@article{development of<i> allium</i><i> cepa</i> potential intron polymorphism markers for molecular breeding of alliums_2024, url={https://publons.com/wos-op/publon/64762757/}, DOI={10.1016/J.SAJB.2023.11.050}, abstractNote={Allium cepa is a widely grown crop for its spice and culinary properties. For molecular breeding of Allium cepa, mining and utilization of various sequence-based markers have been widely reported. Unfortunately, none has reported its molecular breeding using potential intron polymorphism (PIP) markers. Due to advantage of intron positioning prediction and practical utility, the PIP markers used for screening the possible polymorphism and cross-transferability in the Alliums. Screening results showed that among 500 Allium cepa potential intron polymorphism (AcPIP) markers, 275 are cross-transferable and polymorphic. Among the 275 AcPIP, 111 polymorphic markers were physically mapped on to 1st to 8th chromosomes of the Allium cepa. Out of the 275 AcPIP containing functionally significant markers, 118 were mapped in onion with Arabidopsis proteome. A set of 10 Alliums were utilized to interpret the polymorphic possibilities of the 500 AcPIP markers. In totality, 55 % AcPIP markers were polymorphic and cross-transferable among the Alliums. The polymorphic information content (PIC) of AcPIP markers ranged from 0.03 to 0.47 and heterozygosity index (H) varied between 0.16 and 0.80. The constructed phylogenetic tree based on the AcPIP markers of 10 Alliums revealed different clusters due to differences in their taxonomic positions. Out of 275 AcPIP markers, 10 AcPIP markers genotyping based Jaccard dissimilarity-based NJ tree of 96 individuals of Allium cepa showed two distinct groups (high total soluble solid; HTSS and low total soluble solid; LTSS). NJ tree and dissimilarity matrix reveal that group I genotypes are distinct, and dissimilar from group II and III genotypes hence it seems that group II and III genotype evolve from group I genotypes. Further we identified nine diverse Allium cepa subsample among which, genotype number 74 has HTSS and could be used for identification and introgression of HTSS coding genes in elite cultivars. Further DNA fingerprint of Alliums with 20 AcPIP markers suggested geographical reach of the released onion varieties. Hence results suggest that 275 AcPIP markers may be useful for accelerating the breeding programme of the Alliums and other species.}, journal={South African Journal of Botany}, year={2024} }
 @article{seth_2024, title={Editorial: Epigenetic and gene regulation underlying crosstalk in plant development and stress responses}, url={https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2024.1427102/full}, DOI={10.3389/fgene.2024.1427102/full}, journal={Frontiers in Genetics}, author={Seth, Romit}, editor={Seth, Romit and Iorizzo, Massimo and Maritim, Tony and Sharma, Ram KumarEditors}, year={2024}, month={Jul} }
 @article{comparative transcriptome analysis revealed gamma-irradiation mediated disruption of floral integrator gene(s) leading to prolonged vegetative phase in <i>stevia rebaudiana</i> bertoni (vol 148, pg 90, 2020)_2023, url={https://publons.com/wos-op/publon/63829957/}, DOI={10.1016/J.PLAPHY.2023.107863}, journal={Plant Physiology and Biochemistry}, year={2023} }
 @article{pal_2023, title={Genome-wide transcriptional profiling and physiological investigation elucidating the molecular mechanism of multiple abiotic stress response in Stevia rebaudiana Bertoni}, url={https://www.nature.com/articles/s41598-023-46000-7#citeas}, DOI={10.1038/s41598-023-46000-7}, abstractNote={Abstract}, journal={Scientific Reports}, author={Pal, Poonam}, year={2023}, month={Nov} }
 @article{coe_bostan_rolling_turner-hissong_macko-podgorni_senalik_liu_seth_curaba_mengist_et al._2023, title={Population genomics identifies genetic signatures of carrot domestication and improvement and uncovers the origin of high-carotenoid orange carrots}, volume={9}, ISSN={["2055-0278"]}, url={https://doi.org/10.1038/s41477-023-01526-6}, DOI={10.1038/s41477-023-01526-6}, abstractNote={Abstract}, journal={NATURE PLANTS}, author={Coe, Kevin and Bostan, Hamed and Rolling, William and Turner-Hissong, Sarah and Macko-Podgorni, Alicja and Senalik, Douglas and Liu, Su and Seth, Romit and Curaba, Julien and Mengist, Molla Fentie and et al.}, year={2023}, month={Sep} }
 @article{seth_devi_sharma_masand_singh_pal_holkar_sharma_sharma_negi_et al._2022, title={An Integrative Transcriptional Network Revealed Spatial Molecular Interplay Underlying Alantolactone and Inulin Biosynthesis in <i>Inula racemosa</i> Hook f.