Nirala Ramchiary

Global omics offer extensive insights into the diversity of essential biomolecules across various plant developmental stages. Despite advancements in high-throughput technologies, the integrated analysis of global omics such as proteomics, transcriptomics, and metabolomics, is yet to be fully explored in fruits of Capsicum species. In this study, w...

Agriculture has been a vital necessity for human livelihood ever since human domestication around 10 to 12 millenniums back. It serves as a backbone for a strong economic system in developing countries today. Plants are dietary sources of human livelihood along with trees that provide wood for shelter, tools, furniture, and paper. The healthy growt...

The mangrove ecosystems are characterised by high salinity and hypoxia. When viviparous mangrove propagules detach from the mother plants and find a substratum, their roots must respond appropriately to the external environment. Therefore, for an improved understanding of the dynamics of mangrove adaptations to fluctuating intertidal habitats, root...

Capsicum (chili pepper) is a highly valued crop of the Solanaceae family desired for its characteristic sensory and culinary properties around the world. Capsicum fruits exhibit huge variations in the phenotypic traits, such as shape, size, color, texture, shelf life, and so on, that appeal directly to the consumer preference. The fruits of the Cap...

Traditional leafy vegetables (TLVs) are rich in beneficial bioactive compounds and mineral elements. The rural areas of Kerala, India, have a diversity of unconventional TLVs, and only limited research is available on their nutritional and biochemical composition. Therefore, this study was designed to evaluate the mineral elements, metabolites, ant...

Capsicum (chili pepper) is a widely popular and highly consumed fruit crop with beneficial secondary metabolites such as capsaicinoids, carotenoids, flavonoids, and polyphenols, among others. Interestingly, the secondary metabolite profile is a dynamic function of biosynthetic enzymes, regulatory transcription factors, developmental stage, abiotic...

Brassica crops have great economic value due to their rich nutritional content and are therefore grown worldwide as oilseeds, vegetables, and condiments. Deciphering the molecular mechanisms associated with the advantageous phenotype is the major objective of various Brassica improvement programs. As large technological advancements have been achie...

The members of ZRT, IRT-like protein (ZIP) family are involved in the uptake and transportation of several metal ions. Here, we report a comprehensive identification of ZIP transporter genes from Capsicum annuum, C. chinense, and C. baccatum, and their expression analysis under Zn and Fe stress. Changes in root morphology and differential accumulat...

Considering the vast amount of data and information that is made available for phytochemicals in the last few years, the development of consolidated databases, freely available and commercial, has reduced the complications of retrieving and utilizing the resources. Most of the available databases are typical for one kind of information; for example...

Since time immemorial, humans utilize plants for various needs such as food, shelter, fuelwood, and medicine. Plants exhibit medicinal properties due to the presence of several classes of phytochemicals, especially secondary metabolites, also known as specialized metabolites (SMs). Plants are chemical factories and many important drugs used today a...

In a rapidly changing environment along with the growing population, crop production and improvement are the most sought-after sectors in the world. Pepper (Capsicum spp.) is a highly consumed plant species in the form of spice or whole fruit and is widely popular for its pungent flavour and vibrant colours worldwide. Like other crop plants, pepper...

The fruits of the tomato crop (Solanum lycopersicum L.) are increasingly consumed by humans worldwide. Due to their rich nutritional quality, pharmaceutical properties, and flavor, tomato crops have gained a salient role as standout crops among other plants. Traditional breeding and applied functional research have made progress in varying tomato g...

The Capsicum L. belonging to the family Solanaceae is an economically important genus of flowering plants. This genus comprises more than 30 species with its unique characteristic feature of pungency in its fruits, which are used as spices, in raw salads and pickles. People also use the species of Capsicum for ethnomedicinal and ethnoveterinary pur...

Hybrid breeding is one of the efficacious methods of crop improvement. Here, we report our work towards understanding the molecular basis of F1 hybrid heterosis from Capsicum chinense and C. frutescens cross. Bisulfite sequencing identified a total of 70597 CG, 108797 CHG and 38418 CHH differentially methylated regions (DMRs) across F1 hybrid and p...

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...

Capsicum is an important member of the Solanaceae family grown worldwide for its fruits which are utilized as spice as well as a vegetable crop. Capsicum fruits are highly rich in pharmacological compounds such as carotenoids (provitamin A), vitamin C and E, flavonoids and the distinct metabolite alkaloid complex known as capsaicinoids which impart...

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 (...

