Pradeep Singh | IHBT (CSIR) (original) (raw)

Papers by Pradeep Singh

Journal of Plant Biochemistry and Biotechnology

Picrorhiza kurroa is a medicinal perennial herb of economic importance due to its hepatoprotectiv... more Picrorhiza kurroa is a medicinal perennial herb of economic importance due to its hepatoprotective properties mainly accounted by picroside I and picroside II. To fulfill the current demand of the market indiscriminate collection from its natural habitat pose a great threat to this endangered species. To strategize the conservation of natural populations, a set of 20 highly informative novel genic SSR markers were identified. The utility of these makers was successfully tested for the genetic diversity characterization of P. kurroa populations (n = 28) from three geographical locations. These markers produced 136 alleles (average of 6.8) with mean observed heterozygosity, expected heterozygosity, Shannon’s information index, and PIC value of 0.971, 0.798, 1.681, and 0.737 respectively, revealing a higher extent of genetic diversity in P. kurroa. Further, clustering of all the individuals according to their geographical locations indicates at a spatial population structure in P. kurroa. The current study suggests that informative SSR makers identified here can be potentially used for diversity characterization targeting wider geographical locations for selection of elite/quality genotypes for commercial cultivation and genetic rescue of this endangered species.

Conservation Genetics Resources, 2014

Trillium govanianum, an endangered medicinal herb native to the Himalaya, is less studied at the ... more Trillium govanianum, an endangered medicinal herb native to the Himalaya, is less studied at the molecular level due to the non-availability of genomic resources. To facilitate the basic understanding of the key genes and regulatory mechanism of pharmaceutically important biosynthesis pathways, first spatial transcriptome sequencing of T. govanianum was performed. 151,622,376 (~11.5 Gb) high quality reads obtained using paired-end Illumina sequencing were de novo assembled into 69,174 transcripts. Functional annotation with multiple public databases identified array of genes involved in steroidal saponin biosynthesis and other secondary metabolite pathways including brassinosteroid, carotenoid, diterpenoid, flavonoid, phenylpropanoid, steroid and terpenoid backbone biosynthesis, and important TF families (bHLH, MYB related, NAC, FAR1, bZIP, B3 and WRKY). Differentially expressed large number of transcripts, together with CYPs and UGTs suggests involvement of these candidates in tissue specific expression. Combined transcriptome and expression analysis revealed that leaf and fruit tissues are the main site of steroidal saponin biosynthesis. In conclusion, comprehensive genomic dataset created in the current study will serve as a resource for identification of potential candidates for genetic manipulation of targeted bioactive metabolites and also contribute for development of functionally relevant molecular marker resource to expedite molecular breeding and conservation efforts in T. govanianum. Trillium govanianum Wall. ex D. Don (Family: Melanthiaceae), prevalently known as " Nag chhatri " or " Satva " , is an endangered perennial herb with multiple therapeutic properties. It is the only species of the genus Trillium, native to the Himalaya representing scattered distribution from Nanga Parbat to Namcha Barwa at an altitude range of 2700 m to 4000 m 1,2. It is an allotetraploid (2n = 4× = 20) between the genus Trillium and Daiswa, having a very large genome size of 67.125 Gb (1C = 68.64 pg) 3,4. The species is characterized by the presence of three leaves in a whorl just beneath a trimerous flower emerging from a 15–30 cm long solitary stem and bright red berry like globose fruit at the top, containing numerous seeds. Flowering has been reported to occur during the months of May to July followed by seed set in October 3. The short and stout rhizome along with adventitious roots has been used in the Indian system of medicine as " folk medicine " (http://www.medicinalplants.in/folksearch-page) to cure menstrual and other reproductive disorders 5 , general body weakness 6 , dysentery 2 , headache and fever 7 , besides its use as an anthelmintic for livestock 8. Great medicinal importance coupled with high commercial value (15,000 to 20,000 per kg raw botanical drug) in the international markets 9 has led to quantum