}, volume={23}, url={https://www.mdpi.com/1422-0067/23/19/11213}, DOI={10.3390/ijms231911213}, abstractNote={Inula racemosa Hook. f. (Pushkarmula), a perennial Himalayan herb known for its aromatic and phytopharmaceutical attributes, is not yet explored at genomic/transcriptomic scale. In this study, efforts were made to unveil the global transcriptional atlas underlying organ-specific specialized metabolite biosynthesis by integrating RNA-Seq analysis of 433 million sequenced reads with the phytochemical analysis of leaf, stem, and root tissues. Overall, 7242 of 83,772 assembled nonredundant unigenes were identified exhibiting spatial expression in leaf (3761), root (2748), and stem (733). Subsequently, integration of the predicted transcriptional interactome network of 2541 unigenes (71,841 edges) with gene ontology and KEGG pathway enrichment analysis revealed isoprenoid, terpenoid, diterpenoid, and gibberellin biosynthesis with antimicrobial activities in root tissue. Interestingly, the root-specific expression of germacrene-mediated alantolactone biosynthesis (GAS, GAO, G8H, IPP, DMAP, and KAO) and antimicrobial activities (BZR1, DEFL, LTP) well-supported with both quantitative expression profiling and phytochemical accumulation of alantolactones (726.08 μg/10 mg) and isoalantolactones (988.59 μg/10 mg), which suggests “roots” as the site of alantolactone biosynthesis. A significant interaction of leaf-specific carbohydrate metabolism with root-specific inulin biosynthesis indicates source (leaf) to sink (root) regulation of inulin. Our findings comprehensively demonstrate the source-sink transcriptional regulation of alantolactone and inulin biosynthesis, which can be further extended for upscaling the targeted specialized metabolites. Nevertheless, the genomic resource created in this study can also be utilized for development of genome-wide functionally relevant molecular markers to expedite the breeding strategies for genetic improvement of I. racemosa.}, number={19}, journal={International Journal of Molecular Sciences}, author={Seth, Romit and DEVI, AMNA and Sharma, Balraj and Masand, Mamta and Singh, Gopal and Pal, Poonam and Holkar, Ashlesha and Sharma, Shikha and Sharma, Vishal and Negi, Shivanti and et al.}, editor={Seth, RomitEditor}, year={2022}, month={Sep}, pages={11213} }
 @article{parmar_seth_sharma_2022, title={Genome-wide identification and characterization of functionally relevant microsatellite markers from transcription factor genes of Tea (Camellia sinensis (L.) O. Kuntze)}, volume={12}, url={http://dx.doi.org/10.1038/s41598-021-03848-x}, DOI={10.1038/s41598-021-03848-x}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Parmar, Rajni and Seth, Romit and Sharma, Ram Kumar}, year={2022}, month={Jan} }
 @inbook{seth_bhandawat_maritim_sharma_2022, title={Next-Gen Approaches to Understand Plant-Microbe Interactions Providing Abiotic Stress Tolerance in Plants}, url={http://dx.doi.org/10.1201/9781003147091-4}, DOI={10.1201/9781003147091-4}, booktitle={Microbial Based Land Restoration Handbook, Volume 1}, publisher={CRC Press}, author={Seth, Romit and Bhandawat, Abhishek and Maritim, Tony Kipkoech and Sharma, Ram Kumar}, year={2022}, month={Oct}, pages={59–72} }
 @article{devi_seth_masand_singh_holkar_sharma_singh_sharma_2022, title={Spatial Genomic Resource Reveals Molecular Insights into Key Bioactive-Metabolite Biosynthesis in Endangered <i>Angelica glauca</i> Edgew}, volume={23}, url={https://www.mdpi.com/1422-0067/23/19/11064}, DOI={10.3390/ijms231911064}, abstractNote={Angelica glauca Edgew, which is an endangered medicinal and aromatic herb, is a rich source of numerous industrially important bioactive metabolites, including terpenoids, phenolics, and phthalides. Nevertheless, genomic interventions for the sustainable utilization and restoration of its genetic resources are greatly offset due to the scarcity of the genomic resources and key regulators of the underlying specialized metabolism. To unravel the global atlas of the specialized metabolism, the first spatial transcriptome sequencing of the leaf, stem, and root generated 109 million high-quality paired-end reads, assembled de novo into 81,162 unigenes, which exhibit a 61.53% significant homology with the six public protein databases. The organ-specific clustering grouped 1136 differentially expressed unigenes into four subclusters differentially enriched in the leaf, stem, and root tissues. The prediction of the transcriptional-interactome network by integrating enriched gene ontology (GO) and the KEGG metabolic pathways identified the key regulatory unigenes that correspond to terpenoid, flavonoid, and carotenoid biosynthesis in the leaf tissue, followed by the stem and root tissues. Furthermore, the stem and root-specific significant enrichments of phenylalanine ammonia lyase (PAL), cinnamate-4-hydroxylase (C4H), and caffeic acid 3-O-methyltransferase (COMT) indicate that phenylalanine mediated the ferulic acid biosynthesis in the stem and root. However, the root-specific expressions of NADPH-dependent alkenal/one oxidoreductase (NADPH-AOR), S-adenosyl-L-methionine-dependent methyltransferases (SDMs), polyketide cyclase (PKC), and CYP72A15 suggest the “root” as the primary site of phthalide biosynthesis. Additionally, the GC-MS and UPLC analyses corresponded to the organ-specific gene expressions, with higher contents of limonene and phthalide compounds in the roots, while there was a higher accumulation of ferulic acid in the stem, followed by in the root and leaf tissues. The first comprehensive genomic resource with an array of candidate genes of the key metabolic pathways can be potentially utilized for the targeted upscaling of aromatic and pharmaceutically important bioactive metabolites. This will also expedite genomic-assisted conservation and breeding strategies for the revival of the endangered A. glauca.}, number={19}, journal={International Journal of Molecular Sciences}, author={DEVI, AMNA and Seth, Romit and Masand, Mamta and Singh, Gopal and Holkar, Ashlesha and Sharma, Shikha and Singh, Ashok and Sharma, Ram Kumar}, editor={Seth, RomitEditor}, year={2022}, month={Sep}, pages={11064} }
