritional and an ethnomedicinal plant across the world. We further emphasize its ethno medicinal importance across cultures and pharmacological potential.

The genus Capsicum belongs to the Solanaceae family which contains more than 30 species, of which only five, namely, C. annuum L., C. chinense Jacq., C. frutescens L., C. baccatum L. and C. pubescens L. are cultivated. Capsicums are very important crop plants and widely consumed worldwide as they are important source of several nutritional and dietary compounds which includes capsaicinoids, vitamins A and C, pigments, minerals and essential oils. Among the five cultivated spp., C. annuum has gained the maximum attention of researchers. Research on other Capsicum spp. is limited despite they are having wide diversity, and are potential sources of desirable genes for several economically-important traits such as disease resistance, fruit shape, size and color. The improvement of C. annuum by hybridization with C. chinense, C. frutescens, C. baccatum and C. pubescence indicates that these four species may play a significant role as important genetic resources for the transfer of genes of economically-important traits to C. annuum. In this chapter, we have compiled the development and advances made in genetics, breeding and genomics with main emphasis on C. chinense (world’s hottest chili), C. frutescens, C. baccatum and C. pubescens. Highlighted are recent developments in the application of biotechnology especially tissue culture and genetic transformation in Capsicum species.

Impacts of plastic pollution, recognized as a driver of change in the global environment, have been under reported in terrestrial fauna. In this study, we looked at presence of plastic in the diet of Asian elephant and other megaherbivores in the forest habitats of Haridwar and Lansdowne, Uttarakhand state, India. We collected dung and pellet samples from forest edges and forest interiors and quantified plastic particles and other anthropogenic waste present. Each anthropogenic waste item was measured, weighed and sub-categorized into the type of plastic or other categories. Thirty-two percent of the elephant dung samples showed presence of plastic and other waste. Plastic particles comprised of 85% of the waste recovered from the dung with 100% occurrence in elephant dung samples (mean 47.08±12.85 particles per sample). We found twice as many plastic particles (85.27±33.7 per 100g of dung samples) in forest samples as compared to forest edge samples (35.34±11.14 plastic particles/100g of dung samples). Other non-biodegradable anthropogenic waste recovered from elephant dung (glass, metal, rubber bands, clay pottery and tile pieces) was found to be much higher for forest samples (34.79±28.41 items/100g sample) as compared to forest edge samples (9.44±1.91items/100g). This study is the first systematic documentation of occurrence of non-biodegradable waste in the diet of Asian elephants. Dominance of plastic compared to other non-biodegradable material in elephant dung samples highlights its widespread use and poor waste segregation practices. We recommend developing a comprehensive solid waste management strategy to mitigate the threat of plastic pollution around these critical elephant habitats.

Piriformospora indica, a root endophytic fungus, augments plant nutrition and productivity as well as protects plants against pathogens and abiotic stresses. High salinity is a major problem faced by plants as well as by microbes. Until now, the precise mechanism of salt stress tolerance in P. indica has remained elusive. In this study, the transcriptomes of control and salt-treated (0.5 M NaCl) P. indica were sequenced via the RNA-seq approach. A total of 30,567 transcripts and 15,410 unigenes for P. indica were obtained from 7.3 Gb clean reads. Overall 661 differentially expressed genes (DEGs) between control and treated samples were retrieved. Gene ontology (GO) and EuKaryotic Orthologous Groups (KOG) enrichments revealed that DEGs were specifically involved in metabolic and molecular processes, such as “response to salt stress”, “oxidoreductase activity”, “ADP binding”, “translation, ribosomal structure and biogenesis”, “cytoskeleton”, and others. The unigenes involved in “cell wall integrity”, “sterol biosynthesis”, and “oxidative stress” such as Rho-type GTPase, hydroxymethylglutaryl-CoA synthase, and thioredoxin peroxidase were up-regulated in P. indica subjected to salt stress. The salt-responsive DEGs have shown that they might have a potential role in salt stress regulation. Our study on the salt-responsive DEGs established a foundation for the elucidation of molecular mechanisms related to P. indica stress adaptation and a future reference for comparative functional genomics studies of biotechnologically important fungal species.