Stevia is a natural source of commercially important steviol glycosides (SGs), which share biosyn... more Stevia is a natural source of commercially important steviol glycosides (SGs), which share biosynthesis route with gibberellic acids (GAs) through plastidal MEP and cytosolic MVA pathways. Ontogeny-dependent deviation in SGs biosynthesis is one of the key factor for global cultivation of Stevia, has not been studied at transcriptional level. To dissect underlying molecular mechanism, we followed a global transcriptome sequencing approach and generated more than 100 million reads. Annotation of 41,262 de novo assembled transcripts identified all the genes required for SGs and GAs biosynthesis. Differential gene expression and quantitative analysis of important pathway genes (DXS, HMGR, KA13H) and gene regulators (WRKY, MYB, NAC TFs) indicated developmental phase dependent utilization of metabolic flux between SGs and GAs synthesis. Further, identification of 124 CYPs and 45 UGTs enrich the genomic resources, and their PPI network analysis with SGs/GAs biosynthesis proteins identifies putative candidates involved in metabolic changes, as supported by their developmental phase-dependent expression. These putative targets can expedite molecular breeding and genetic engineering efforts to enhance SGs content, biomass and yield. Futuristically, the generated dataset will be a useful resource for development of functional molecular markers for diversity characterization, genome mapping and evolutionary studies in Stevia.

Scientific Reports, 2017

Trillium govanianum, an endangered medicinal herb native to the Himalaya, is less studied at the ... more Trillium govanianum, an endangered medicinal herb native to the Himalaya, is less studied at the molecular level due to the non-availability of genomic resources. To facilitate the basic understanding of the key genes and regulatory mechanism of pharmaceutically important biosynthesis pathways, first spatial transcriptome sequencing of T. govanianum was performed. 151,622,376 (~11.5 Gb) high quality reads obtained using paired-end Illumina sequencing were de novo assembled into 69,174 transcripts. Functional annotation with multiple public databases identified array of genes involved in steroidal saponin biosynthesis and other secondary metabolite pathways including brassinosteroid, carotenoid, diterpenoid, flavonoid, phenylpropanoid, steroid and terpenoid backbone biosynthesis, and important TF families (bHLH, MYB related, NAC, FAR1, bZIP, B3 and WRKY). Differentially expressed large number of transcripts, together with CYPs and UGTs suggests involvement of these candidates in tissue specific expression. Combined transcriptome and expression analysis revealed that leaf and fruit tissues are the main site of steroidal saponin biosynthesis. In conclusion, comprehensive genomic dataset created in the current study will serve as a resource for identification of potential candidates for genetic manipulation of targeted bioactive metabolites and also contribute for development of functionally relevant molecular marker resource to expedite molecular breeding and conservation efforts in T. govanianum.

Frontiers in plant science, 2016

Bamboo, one of the fastest growing plants, can be a promising model system to understand growth. ... more 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...

Aquilaria malaccensis is a critically endangered species in Asia because of its overexploitation ... more Aquilaria malaccensis is a critically endangered species in Asia because of its overexploitation to obtain high valued agarwood, used in medicine, perfume, and incense production. Its genetic improvement faces serious problem due to lack of genomic resources. In this study, eighteen novel highly polymorphic microsatellite markers derived from enriched genomic libraries were characterized using 45 individuals of three populations, would be an asset to its non-existing marker recourse. Allelic variations per locus ranged from 2 to 6 with mean allele number was 3.28. The average observed and expected heterozygosity varied from 0.811 and 0.597, respectively. Reproducibility rate, polymorphic potential and ability to detect heterozygosity, novel microsatellites markers would contribute in evaluation of genetic diversity and population structure, and selection of elite germplasm for conservation of genetic resources and commercial utilization.

The endangered Aquilaria malaccensis, is an important plant with high economic values. Characteri... more The endangered Aquilaria malaccensis, is an important plant with high economic values. Characterization of genetic diversity and population structure is receiving tremendous attention for effective conservation of genetic resources. Considering important repositories of biological diversity, the genetic relationships of 127 A. malaccensis accessions from 10 home gardens of three states of northeast India were assessed using amplified fragment length polymorphism (AFLP). Of the 1153 fragments amplified with four AFLP primer combinations, 916 (79.4%) were found to be polymorphic. Polymorphic information content (PIC) and marker index (MI) of each primer combination correlate significantly with the number of genotypes resolved. Overall, a high genetic diversity (avg. 71.85%) was recorded. Further, high gene flow (N m : 3.37), low genetic differentiation (F ST : 0.069) and high within population genetic variation (93%) suggests that most of the genetic diversity is restricted within population. Neighbour joining (NJ), principal coordinate analysis (PCoA) and Bayesian-based STRUCTURE grouped all the accessions in two clusters with significant intermixing between populations, therefore, revealed that two genetically distinct gene pools are operating in the A. malaccensis populations cultivated in home gardens. Based on the various diversity inferences , five diverse populations (JOH, FN, HLF, DHM and ITN) were identified, which can be potentially exploited to develop conservation strategies for A. malaccensis. diversity and population structure of endangered Aquilaria malaccensis revealed potential for future conservation. J. Genet. 94, 697–704]