 @article{kiran_sharma_awasthi_nayyar_seth_chandel_siddique_zinta_sharma_2021, title={Disruption of carbohydrate and proline metabolism in anthers under low temperature causes pollen sterility in chickpea}, volume={188}, ISSN={0098-8472}, url={http://dx.doi.org/10.1016/j.envexpbot.2021.104500}, DOI={10.1016/j.envexpbot.2021.104500}, abstractNote={Chickpea (Cicer arietinum L.) is the third most important food legume globally and is an important source of high-quality proteins to both humans and animals. It is highly sensitive to low temperature (LT) resulting in large scale yield losses. LT induces flower abortion in chickpea by disruption of gamete development and induction of pollen sterility. However, molecular mechanisms governing LT induced pollen sterility in chickpea are unknown. Disruption of carbohydrate metabolism has been implicated in LT induced damage to crops whereas proline and antioxidants protect plants from LT stress. In this study, the impact of LT on carbohydrates, proline and enzymatic antioxidants and expression of genes of these metabolite pathways were investigated in anthers at vacuolated pollen stage. The study included two genotypes, a cold-sensitive (GPF2) and a cold-tolerant (ICC 16349) that differed for pollen sterility under LT. Metabolite profiling revealed a reduction in starch and proline content in GPF2 under LT, whereas these parameters did not change but non-reducing sugars increased in ICC 16349. At the transcriptional level, cold initially lowered the transcription of all genes (19) under study in GPF2 and 14 genes out of 19 in ICC 16349. Initial down-regulation was followed by differential reactivation of transcription machinery in GPF2 and ICC 16349 at 30 min. Under LT, expression of starch synthesis, starch degradation, sucrose synthesis and sucrose transport genes showed a contrasting response in the two genotypes, where GPF2 showed downregulation of these genes while ICC 16,349 showed upregulation. The proline transport gene (proline transporter 1) showed higher downregulation in GPF2 than ICC 16349. Overall, pollen viability under LT in ICC 16349 was linked to the maintenance of starch, reducing sugars and proline levels and over-expression of UDP glucose pyrophosphorylase and cell wall invertase, while these processes were compromised in the GPF2 possibly leading to pollen sterility.}, journal={Environmental and Experimental Botany}, publisher={Elsevier BV}, author={Kiran, Asha and Sharma, P.N. and Awasthi, Rashmi and Nayyar, Harsh and Seth, Romit and Chandel, Surender Singh and Siddique, Kadambot H.M. and Zinta, Gaurav and Sharma, Kamal Dev}, year={2021}, month={Aug}, pages={104500} }
 @article{sharma_seth_thakur_parmar_masand_devi_singh_dhyani_choudhary_sharma_2021, title={Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook}, volume={187}, ISSN={0031-9422}, url={http://dx.doi.org/10.1016/j.phytochem.2021.112772}, DOI={10.1016/j.phytochem.2021.112772}, abstractNote={Fritillaria roylei Hook. is a critically endangered high altitude Himalayan medicinal plant species with rich source of pharmaceutically active structurally diverse steroidal alkaloids. Nevertheless, except few marker compounds, the chemistry of the plant remains unexplored. Therefore, in the current study, transcriptome sequencing efforts were made to elucidate isosteroidal alkaloids biosynthesis by creating first organ-specific genomic resource using bulb, stem, and leaf tissues derived from natural populations of Indian Himalayan region. Overall, 349.9 million high quality paired-end reads obtained using NovaSeq 6000 platform were assembled (de novo) into 82,848 unigenes and 31,061 isoforms. Functional annotation and organ specific differential expression (DE) analysis identified 2488 significant DE transcripts, grouped into three potential sub-clusters (sub-cluster I: 728 transcripts; sub-cluster II: 446 transcripts and Sub-cluster III: 1314 transcripts). Subsequently, pathway enrichment (GO, KEGG) and protein-protein network analysis revealed significantly higher enrichment of phenyl-propanoid and steroid backbone including terpenoid, sesquiterpenoid and triterpenoid biosynthesis in bulb. Additionally, upregulated expression of cytochrome P450, UDP-dependent Glucuronosyltransferase families and key transcription factor families (FAR1, bHLH, GRAS, C2H2, TCP and MYB) suggests ‘bulb’ as a primary site of MVA mediated isosteroidal alkaloids biosynthesis. The comprehensive elucidation of molecular insights in this study is a first step towards the understanding of isosteroidal alkaloid biosynthesis pathway in F. roylei. Furthermore, key genes and regulators identified here can facilitate metabolic engineering of potential bioactive compounds at industrial scale.}, journal={Phytochemistry}, publisher={Elsevier BV}, author={Sharma, Balraj and Seth, Romit and Thakur, Sapna and Parmar, Rajni and Masand, Mamta and Devi, Amna and Singh, Gopal and Dhyani, Praveen and Choudhary, Shruti and Sharma, Ram Kumar}, editor={Seth, RomitEditor}, year={2021}, month={Jul}, pages={112772} }