Pepper is one of the most important spice crops in the world today with an enormous economic value. The pepper fruits are rich in pharmaceutically important compounds such as carotenoids and capsaicinoids. Over the years, crops of pepper have suffered significant losses in terms of yield and quality due to a myriad of pathogen infections including...

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 understandin...

Improvement in crop yields in Brassica juncea has been stagnating for some time, a trend that is likely to exacerbate further due to the effects of various biotic and abiotic stresses like insects or diseases, drought, submergence, salinity and high temperature. The crucial increase in the crop production should necessarily come from higher yields,...

Genetic maps are a prerequisite for understanding genome organization, map-based cloning, and marker-assisted selection of agronomically important traits in crops. The application of genetic markers to genetic mapping and quantitative trait locus analyses in Brassica juncea is now well-established. Extensive genetic mapping efforts have been made i...

Mangroves are globally recognized for their ecological, economic, social, and cultural importance. They provide a variety of goods and services to humanity. Mangroves are a group of trees and shrubs sheltered in the intertidal zones of tropical, subtropical, and warm temperate regions of the planet. They are adapted to a wide range of environmental...

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...

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 diet...

Purslane (Portulaca oleracea L.) is a popular orphan crop used for its nutritional properties in various parts of the world. It is considered one of the richest terrestrial sources of omega-3 and omega-6-fatty acids (ω-3 and 6-FAs) suggesting its importance for human health. This ethnomedicinal plant is also an important part of traditional healing...

Till date, no systematic study of phosphate transporter (PHT) genes is reported in Capsicumspecies. For the first time, we report genomewide 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 tande...

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 eleme...

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, ter...

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, C...

MicroRNAs (miRNAs) are crucial elements of convoluted gene regulatory network that governs plant development and stress responses. The role of small RNAs (sRNA) especially in C. chinense (Bhut Jolokia) and C. frutescens (Kon Jolokia) of Capsicum genus are still unexplored. Therefore, to identify miRNAs small RNA sequencing was performed from leaf,...

The sustainable development goals (SDGs) are a set of 17 goals with 169 targets. The Agenda 2030 of the United Nations envisages a holistic approach to achieve these goals by focusing on humankind and the planet. In this review, we analyzed the scientific literature and technical reports of international bodies such as the United Nations and Food a...

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 transcr...

Capsaicinoids, a group of secondary metabolites (alkaloids) which imparts hot property, are unique to the Capsicum fruits and have high value in the pharmaceutical and food industries. In spite of having high capsaicinoids content with ethnopharmacological and economic importance, the C. chinense and C. frutescens of the Northeast India, are undere...

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, Cap...

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 propo...

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 chromoso...

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. chi...

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 the physiological maturity of the fruit across the developmental stages which has not been well reported till now. A cold temperature (4°C) treatment wa...

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 early 1980s, DNA sequencing was heralded as a game changer in the way we look at biology. However, the cost of operation and scale of handling large contiguous reads were the biggest bottleneck. Therefore, research and experimentation were coerced to relatively simpler genomes of prokaryotes and organelle genomes of eukaryotes such as mitochondr...

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...

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 q...

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-el...

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 t...

Noncoding RNAs were not only classified based on their structural variation but also on the basis of their regulatory roles in diverse cellular pathways. During the last two decades, several studies on noncoding RNAs have been reported and now it is well known that they regulate expression of genes involved in diverse biological functions. Therefor...

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 determ...

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 c...

The genus Capsicum (chili), one of the important Solanaceae crop plants, is grown widely for producing vegetables and spices and for extraction of the coloring agent. Chili fruits contain a vast number of metabolites that are crucial for human health, viz., carotenoids (provitamin A), vitamin E, vitamins C, flavonoids, and capsaicinoids (destroy fr...

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 invitro conditions using molecular markers. Embryos from 27 polyembryonic and 7 monoembryonic seeds o...

Key message: QTLs and candidate gene markers associated with leaf morphological and color traits were identified in two immortalized populations of Brassica rapa, which will provide genetic information for marker-assisted breeding. Brassica rapa is an important leafy vegetable consumed worldwide and morphology is a key character for its breeding....

Bhut jolokia, commonly known as Ghost chili, a native Capsicum species found in North East India was recorded as the naturally occurring hottest chili in the world by the Guinness Book of World Records in 2006. Although few studies have reported variation in pungency content of this particular species, no study till date has reported detailed expre...

Next-generation sequencing (NGS) technologies make possible the sequencing of the whole genome of a species decoding a complete gene catalogue and transcriptome to al‐ low the study of expression pattern of entire genes. The huge data generated through whole genome and transcriptome sequencing not only provide a basis to study variation at gene seq...