Journal of Plant Biochemistry and Biotechnology

Picrorhiza kurroa is a medicinal perennial herb of economic importance due to its hepatoprotectiv... more Picrorhiza kurroa is a medicinal perennial herb of economic importance due to its hepatoprotective properties mainly accounted by picroside I and picroside II. To fulfill the current demand of the market indiscriminate collection from its natural habitat pose a great threat to this endangered species. To strategize the conservation of natural populations, a set of 20 highly informative novel genic SSR markers were identified. The utility of these makers was successfully tested for the genetic diversity characterization of P. kurroa populations (n = 28) from three geographical locations. These markers produced 136 alleles (average of 6.8) with mean observed heterozygosity, expected heterozygosity, Shannon’s information index, and PIC value of 0.971, 0.798, 1.681, and 0.737 respectively, revealing a higher extent of genetic diversity in P. kurroa. Further, clustering of all the individuals according to their geographical locations indicates at a spatial population structure in P. kurroa. The current study suggests that informative SSR makers identified here can be potentially used for diversity characterization targeting wider geographical locations for selection of elite/quality genotypes for commercial cultivation and genetic rescue of this endangered species.

Conservation Genetics Resources, 2014

Trillium govanianum, an endangered medicinal herb native to the Himalaya, is less studied at the ... more Trillium govanianum, an endangered medicinal herb native to the Himalaya, is less studied at the molecular level due to the non-availability of genomic resources. To facilitate the basic understanding of the key genes and regulatory mechanism of pharmaceutically important biosynthesis pathways, first spatial transcriptome sequencing of T. govanianum was performed. 151,622,376 (~11.5 Gb) high quality reads obtained using paired-end Illumina sequencing were de novo assembled into 69,174 transcripts. Functional annotation with multiple public databases identified array of genes involved in steroidal saponin biosynthesis and other secondary metabolite pathways including brassinosteroid, carotenoid, diterpenoid, flavonoid, phenylpropanoid, steroid and terpenoid backbone biosynthesis, and important TF families (bHLH, MYB related, NAC, FAR1, bZIP, B3 and WRKY). Differentially expressed large number of transcripts, together with CYPs and UGTs suggests involvement of these candidates in tissue specific expression. Combined transcriptome and expression analysis revealed that leaf and fruit tissues are the main site of steroidal saponin biosynthesis. In conclusion, comprehensive genomic dataset created in the current study will serve as a resource for identification of potential candidates for genetic manipulation of targeted bioactive metabolites and also contribute for development of functionally relevant molecular marker resource to expedite molecular breeding and conservation efforts in T. govanianum. Trillium govanianum Wall. ex D. Don (Family: Melanthiaceae), prevalently known as " Nag chhatri " or " Satva " , is an endangered perennial herb with multiple therapeutic properties. It is the only species of the genus Trillium, native to the Himalaya representing scattered distribution from Nanga Parbat to Namcha Barwa at an altitude range of 2700 m to 4000 m 1,2. It is an allotetraploid (2n = 4× = 20) between the genus Trillium and Daiswa, having a very large genome size of 67.125 Gb (1C = 68.64 pg) 3,4. The species is characterized by the presence of three leaves in a whorl just beneath a trimerous flower emerging from a 15–30 cm long solitary stem and bright red berry like globose fruit at the top, containing numerous seeds. Flowering has been reported to occur during the months of May to July followed by seed set in October 3. The short and stout rhizome along with adventitious roots has been used in the Indian system of medicine as " folk medicine " (http://www.medicinalplants.in/folksearch-page) to cure menstrual and other reproductive disorders 5 , general body weakness 6 , dysentery 2 , headache and fever 7 , besides its use as an anthelmintic for livestock 8. Great medicinal importance coupled with high commercial value (15,000 to 20,000 per kg raw botanical drug) in the international markets 9 has led to quantum

Stevia is a natural source of commercially important steviol glycosides (SGs), which share biosyn... more Stevia is a natural source of commercially important steviol glycosides (SGs), which share biosynthesis route with gibberellic acids (GAs) through plastidal MEP and cytosolic MVA pathways. Ontogeny-dependent deviation in SGs biosynthesis is one of the key factor for global cultivation of Stevia, has not been studied at transcriptional level. To dissect underlying molecular mechanism, we followed a global transcriptome sequencing approach and generated more than 100 million reads. Annotation of 41,262 de novo assembled transcripts identified all the genes required for SGs and GAs biosynthesis. Differential gene expression and quantitative analysis of important pathway genes (DXS, HMGR, KA13H) and gene regulators (WRKY, MYB, NAC TFs) indicated developmental phase dependent utilization of metabolic flux between SGs and GAs synthesis. Further, identification of 124 CYPs and 45 UGTs enrich the genomic resources, and their PPI network analysis with SGs/GAs biosynthesis proteins identifies putative candidates involved in metabolic changes, as supported by their developmental phase-dependent expression. These putative targets can expedite molecular breeding and genetic engineering efforts to enhance SGs content, biomass and yield. Futuristically, the generated dataset will be a useful resource for development of functional molecular markers for diversity characterization, genome mapping and evolutionary studies in Stevia.