 @article{maritim_seth_parmar_sharma_2021, title={Multiple-genotypes transcriptional analysis revealed candidates genes and nucleotide variants for improvement of quality characteristics in tea (Camellia sinensis (L.) O. Kuntze)}, volume={113}, url={http://dx.doi.org/10.1016/j.ygeno.2020.12.020}, DOI={10.1016/j.ygeno.2020.12.020}, abstractNote={Tea quality is a polygenic trait that exhibits tremendous genetic variability due to accumulation of array of secondary metabolites. To elucidate global molecular insights controlling quality attributes, metabolite profiling and transcriptome sequencing of twelve diverse tea cultivars was performed in tea shoots harvested during quality season. RP-HPLC-DAD analysis of quality parameters revealed significant difference in catechins, theanine and caffeine contents. Transcriptome sequencing resulted into 50,107 non-redundant transcripts with functional annotations of 81.6% (40,847) of the transcripts. Interestingly, 2872 differentially expressed transcripts exhibited significant enrichment in 38 pathways (FDR ≤ 0.05) including secondary metabolism, amino acid and carbon metabolism. Thirty-eight key candidates reportedly involved in biosynthesis of fatty acid derived volatiles, volatile terpenes, glycoside hydrolysis and key quality related pathways (flavonoid, caffeine and theanine-biosynthesis) were highly expressed in catechins-rich tea cultivars. Furthermore, enrichment of candidates involved in flavonoid biosynthesis, transcriptional regulation, volatile terpene and biosynthesis of fatty acid derived volatile in Protein-Protein Interactome network revealed well-coordinated regulation of quality characteristics in tea. Additionally, ascertainment of 23,649 non-synonymous SNPs and validation of candidate SNPs present in quality related genes suggests their potential utility in genome-wide mapping and marker development for expediting breeding of elite compound-rich tea cultivars.}, number={1}, journal={Genomics}, publisher={Elsevier BV}, author={Maritim, Tony Kipkoech and Seth, Romit and Parmar, Rajni and Sharma, Ram Kumar}, editor={Seth, RomitEditor}, year={2021}, month={Jan}, pages={305–316} }
 @article{maritim_masand_seth_sharma_2021, title={Transcriptional analysis reveals key insights into seasonal induced anthocyanin degradation and leaf color transition in purple tea (Camellia sinensis (L.) O. Kuntze)}, volume={11}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/s41598-020-80437-4}, DOI={10.1038/s41598-020-80437-4}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Maritim, Tony Kipkoech and Masand, Mamta and Seth, Romit and Sharma, Ram Kumar}, editor={Seth, RomitEditor}, year={2021}, month={Jan} }
 @article{seth_maritim_parmar_sharma_2021, title={Underpinning the molecular programming attributing heat stress associated thermotolerance in tea (Camellia sinensis (L.) O. Kuntze)}, volume={8}, url={https://www.nature.com/articles/s41438-021-00532-z}, DOI={10.1038/s41438-021-00532-z}, abstractNote={Abstract}, number={1}, journal={Horticulture Research}, publisher={Springer Science and Business Media LLC}, author={Seth, Romit and Maritim, Tony Kipkoech and Parmar, Rajni and Sharma, Ram Kumar}, editor={Seth, RomitEditor}, year={2021}, month={May} }
 @misc{seth_sharma_2021, title={Unravelling Transcriptional Network Underlying Heat Stress Associated Thermotolerance in Tea (Camellia sinensis (L) O. Kuntze)}, journal={5th Seminar Student Series}, author={Seth, R. and Sharma, R.K.}, year={2021} }
 @inproceedings{seth_sharma_2021, title={Unravelling Transcriptional Network Underlying Pollen-Pistil Communication in Tea (Camellia sinensis (L) O. Kuntze)}, booktitle={Advances in Plant Biotechnology and Genome editing}, author={Seth, R. and Sharma, R.K.}, year={2021} }
 @article{singh_pal_masand_seth_kumar_singh_sharma_2020, title={Comparative transcriptome analysis revealed gamma-irradiation mediated disruption of floral integrator gene(s) leading to prolonged vegetative phase in Stevia rebaudiana Bertoni}, volume={148}, url={https://doi.org/10.1016/j.plaphy.2020.01.004}, DOI={10.1016/j.plaphy.2020.01.004}, abstractNote={Stevia rebaudiana Bert. is getting global attention because of its ability to synthesize commercially important low/no calorie natural sweeteners (LNCSs) steviol glycosides (SGs). Considering, higher accumulation of SGs in vegetative phase followed by decrement during reproductive phase necessitate the understanding of different molecular components of floral transition to develop superior varieties/cultivars with prolonged vegetative phase in Stevia. Current comparative transcriptional analysis of low dose (5 kR) gamma-irradiated mutant genotype (SMG) with prolonged vegetative phase vis-à-vis background genotype (SBG) identified DGEs of major floral transition pathways, and expressed according to their physiological fate irrespective to SMG & SBG. Contrarily, reduced expression of floral integrator genes (FT and LEAFY) in mutant genotype suggests their involvement in prolonged vegetative phase phenotype. Likewise, GO and KEGG enrichment of photosynthesis and carbon assimilation efficiency might be associated with prolonged vegetative phase and higher accumulation of Stevioside content in mutant genotype. Furthermore, deviation of flowering related transcription factors (higher expressions except MIKS-type MADS-box SMG_PV compared to SBG_F) may possibly be correlated with low expression of floral integrator genes. Findings of current studies will facilitate the genetic manipulations and crop improvement efforts in Stevia through conventional breeding and genome editing approaches for increased SGs biosynthesis.}, journal={Plant Physiology and Biochemistry}, publisher={Elsevier BV}, author={Singh, Gopal and Pal, Poonam and Masand, Mamta and Seth, Romit and Kumar, Ashok and Singh, Sanatsujat and Sharma, Ram Kumar}, year={2020}, month={Mar}, pages={90–102} }