Capsicum species commonly known as Chilli pepper is one of the world’s most important vegetable and spice crop. India is the world’s largest producer, consumer and exporter of chilli pepper. Despite comprising 38 species, only six species of Capsicum namely, Capsicum annuum, C. assamicum, C. baccatum, C. frutescence, C. chinense and C. pubescens ar...

The YacK gene from Yersinia enterocolitica strain 7, cloned in pET28a vector and expressed in Escherichia coli BL21 (DE3), showed laccase activity when oxidized with 2,2’-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) and guaiacol. The recombinant laccase protein was purified and characterized biochemically with a molecular mass of ≈58 KDa...

Cabbage belonging to Brassicaceae family is one of the most important vegetables cultivated worldwide. The economically important part of cabbage crop is head, formed by leaves which may be of splitting and non-splitting types. Cabbage varieties showing head splitting causes huge loss to the farmers and therefore finding the molecular and structura...

Cabbage head splitting can greatly affect both the quality and commercial value of cabbage (Brassica oleracea). To detect the genetic basis of head-splitting resistance, a genetic map was constructed using an F 2 population derived by crossing ''748'' (head-splitting-resistant inbred line) and ''747'' (head-splitting-susceptible inbred line). The m...

Key message The resistance to Diamondback moth insect in cabbage is governed by many minor loci in quantitative nature, and at least four genetic loci should be incorporated in marker-assisted breeding program for developing partially resistant DBM cabbage cultivars. Abstract The Diamondback moth (DBM), Plutella xylostella (L.), is the most dest...

Strains of Ganoderma lucidum MDU-7 produces multiple extracellular isoforms of laccase in submerged culture condition using malt extract as a carbon source and copper sulfate as an inducer. SDS- PAGE followed by MALDI-TOF peptide fingerprinting confirmed laccase isozyme with molecular mass of 24-66 kDa. Two laccase isozymes (Glac H1 and Glac L1) we...

One of the main characteristics of chili pepper fruit is its pungent taste due to the presence of a group of compounds known as capsaicinoids. Capsaicinoids biosynthesis in chili plant is defined by two pathways: phenylpropanoid, which determines phenolic structure; and fatty acid metabolism, which determines the molecule’s fatty acids. The potency...

Capsicum species commonly known as Chili peppers are economically important group of plants belonging to the Solanaceae family. Of the 38 species reported, only six species namely, Capsicum annuum, C. assamicum, C. baccatum, C. frutescence, C. chinense and C. pubescens are cultivated. They are very important component of the human being as peppers...

Fusarium wilt (FW), caused by the soil-borne fungal pathogen Fusarium oxysporum is a serious disease in cruciferous plants, including the radish (Raphanus sativus). To identify quantitative trait loci (QTL) or gene(s) conferring resistance to FW, we constructed a genetic map of R. sativus using an F2 mapping population derived by crossing the inbre...

MicroRNAs (miRNAs) are recently discovered, noncoding, small regulatory RNA molecules that negatively regulate gene expression. Although many miRNAs are identified and validated in many plant species, they remain largely unknown in Brassica rapa (AA 2n =, 20). B. rapa is an important Brassica crop with wide genetic and morphological diversity resul...

MicroRNAs (miRNAs) are recently discovered, noncoding, small regulatory RNA molecules that negatively regulate gene expression. Although many miRNAs are identified and validated in many plant species, they remain largely unknown in Brassica rapa (AA 2n =, 20). B. rapa is an important Brassica crop with wide genetic and morphological diversity resul...

MicroRNAs (miRNAs) are recently discovered, noncoding, small regulatory RNA molecules that negatively regulate gene expression. Although many miRNAs are identified and validated in many plant species, they remain largely unknown in Brassica rapa (AA 2n =, 20). B. rapa is an important Brassica crop with wide genetic and morphological diversity resul...

MicroRNAs (miRNAs) are recently discovered, noncoding, small regulatory RNA molecules that negatively regulate gene expression. Although many miRNAs are identified and validated in many plant species, they remain largely unknown in Brassica rapa (AA 2n =, 20). B. rapa is an important Brassica crop with wide genetic and morphological diversity resul...

Brassica rapa is an important crop species that produces vegetables, oilseed, and fodder. Although many studies reported quantitative trait loci (QTL) mapping, the genes governing most of its economically important traits are still unknown. In this study, we report QTL mapping for morphological and yield component traits in B. rapa and comparative...