Scientific Reports, 2017

Trillium govanianum, an endangered medicinal herb native to the Himalaya, is less studied at the ... more Trillium govanianum, an endangered medicinal herb native to the Himalaya, is less studied at the molecular level due to the non-availability of genomic resources. To facilitate the basic understanding of the key genes and regulatory mechanism of pharmaceutically important biosynthesis pathways, first spatial transcriptome sequencing of T. govanianum was performed. 151,622,376 (~11.5 Gb) high quality reads obtained using paired-end Illumina sequencing were de novo assembled into 69,174 transcripts. Functional annotation with multiple public databases identified array of genes involved in steroidal saponin biosynthesis and other secondary metabolite pathways including brassinosteroid, carotenoid, diterpenoid, flavonoid, phenylpropanoid, steroid and terpenoid backbone biosynthesis, and important TF families (bHLH, MYB related, NAC, FAR1, bZIP, B3 and WRKY). Differentially expressed large number of transcripts, together with CYPs and UGTs suggests involvement of these candidates in tissue specific expression. Combined transcriptome and expression analysis revealed that leaf and fruit tissues are the main site of steroidal saponin biosynthesis. In conclusion, comprehensive genomic dataset created in the current study will serve as a resource for identification of potential candidates for genetic manipulation of targeted bioactive metabolites and also contribute for development of functionally relevant molecular marker resource to expedite molecular breeding and conservation efforts in T. govanianum.

Frontiers in plant science, 2016

Bamboo, one of the fastest growing plants, can be a promising model system to understand growth. ... more 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...

Aquilaria malaccensis is a critically endangered species in Asia because of its overexploitation ... more Aquilaria malaccensis is a critically endangered species in Asia because of its overexploitation to obtain high valued agarwood, used in medicine, perfume, and incense production. Its genetic improvement faces serious problem due to lack of genomic resources. In this study, eighteen novel highly polymorphic microsatellite markers derived from enriched genomic libraries were characterized using 45 individuals of three populations, would be an asset to its non-existing marker recourse. Allelic variations per locus ranged from 2 to 6 with mean allele number was 3.28. The average observed and expected heterozygosity varied from 0.811 and 0.597, respectively. Reproducibility rate, polymorphic potential and ability to detect heterozygosity, novel microsatellites markers would contribute in evaluation of genetic diversity and population structure, and selection of elite germplasm for conservation of genetic resources and commercial utilization.

The endangered Aquilaria malaccensis, is an important plant with high economic values. Characteri... more The endangered Aquilaria malaccensis, is an important plant with high economic values. Characterization of genetic diversity and population structure is receiving tremendous attention for effective conservation of genetic resources. Considering important repositories of biological diversity, the genetic relationships of 127 A. malaccensis accessions from 10 home gardens of three states of northeast India were assessed using amplified fragment length polymorphism (AFLP). Of the 1153 fragments amplified with four AFLP primer combinations, 916 (79.4%) were found to be polymorphic. Polymorphic information content (PIC) and marker index (MI) of each primer combination correlate significantly with the number of genotypes resolved. Overall, a high genetic diversity (avg. 71.85%) was recorded. Further, high gene flow (N m : 3.37), low genetic differentiation (F ST : 0.069) and high within population genetic variation (93%) suggests that most of the genetic diversity is restricted within population. Neighbour joining (NJ), principal coordinate analysis (PCoA) and Bayesian-based STRUCTURE grouped all the accessions in two clusters with significant intermixing between populations, therefore, revealed that two genetically distinct gene pools are operating in the A. malaccensis populations cultivated in home gardens. Based on the various diversity inferences , five diverse populations (JOH, FN, HLF, DHM and ITN) were identified, which can be potentially exploited to develop conservation strategies for A. malaccensis. diversity and population structure of endangered Aquilaria malaccensis revealed potential for future conservation. J. Genet. 94, 697–704]