 @article{dhyani_sharma_singh_masand_seth_sharma_2020, title={Genome-wide discovery of microsatellite markers and, population genetic diversity inferences revealed high anthropogenic pressure on endemic populations of Trillium govanianum}, volume={154}, url={https://doi.org/10.1016/j.indcrop.2020.112698}, DOI={10.1016/j.indcrop.2020.112698}, abstractNote={Trillium govanianum ethnobotanical perspectives include the treatment of cancer, hypertension, neurasthenia, giddiness, arthritis, dysentery, and inflammation. As its industrial demand for steroidal content is increasing, the endemic species have been subjected to severe habitat degradation and fragmentation by the illicit trade in Indian Himalayan Region (IHR). Additionally, molecular genetics efforts in T. govanianum has also lagged, mainly because of the non-availability of genome-wide molecular marker resources. Apropos, using tissue-specific transcriptomic data derived from the rhizome, stem, leaf, and fruit, the present study identified 5337 novel functionally relevant genome-wide SSR markers. The tri repeats were most abundant (41%) with a higher occurrence of CCG/CGG repeat motif, mostly located in the CDS region. Based on functional annotations of SSR transcripts with multifarious public databases (NR, TAIR, KEGG, KOG, SwissProt & PTFdb), a set of 288 SSR markers encompassing important roles in steroidal saponins pathway, cellular and metabolic processes such as response to stress, binding, and catalytic activity were validated, successfully. Genetic diversity and population structure analysis of 290 genotypes of 14 geographically distinct populations representing eight different valleys (2086−3500 m amsl) of the IHR amplified an average of 4.33 alleles per locus. Overall, a low genetic diversity (He: 0.25), high genetic divergence (GST: 0.23), high within populations molecular variance (72 %), limited gene flow (0.792), and slight positive isolation by distance (Rxy = 0.260; p = 0.030) is recorded in T. govanianum populations. Further, neighbor-joining (NJ) based hierarchical clustering, PCoA, and Bayesian structure clustering identified two major groups in the tested populations. Novel microsatellite marker resources and population diversity inferences studied for the first time revealed that there is a need to recuperate diversity in situ and maintain effective population size, a much-required step to mitigate high anthropogenic pressure on T. govanianum in Indian Himalayan Region.}, journal={Industrial Crops and Products}, publisher={Elsevier BV}, author={Dhyani, Praveen and Sharma, Balraj and Singh, Pradeep and Masand, Mamta and Seth, Romit and Sharma, Ram Kumar}, year={2020}, month={Oct}, pages={112698} }
 @article{nag_choudhary_masand_parmar_bhandawat_seth_singh_dhyani_sharma_2020, title={Spatial transcriptional dynamics of geographically separated genotypes revealed key regulators of podophyllotoxin biosynthesis in Podophyllum hexandrum}, volume={147}, url={https://doi.org/10.1016/j.indcrop.2020.112247}, DOI={10.1016/j.indcrop.2020.112247}, abstractNote={Podophyllum hexandrum is the major source of podophyllotoxin (PTOX), a highly bioactive lignan of great pharmacological importance with anti-cancerous activities. The industrial demand of PTOX relies on the highly endangered natural resources only. It is therefore, desirable to elucidate global molecular processes and identify key genes for enhancing PTOX biosynthesis by overexpressing the targeted candidates. Transcriptome of leaf, rhizome, and stalk was generated to analyse the spatial regulation of PTOX biosynthesis in genetically diverse genotypes. Overall, 198 million high-quality paired-end reads were assembled into 85,531 transcripts. In addition, 32,341 transcripts were assigned gene ontologies with 6570 hits in distinct pathways and 15,886 transcription factors representing 70 families. Interestingly, comparative expression analyses revealed that 12 of 31 genes of PTOX biosynthesis were upregulated in rhizome. However, shikimate and phenylalanine pathways that generate PTOX precursors were abundantly upregulated in leaves. Thus, a further insight on the inducers of these genes can be extended to enrich the aerial tissues for downstream pathway through genetic manipulations. Additionally, higher expression of transcription factors WRKY, MYB, bZIP, bHLH, and AP2, transporters ABCB and ABCC, UGTs, CYP450s, and jasmonate pathway in rhizome supported the secondary metabolism. The comprehensive genomic resource created during this study will provide deeper understanding of lignan biosynthesis and its regulation. This will further enable selection of the elite genotypes and potential genes that can be directed to enhance PTOX production and yield at an industrial scale.}, journal={Industrial Crops and Products}, publisher={Elsevier BV}, author={Nag, Akshay and Choudhary, Shruti and Masand, Mamta and Parmar, Rajni and Bhandawat, Abhishek and Seth, Romit and Singh, Gopal and Dhyani, Praveen and Sharma, Ram Kumar}, year={2020}, month={May}, pages={112247} }