Brassica rapa L. (AA, 2n = 20), an A genome diploid species of Brassica genus is of researchers interest recent days since enormous amount of data is available about the genome. Since EST analysis is a powerful tool in gene discovery we compared different existing methods and developed a new pipeline for EST computational analysis to analyze the av...

Sequencing of the chloroplast (cp) genome using traditional sequencing methods has been difficult because of its size (>120 kb) and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the cp genome using DNA extracted from whole cells and Solexa sequencing technology, we sequenced whole cellular DNA is...

Errors and insertion/deletions (InDels) in assemblies guided by cp sequence of A. thaliana or N. tabacum.

Annotated genes in B. rapa cp genome.

Gaps in assemblies guided by cp sequences of B. rapa, A. thaliana, or N. tabacum.

Single nucleotide polymorphisms (SNPs) and insertion/deletions (InDels) identified for B. rapa accessions Chiifu-402-41, Z16, and FT.

Chlorophyll a and chlorophyll b present in the chloroplasts of higher plants are the main pigments of leaf photosynthesis. The aim of this study was to localize the genetic factors affecting chlorophyll a and chlorophyll b content in the Chinese cabbage (Brassica rapa ssp. pekinensis) genome. To achieve this goal, we updated our previous genetic ma...

The inheritance of leaf and heading-related traits in Chinese cabbage (Brassica rapa ssp. pekinensis) are poorly understood since only a handful of studies of these traits are available till date. In this study, QTL mapping was done for seven leaf and heading related traits that includes gross weight, number of non-wrapper leaves, head weight, head...

We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structur...

Genic microsatellite markers, also known as functional markers, are preferred over anonymous markers as they reveal the variation in transcribed genes among individuals. In this study, we developed a total of 707 expressed sequence tag-derived simple sequence repeat markers (EST-SSRs) and used for development of a high-density integrated map using...

Brassica napus (AACC genome) is an important oilseed crop that was formed by the fusion of the diploids B. rapa (AA) and B. oleracea (CC). The complete genomic sequence of the Brassica A genome will be available soon from the B. rapa genome sequencing project, but it is not clear how informative the A genome sequence in B. rapa (A(r)) will be for p...

MicroRNAs (miRNAs) are recently discovered, noncoding, small regulatory RNA molecules that negatively regulate gene expression. Although many miRNAs are identified and validated in many plant species, they remain largely unknown in Brassica rapa (AA 2n =, 20). B. rapa is an important Brassica crop with wide genetic and morphological diversity resul...

Brassica rapa plants are highly important as vegetables, sources of oilseeds and fodder crop. Here, we developed 450 unigene derived microsatellite (UGMS) markers in B. rapa using unigenes downloaded from the National Center for Biotechnology Information database. Of the 450 UGMS primer pairs, 428 (95.1%) produced repeatable and reliable amplificat...

Brassica rapa (2n = 20, AA) is one among the six economically important cultivated Brassica species of U’s triangle. The presence of wide genetic and morphological diversity in the form of several subspecies in different geographical regions allows growing of this species for producing leafy vegetables, vegetable oils, turnips roots, turnip greens,...

We constructed a high-density Brassica rapa integrated linkage map by combining a reference genetic map of 78 doubled haploid lines derived from Chiifu-401-42 × Kenshin (CKDH) and a new map of 190 F2 lines derived from Chiifu-401-42 × rapid cycling B. rapa (CRF2). The integrated map contains 1017 markers and covers 1262.0 cM of the B. rapa genome,...

The species Brassica rapa includes important vegetable and oil crops. It also serves as an excellent model system to study polyploidy-related genome evolution because of its paleohexaploid ancestry and its close evolutionary relationships with Arabidopsis thaliana and other Brassica species with larger genomes. Therefore, its genome sequence will b...

Figures S1, S2, S3, and S4. Figure S1: genetic versus physical distance on chromosome A3. The genetic map was constructed using the VCS population. Figure S2: frequency distribution of genes in multigene families with tandem duplicated paralog arrangements. Tandem duplicated paralogs on chromosome A3 were identified using BLASTP analysis with a min...

Tables S1, S2, S3, and S4. Table S1: summary of sequence contigs along with constituent BAC associations on minimum tiling path for chromosome A3. Table S2: comparison of repetitive sequences identified on chromosome A3 and seed BAC sequences of B. rapa. Table S3: miRNAs identified on chromosome A3. Table S4: synteny alignment between B. rapa chrom...