Capsaicinoids are a group of molecules, which impart pungency (hotness) to Capsicum fruits. The capsaicinoids are synthesized in the placenta of the Capsicum fruits. During the past few decades, there is an increasing interest in elucidation of the biosynthetic pathway of capsaicinoids. The whole genome sequencing of the highly pungent species, Capsicum chinense has revealed several important genes that are responsible for the biosynthesis of capsaicin and dihydrocapsaicin, the two major active constituents of the pungency complex, also known as capsaicinoid complex. The capsaicinoids have recently attracted a wide attention, because of its huge pharmacotherapeutic potential in treating several diseases, such as diabetes, cancer, obesity, cardiovascular, respiratory, gastric diseases and urological disorders. Further, capsaicin has been increasingly used as a molecule of choice for pain relief and many other diseases. In this chapter, we have presented briefly the sources and types of capsaicinoids, its biosynthesis, quantification of pungency and the genes responsible for its biosynthesis. Further, we have highlighted the candidate genes that are important for the biosynthesis of capsaicin and can be used for further manipulation experiments. At the end, this chapter focuses on the therapeutic potential of capsaicin in treating several diseases, such as diabetes, cancer, obesity, cardiovascular, respiratory, gastric diseases and urological disorders and its increasing role in pain relief. Finally, we have briefly discussed the mode of action of capsaicin against cancer, cardiovascular diseases, obesity management, pain relief and urological disorders.

Apart from using traditionally in culinary preparations, chili peppers are also important constituents of herbal medicines. Although the bioactive components are studied mostly in the fruits of Capsicum annuum, no such study reports till date is available for Ghost chili (C. chinense) from North East India. Therefore, the aim of this study was to carry out an analysis of the bioactive constituents in the naturally occurring hottest chili Ghost chili (C. chinense), and evaluate its antioxidant, pro/anti-genotoxic, and apoptotic effects in in vitro and in vivo models. Three different antioxidant assays showed that lower doses of Ghost chili extract showed higher DNA protective and antioxidant activities. Furthermore, the administration for 7 alternate days into 6 week old Swiss albino mice showed that the lower doses (50 and 100 mg/kg bw) reduced DMBA induced genotoxicity beside significantly enhancing the activities of hepatic antioxidant enzymes, while higher dose (200 mg/kg bw) induced genotoxic effect in bone marrow cells. The administration of higher dose (200 mg/kg bw) also induced apoptosis and upregulation of Bax (pro) and downregulation of Bcl-2 (anti) apoptotic genes. Dose dependent increase of apoptosis was also observed in Hep G2 and Hep 3B liver cancer cell lines. Our findings in the present study suggest that low doses of C. chinense can exert cancer chemopreventive effects. The induction of apoptosis in both cancer cell lines and mouse bone marrow cells, and up-regulation of proapoptotic genes suggests that the higher dose of C. chinense can be used for targeted cancer therapy.

The objective of this work was to evaluate the occurrence of polyembryonic seedlings and other morphological parameters in Khasi mandarin during three harvest years and to identify zygotic (sexual) seedlings from nucellar (asexual) ones grown under in-vitro conditions using molecular markers. Embryos from 27 polyembryonic and 7 monoembryonic seeds of Khasi mandarin were grown in-vitro. DNA from seedlings and mother parent was analyzed using 16 ISSR and 5 RAPD primers, of which 4 ISSR and a set of 3 RAPD primers were effective to identify zygotic or nucellar origin of the seedlings. In-vitro culture enables maximum embryos of each seed to grow, favouring the origin of seedlings to be identified as zygotic. Among 69 tested individuals, 37 zygotic and 32 nucellar seedlings were recognized. In polyembryonic and monoembryonic seeds, 59.6% and 42.8% of the seedlings, respectively, have the sexual origin. Morphological characteristics of seeds and the seedlings generated varied significantly and were not correlated with polyembryony except for the clutch size and the number of branches. Polyembryonic seeds in the cultivar are high, ranging from 50.0%, 55.5% to 83.3% over three harvest years with more clutch size and the possibility of obtaining zygotic plants from them is high. In polyembryonic seeds not all zygotic seedlings were produced by small embryos located at the micropyle. Identification of zygotic seedlings by ISSR and RAPD markers in Khasi mandarin cultivar is efficient and reliable at an early developmental stage.

Till date, no systematic study of phosphate transporter (PHT) genes is reported in Capsicum species. For the first time, we report the identification and homology modelling of C. annuum PHT genes (CaPHT) belonging to CaPHT1, CaPHT2, CaPHT3, CaPHT4, CaPHT5 and CaPHO family. Further, gene duplication analysis identified 14 segmental and 5 tandemly duplicated gene pairs. Synteny analysis showed high collinearity of CaPHTs with tomato and potato. The 3D structures of CaPHT genes were highly similar to the reference model suggesting potential functional similarities of PHT genes in Capsicum. Analysis in fruit transcriptomes and validation using quantitative real-time PCR showed differential expressions (DE) of CaPHTs in leaf, stem, root, flower and fruit tissues of C. annuum. During P-stress conditions CaPHT1;3 to CaPHT1;7, CaPHT3;1 to CaPHT3;4 and six members of CaPHO family showed DE patterns between leaf and root tissues. Metabolite profiling of plants grown under P-stress conditions showed significantly (p-value