 @article{bhandawat_sharma_singh_seth_nag_kaur_sharma_2019, title={Discovery and Utilization of EST-SSR Marker Resource for Genetic Diversity and Population Structure Analyses of a Subtropical Bamboo, Dendrocalamus hamiltonii}, volume={57}, ISSN={0006-2928 1573-4927}, url={http://dx.doi.org/10.1007/s10528-019-09914-4}, DOI={10.1007/s10528-019-09914-4}, abstractNote={Dendrocalamus hamiltonii is a giant bamboo species native to Indian subcontinent with high economic importance. Nevertheless, highly outcross nature and flowering once in decades impose severe limitation in its propagation. Identification and mixed cultivation of genetically diverse genotypes may assist successful breeding and natural recombination of desirable traits. Characterization of existing genetic diversity and population structure are indispensable for efficient implementation of such strategies, which is facing a major challenge due to non-availability of sequence-based markers for the species. In this study, 8121 EST-SSR markers were mined from D. hamiltonii transcriptome data. Among all, tri-repeats were most represented (52%), with the abundance of CCG/CGG repeat motif. A set of 114 polymorphic markers encompassing epigenetic regulators, transcription factors, cell cycle regulators, signaling, and cell wall biogenesis, detected polymorphism and interaction (in silico) with important genes, that might have role in bamboo growth and development. Genetic diversity and population structure of the three D. hamiltonii populations (72 individuals) revealed moderate to high-level genetic diversity (mean alleles per locus: 5.8; mean PIC: 0.44) using neutral EST-SSR markers. AMOVA analysis suggests maximum diversity (59%) exists within population. High genetic differentiation (G st  = 0.338) and low gene flow (N m  = 0.49) were evident among populations. Further, PCoA, dendrogram, and Bayesian STRUCTURE analysis clustered three populations into two major groups based on geographical separations. In future, SSR marker resources created can be used for systematic breeding and implementation of conservation plans for sustainable utilization of bamboo complex.}, number={5}, journal={Biochemical Genetics}, publisher={Springer Science and Business Media LLC}, author={Bhandawat, Abhishek and Sharma, Vikas and Singh, Pradeep and Seth, Romit and Nag, Akshay and Kaur, Jagdeep and Sharma, Ram Kumar}, year={2019}, month={Apr}, pages={652–672} }
 @article{bhandawat_sharma_singh_seth_nag_kaur_sharma_2019, title={Discovery and Utilization of EST-SSR Marker Resource for Genetic Diversity and Population Structure Analyses of a Subtropical Bamboo, Dendrocalamus hamiltonii}, journal={Biochemical Genetics}, publisher={Springer}, author={Bhandawat, Abhishek and Sharma, Vikas and Singh, Pradeep and Seth, Romit and Nag, Akshay and Kaur, Jagdeep and Sharma, Ram Kumar}, year={2019}, pages={1–21} }
 @article{singh_singh_seth_parmar_singh_singh_kumar_sharma_2019, title={Functional annotation and characterization of hypothetical protein involved in blister blight tolerance in tea (Camellia sinensis (L) O. Kuntze)}, volume={28}, ISSN={0971-7811 0974-1275}, url={http://dx.doi.org/10.1007/s13562-019-00492-5}, DOI={10.1007/S13562-019-00492-5}, number={4}, journal={Journal of Plant Biochemistry and Biotechnology}, publisher={Springer Science and Business Media LLC}, author={Singh, Gagandeep and Singh, Gopal and Seth, Romit and Parmar, Rajni and Singh, Pradeep and Singh, Vikram and Kumar, Sanjay and Sharma, Ram Kumar}, year={2019}, month={Mar}, pages={447–459} }
 @article{singh_singh_seth_parmar_singh_singh_kumar_sharma_2019, title={Functional annotation and characterization of hypothetical protein involved in blister blight tolerance in tea (Camellia sinensis (L) O. Kuntze)}, journal={Journal of Plant Biochemistry and Biotechnology}, publisher={Springer}, author={Singh, Gagandeep and Singh, Gopal and Seth, Romit and Parmar, Rajni and Singh, Pradeep and Singh, Vikram and Kumar, Sanjay and Sharma, Ram Kumar}, editor={Seth, RomitEditor}, year={2019}, pages={1–13} }
 @article{seth_bhandawat_parmar_singh_kumar_sharma_2019, title={Global Transcriptional Insights of Pollen-Pistil Interactions Commencing Self-Incompatibility and Fertilization in Tea [<i>Camellia sinensis</i> (L.) O. Kuntze]}, volume={20}, url={http://www.mdpi.com/1422-0067/20/3/539}, DOI={10.3390/ijms20030539}, abstractNote={This study explicates molecular insights commencing Self-Incompatibility (SI) and CC (cross-compatibility/fertilization) in self (SP) and cross (CP) pollinated pistils of tea. The fluorescence microscopy analysis revealed ceased/deviated pollen tubes in SP, while successful fertilization occurred in CP at 48 HAP. Global transcriptome sequencing of SP and CP pistils generated 109.7 million reads with overall 77.9% mapping rate to draft tea genome. Furthermore, concatenated de novo assembly resulted into 48,163 transcripts. Functional annotations and enrichment analysis (KEGG & GO) resulted into 3793 differentially expressed genes (DEGs). Among these, de novo and reference-based expression analysis identified 195 DEGs involved in pollen-pistil interaction. Interestingly, the presence of 182 genes [PT germination & elongation (67), S-locus (11), fertilization (43), disease resistance protein (30) and abscission (31)] in a major hub of the protein-protein interactome network suggests a complex signaling cascade commencing SI/CC. Furthermore, tissue-specific qRT-PCR analysis affirmed the localized expression of 42 DE putative key candidates in stigma-style and ovary, and suggested that LSI initiated in style and was sustained up to ovary with the active involvement of csRNS, SRKs & SKIPs during SP. Nonetheless, COBL10, RALF, FERONIA-rlk, LLG and MAPKs were possibly facilitating fertilization. The current study comprehensively unravels molecular insights of phase-specific pollen-pistil interaction during SI and fertilization, which can be utilized to enhance breeding efficiency and genetic improvement in tea.}, number={3}, journal={International Journal of Molecular Sciences}, author={Seth, Romit and Bhandawat, Abhishek and Parmar, Rajni and Singh, Pradeep and Kumar, Sanjay and Sharma, Ram Kumar}, editor={Seth, RomitEditor}, year={2019}, month={Jan}, pages={539} }
 @inproceedings{parmar_seth_singh_singh_sharma_2019, title={High Throughput NGS Efforts to Dissect Drought Tolerance and Mining of Functional Variation in Tea}, booktitle={Plant and animal genome (PAG) conference}, author={Parmar, R. and Seth, R. and Singh, P. and Singh, G. and Sharma, R.K.}, year={2019} }
 @article{parmar_seth_singh_singh_kumar_sharma_2019, title={Transcriptional profiling of contrasting genotypes revealed key candidates and nucleotide variations for drought dissection in Camellia sinensis (L.) O. Kuntze}, volume={9}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/s41598-019-43925-w}, DOI={10.1038/s41598-019-43925-w}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Parmar, Rajni and Seth, Romit and Singh, Pradeep and Singh, Gopal and Kumar, Sanjay and Sharma, Ram Kumar}, editor={Seth, RomitEditor}, year={2019}, month={May} }
 @inproceedings{seth_bhandawat_parmar_singh_kumar_sharma_2017, title={Genome-wide approach for molecular dissection and identification of functionally relevant variations involved in selfincompatibility in tea (Camellia sinensis (L) O. Kuntze)}, booktitle={Har Gobind Khorana Memorial Symposium on Genes, Genomes & Membrane Biology}, author={Seth, R. and Bhandawat, A. and Parmar, R. and Singh, P. and Kumar, S. and Sharma, R.K.}, year={2017} }
 @article{bhandawat_singh_seth_singh_sharma_2017, title={Genome-wide transcriptional profiling to elucidate key candidates involved in bud burst and rattling growth in a subtropical bamboo (Dendrocalamus hamiltonii)}, volume={7}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85009726039&partnerID=MN8TOARS}, DOI={10.3389/fpls.2016.02038}, abstractNote={Bamboo, one of the fastest growing plants, can be a promising model system to understand growth. The study provides an insight into the complex interplay between environmental signaling and cellular machineries governing initiation and persistence of growth in a subtropical bamboo (Dendrocalamus hamiltonii). Phenological and spatio-temporal transcriptome analysis of rhizome and shoot during the major vegetative developmental transitions of D. hamiltonii was performed to dissect factors governing growth. Our work signifies the role of environmental cues, predominantly rainfall, decreasing day length, and high humidity for activating dormant bud to produce new shoot, possibly through complex molecular interactions among phosphatidylinositol, calcium signaling pathways, phytohormones, circadian rhythm, and humidity responses. We found the coordinated regulation of auxin, cytokinin, brassinosteroid signaling and cell cycle modulators; facilitating cell proliferation, cell expansion, and cell wall biogenesis supporting persistent growth of emerging shoot. Putative master regulators among these candidates were identified using predetermined Arabidopsis thaliana protein-protein interaction network. We got clues that the growth signaling begins far back in rhizome even before it emerges out as new shoot. Putative growth candidates identified in our study can serve in devising strategies to engineer bamboos and timber trees with enhanced growth and biomass potentials.}, journal={Frontiers in Plant Science}, author={Bhandawat, A. and Singh, G. and Seth, R. and Singh, P. and Sharma, R.K.}, year={2017} }