Capsicum fruits are rich sources of mineral nutrients with several health benefits. However, a thorough investigation of mineral elements in Capsicum fruits at green, breaker and mature developmental stages in comparatively larger germplasm has not been reported yet. This study reports profiling of 9 mineral elements i.e. Mg, P, K, Ca, B, Mn, Fe, Cu and Zn in 20 Capsicum accessions belonging to Capsicum annuum, C. chinense and C. frutescens from Northeast India. Briefly, the highest content of P (1798 ± 39) and K (7560 ± 76 mg 100g−1) at the green and breaker stages of Capsicum accession Acc-Ca9, Fe (13 ± 2) and Zn (4 ± 0.1) at the breaker stage of Acc-Ca2; and Cu at the mature stage of Acc-Cc2 (3 ± 0.4) and Acc-Cc3 (3.4 ± 0.04 mg 100g−1) were observed and showed significant differences (p

Indigenous communities across the globe, especially in rural areas, consume locally available plants known as Traditional Food Plants (TFPs) for their nutritional and health-related needs. Recent research shows that many TFPs are highly nutritious as they contain health beneficial metabolites, vitamins, mineral elements and other nutrients. Excessive reliance on the mainstream staple crops has its own disadvantages. Traditional food plants are nowadays considered important crops of the future and can act as supplementary foods for the burgeoning global population. They can also act as emergency foods in situations such as COVID-19 and in times of other pandemics. The current situation necessitates locally available alternative nutritious TFPs for sustainable food production. To increase the cultivation or improve the traits in TFPs, it is essential to understand the molecular basis of the genes that regulate some important traits such as nutritional components and resilience to biotic and abiotic stresses. The integrated use of modern omics and gene editing technologies provide great opportunities to better understand the genetic and molecular basis of superior nutrient content, climate-resilient traits and adaptation to local agroclimatic zones. Recently, realizing the importance and benefits of TFPs, scientists have shown interest in the prospection and sequencing of TFPs for their improvements, cultivation and mainstreaming. Integrated omics such as genomics, transcriptomics, proteomics, metabolomics and ionomics are successfully used in plants and have provided a comprehensive understanding of gene-protein-metabolite networks. Combined use of omics and editing tools has led to successful editing of beneficial traits in several TFPs. This suggests that there is ample scope for improvement of TFPs for sustainable food production. In this article, we highlight the importance, scope and progress towards improvement of TFPs for valuable traits by integrated use of omics and gene editing techniques.

Foxtail millet (Setaria italica), the second largest cultivated millet crop after pearl millet, is utilized for food and forage globally. Further, it is also considered as a model crop for studying agronomic, nutritional and biofuel traits. In the present study, a genome-wide association study (GWAS) was performed for ten important agronomic traits in 142 foxtail millet core eco-geographically diverse genotypes using 10 K SNPs developed through GBS-ddRAD approach. Number of SNPs on individual chromosome ranged from 844 (chromosome 5) to 2153 (chromosome 8) with an average SNP frequency of 25.9 per Mb. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations was found to decay rapidly with the genetic distance of 177 Kb. However, for individual chromosome, LD decay distance ranged from 76 Kb (chromosome 6) to 357 Kb (chromosome 4). GWAS identified 81 MTAs (marker-trait associations) for ten traits across the genome. High confidence MTAs for three important agronomic traits including FLW (flag leaf width), GY (grain yield) and TGW (thousand-grain weight) were identified. Significant pyramiding effect of identified MTAs further supplemented its importance in breeding programs. Desirable alleles and superior genotypes identified in the present study may prove valuable for foxtail millet improvement through marker-assisted selection.