 @article{bhandawat_singh_seth_singh_sharma_2017, title={Genome-wide transcriptional profiling to elucidate key candidates involved in bud burst and rattling growth in a subtropical bamboo (Dendrocalamus hamiltonii)}, volume={7}, url={http://journal.frontiersin.org/article/10.3389/fpls.2016.02038/full}, DOI={https://doi.org/10.3389/fpls.2016.02038}, abstractNote={Bamboo, one of the fastest growing plants, can be a promising model system to understand growth. The study provides an insight into the complex interplay between environmental signaling and cellular machineries governing initiation and persistence of growth in a subtropical bamboo (Dendrocalamus hamiltonii). Phenological and spatio-temporal transcriptome analysis of rhizome and shoot during the major vegetative developmental transitions of D. hamiltonii was performed to dissect factors governing growth. Our work signifies the role of environmental cues, predominantly rainfall, decreasing day length, and high humidity for activating dormant bud to produce new shoot, possibly through complex molecular interactions among phosphatidylinositol, calcium signaling pathways, phytohormones, circadian rhythm, and humidity responses. We found the coordinated regulation of auxin, cytokinin, brassinosteroid signaling and cell cycle modulators; facilitating cell proliferation, cell expansion, and cell wall biogenesis supporting persistent growth of emerging shoot. Putative master regulators among these candidates were identified using predetermined Arabidopsis thaliana protein-protein interaction network. We got clues that the growth signaling begins far back in rhizome even before it emerges out as new shoot. Putative growth candidates identified in our study can serve in devising strategies to engineer bamboos and timber trees with enhanced growth and biomass potentials.}, journal={Frontiers in Plant Science}, publisher={Frontiers}, author={Bhandawat, Abhishek and Singh, Gagandeep and Seth, Romit and Singh, Pradeep and Sharma, Ram Kumar}, year={2017}, month={Jan}, pages={2038} }
 @article{singh_singh_bhandawat_singh_parmar_seth_sharma_2017, title={Spatial transcriptome analysis provides insights of key gene(s) involved in steroidal saponin biosynthesis in medicinally important herb Trillium govanianum}, volume={7}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85016327439&partnerID=MN8TOARS}, DOI={10.1038/srep45295}, abstractNote={Abstract}, journal={Scientific Reports}, author={Singh, P. and Singh, G. and Bhandawat, A. and Singh, G. and Parmar, R. and Seth, R. and Sharma, R.K.}, year={2017} }
 @article{jayaswall_mahajan_singh_parmar_seth_raina_swarnkar_singh_shankar_sharma_2016, title={Transcriptome Analysis Reveals Candidate Genes involved in Blister Blight defense in Tea (Camellia sinensis (L) Kuntze)}, volume={6}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/srep30412}, DOI={10.1038/srep30412}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Jayaswall, Kuldip and Mahajan, Pallavi and Singh, Gagandeep and Parmar, Rajni and Seth, Romit and Raina, Aparnashree and Swarnkar, Mohit Kumar and Singh, Anil Kumar and Shankar, Ravi and Sharma, Ram Kumar}, year={2016}, month={Jul} }
 @article{seth_2016, title={Transcriptome Analysis Reveals Candidate Genes involved in Blister Blight defense in Tea (Camellia sinensis (L) Kuntze)}, url={http://www.nature.com/articles/srep30412}, DOI={doi: 10.1038/srep30412 (2016).}, abstractNote={Abstract}, journal={Nature Scientific Reports}, year={2016}, month={Jul} }
 @inproceedings{sharma_parmar_singh_raina_kuldip_bhandawat_seth_sharma_singh_ahuja_2015, title={Exploiting Next generation sequencing for creation of genomic resources in Tea}, booktitle={5th International Conference on Next Generation Genomics & Integrated Breeding for Crop improvement}, author={Sharma, R.K. and Parmar, R. and Singh, G. and Raina, A.S. and Kuldip, A. and Bhandawat, A and Seth, R. and Sharma, H. and Singh, A.K. and Ahuja, P.S.}, year={2015} }
 @inproceedings{parmar_singh_raina_kuldip_bhandawat_seth_sharma_2015, title={NGS Based Transcriptome Sequencing of Multiple Diverse Genotypes: An Efficient Approach to Develop Functionally Relevant Marker Resource in Tea}, booktitle={International Plant Physiology Congress}, author={Parmar, R. and Singh, G. and Raina, S. and Kuldip, A. and Bhandawat, A. and Seth, R. and Sharma, R.K.}, year={2015} }
 @inproceedings{seth_raina_bhandawat_parmar_singh_sharma_2015, title={Next generation transcriptome sequencing to elucidate molecular mechanism of Self-incompatibility in tea}, booktitle={Plant Physiology Congress}, author={Seth, R. and Raina, A.S. and Bhandawat, A. and Parmar, R. and Singh, G. and Sharma, R.K.}, year={2015} }
 @inproceedings{sharma_kuldip_parmar_sharma_singh_seth_raina_singh_ahuja_2014, title={Genomic opportunities for genetic improvement and rejuvenation of tea cultivation in Himachal Pradesh}, booktitle={Role of Science & Technology in Sustainable Development}, author={Sharma, R.K. and Kuldip, A. and Parmar, R. and Sharma, H. and Singh, G. and Seth, R. and Raina, A.S. and Singh, S. and Ahuja, P.S.}, year={2014} }
 @inproceedings{kuldeep_mahajan_parmar_seth_swarnkar_singh_ravishankar_singh_ahuja_sharma_2014, title={Transcriptional profiling of tea to reveal the defence mechanism against blister blight disease and marker development}, booktitle={National Conference on Science of OMICS for Agricultural Productivity: Future Perspective}, author={Kuldeep, S. and Mahajan, P. and Parmar, R. and Seth, R. and Swarnkar, M. and Singh, S. and Ravishankar, A. and Singh, A.K. and Ahuja, P.S. and Sharma, R.K.}, year={2014} }
 @article{population genomics and genomics-assisted trait improvement in tea (camellia sinensis (l.) o. kuntze), url={https://publons.com/wos-op/publon/65165648/}, DOI={10.1007/1383} }