The uncertainties of climatic variability and global warming are leading to rising concerns towards ensuring global food security of an expanding population. Unfavorable climatic conditions, like extremes of temperature, drought, flood, and salinity, in addition to the elevated greenhouse gases adversely affect the physiology, and accordingly the quantitative and qualitative characteristics of plants. Mustard (Brassica juncea) and rape (Brassica rapa), the two important oilseed crops of the Indian subcontinent, are also cultivated in Eastern Europe, Russia, China, and Canada. These oilseed crops are affected by various biotic and abiotic stress during different growth and developmental stages, that severely influences agricultural productivity. Extensive breeding efforts toward the development of Brassica cultivars that can resist these climatic variabilities are under various stages of progress. The Brassica germplasm and the wild relatives of B. juncea and B. rapa, which constitute important genetic stocks, are also being utilized in these breeding programs. An integrated approach is required that will study plant–insect pest and disease–climate interactions for conceiving future strategies to develop disease-, insect-resistant, and climate-resilient plant varieties. Developing mustard varieties, efficient in the utilization of soil nutrients, are also required for improving productivity in impoverished soils and for better uptake/utilization of nutrients in soils rich in resources. Future research in oilseed mustard and rape should, therefore, involve examining the influence of climate-smart traits on yield/production in targeted environments, so that climate-resilient cultivars adapted to climate change conditions could be developed. This chapter summarizes the advances in breeding of climate-smart traits such as, tolerance to drought, heat, salinity, flooding and frost, and efficient nutrient utilization, in oilseed mustard and rape, that could assist in the genomic designing for climate-smart crops.

People have an intimate association with plants since the onset of civilizations on this planet for various purposes, such as food, shelter, dye and healing. The use of plants for medicinal purposes in ancient times involved trial-and-error methods for their bioactivities. The therapeutic potential of medicinal plants has been well acknowledged in recent times with increasing experimental proofs. This has led to increased interest in their use for nutraceutical as well as medicinal purposes. It is not surprising that many of the modern medicines used currently are derived from plants. For this reason, there is an increased interest in the bioprospecting, usage and drug formulations of medicinal plants because of the presence of specialized metabolites in them. This upsurge in the interest on the usage of medicinal plants is attributed to their easy availability, developments in the recent high-throughput omics approaches, increased disease burden and increased participation of pharmaceutical companies in the business of producing phytomedicinal products for delivering plant-based healthcare services. To date, the primary focus of research with regard to medicinal plants has been in the areas of phytochemistry, pharmacognosy and horticulture. However, recent breakthroughs in high-throughput approaches have revolutionized this area of research and shifted the focus towards omics approaches, such as genomics, transcriptomics, proteomics, metabolomics, epigenomics, trichomics and ionomics. Thus, the present chapter discusses the high-throughput omics approaches in identifying genes, proteins and metabolites of medicinal plant species.

At DNA level, methylation is one of the most studied epigenetic marks and plays an important role in plant growth and development via regulating gene expression, integrity, and mobility of genome as well as transposons. The epigenetic studies especially the DNA methylation have been investigated only in a few members of the Solanaceae family like tomato and potato. So far, cytosine methylation landscape in Capsicum, a diploid, self-pollinating crop of the Solanaceae family grown worldwide for fresh and processed products, is far less documented. In our research study in the laboratory, we found the overall high cytosine methylation in Capsicum fruit as compared to other plants. The Capsicum fruit shows at an average 89.1% of CG, 84.85% of CHG, and 24.9% CHH cytosine methylation globally. The variation in genome size reflects the variations in the global cytosine methylation across different species. The Capsicum genome which is 3–4-fold larger than that of tomato and potato is found to have ~1.2–2.7-fold higher cytosine methylation at all methylation contexts. The abundance of repetitive elements (REs) generally affects the variations in genome size across species and generally has dense cytosine methylation. The intraspecific variations in cytosine methylation as well as the miRNA-regulated methylation are unexplored in Capsicum, which could provide plausible evolutionary relationship between different species of Solanaceae family. DNA methylation is considered as one of the requisites for various developmental and transcriptional gene expression regulation, while it is also important for reprogramming of various biological processes and transcriptional gene regulation by trimming down their methylation profiles. Therefore, the collaborative role of methylation and demethylation phenomenon in DNA results in the global dynamic nature of cytosine methylation.

Capsicum is one of the most important vegetable crops of the family Solanaceae and is widely used as spice due to its pungent nature. Besides, Capsicum fruit rich in metabolites and vitamins; and also has anticancerous property, which further increases the importance of this crop. However, Capsicum crop is highly affected by abiotic/biotic stresses such as drought, heat, cold, salinity, and pathogens. To overcome these stresses, plants adapted several mechanisms such as the production of osmoprotectant, proline, galactinol and raffinose, and the reduction of reactive oxygen species. Autophagy also plays an important role to provide tolerance against stresses through degradation of toxins. Among the others, transcription factors and plasma membrane intrinsic proteins, and plant endophytes are found to be involved in regulating stress tolerance mechanism. Furthermore, in Capsicum genome, a number of genes and quantitative trait loci (QTLs) involved in stress tolerance mechanism have been identified. In this chapter, a detail compilation of important molecular mechanisms and associated genes/QTLs involved toward imparting abiotic and biotic stress tolerance in Capsicum genome is made.