Publications by authors named "Nagendra Singh"

266 Publications

Exploring the edible gum (galactomannan) biosynthesis and its regulation during pod developmental stages in clusterbean using comparative transcriptomic approach.

Sci Rep 2021 Feb 17;11(1):4000. Epub 2021 Feb 17.

ICAR-National Institute for Plant Biotechnology, New Delhi, India.

Galactomannan is a polymer of high economic importance and is extracted from the seed endosperm of clusterbean (C. tetragonoloba). In the present study, we worked to reveal the stage-specific galactomannan biosynthesis and its regulation in clusterbean. Combined electron microscopy and biochemical analysis revealed high protein and gum content in RGC-936, while high oil bodies and low gum content in M-83. A comparative transcriptome study was performed between RGC-936 (high gum) and M-83 (low gum) varieties at three developmental stages viz. 25, 39, and 50 days after flowering (DAF). Total 209,525, 375,595 and 255,401 unigenes were found at 25, 39 and 50 DAF respectively. Differentially expressed genes (DEGs) analysis indicated a total of 5147 shared unigenes between the two genotypes. Overall expression levels of transcripts at 39DAF were higher than 50DAF and 25DAF. Besides, 691 (RGC-936) and 188 (M-83) candidate unigenes that encode for enzymes involved in the biosynthesis of galactomannan were identified and analyzed, and 15 key enzyme genes were experimentally validated by quantitative Real-Time PCR. Transcription factor (TF) WRKY was observed to be co-expressed with key genes of galactomannan biosynthesis at 39DAF. We conclude that WRKY might be a potential biotechnological target (subject to functional validation) for developing high gum content varieties.
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http://dx.doi.org/10.1038/s41598-021-83507-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7890066PMC
February 2021

An Apical Meristem-Targeted Transformation Method for the Development of Transgenics in Flax (): Optimization and Validation.

Front Plant Sci 2020 28;11:562056. Epub 2021 Jan 28.

ICAR-National Institute for Plant Biotechnology, New Delhi, India.

Efficient regeneration of explants devoid of intrinsic somaclonal variations is a cardinal step in plant tissue culture, thus, a vital component of transgenic technology. However, recalcitrance of economically important crops to tissue culture-based organogenesis ensues a setback in the use of transgenesis in the genetic engineering of crop plants. The present study developed an optimized, genotype-independent, nonconventional tissue culture-independent strategy for the genetic transformation of flax/linseed. This apical meristem-targeted transformation protocol will accelerate value addition in the dual purpose industrially important but recalcitrant fiber crop flax/linseed. The study delineated optimization of mediated transformation and stable T-DNA (pCambia2301::) integration in flax. It established successful use of a stringent soilrite-based screening in the presence of 30 mg/L kanamycin for the identification of putative transformants. The amenability, authenticity, and reproducibility of soilrite-based kanamycin screening were further verified at the molecular level by GUS histochemical analysis of T seedlings, and gene-specific PCR, genomic Southern hybridization for stable integration of T-DNA, and expression analysis of transgenes by sqRT-PCR. This method resulted in a screening efficiency of 6.05% in the presence of kanamycin, indicating amenability of flax transformation. The strategy can be a promising tool for the successful development of transgenics in flax.
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http://dx.doi.org/10.3389/fpls.2020.562056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7876084PMC
January 2021

Evaluating WHO prescribed sanitary inspection templates for assessing contamination risks in tubewells with handpump - case of 9 Indian districts.

Arch Environ Occup Health 2021 Feb 13:1-9. Epub 2021 Feb 13.

Environmental Engineering Division, Department of Civil Engineering, National Institute of Technology, MANIT, Bhopal, India.

WHO prescribes Sanitary Inspections in recommended formats for assessing contamination risks in Tubewells installed with handpump that often constitute primary drinking water sources in rural and remote areas. Sanitary inspections are easy alternatives to costlier and technically demanding laboratory water quality analysis. However, their efficacy remains uncertain despite decades of widespread usage. This study evaluates sanitary inspections by assessing contamination risk in 324 Tubewells with handpump across 9 districts in India. Results indicate that 62% of sampled sources were safe in lab analysis, despite sanitary inspections indicating varying risks. This implies that WHO prescribed inspections yield higher risks, and overestimated risk perception are likely to skew planning and policy, resulting in budgetary over-allocations and financial mismanagement in water-supplies. There is thus an urgent need to review and revise WHO prescribed sanitary inspection templates.
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http://dx.doi.org/10.1080/19338244.2021.1886033DOI Listing
February 2021

identification and validation of natural antiviral compounds as potential inhibitors of SARS-CoV-2 methyltransferase.

J Biomol Struct Dyn 2021 Feb 15:1-11. Epub 2021 Feb 15.

School of Biotechnology, Gautam Buddha University, Greater Noida, India.

The novel Coronavirus disease 2019 (COVID-19) is potentially fatal and caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Due to the unavailability of any proven treatment or vaccination, the outbreak of COVID-19 is wreaking havoc worldwide. Hence, there is an urgent need for therapeutics targeting SARS-CoV-2. Since, botanicals are an important resource for several efficacious antiviral agents, natural compounds gaining significant attention for COVID-19 treatment. In the present study, methyltranferase (MTase) of the SARS-CoV-2 is targeted using computational approach. The compounds were identified using molecular docking, virtual screening and molecular dynamics simulation studies. The binding mechanism of each compound was analyzed considering the stability and energetic parameter using methods. We have found four natural antiviral compounds Amentoflavone, Baicalin, Daidzin and Luteoloside as strong inhibitors of methyltranferase of SARS-CoV-2. ADMET prediction and target analysis of the selected compounds showed favorable results. MD simulation was performed for four top-scored molecules to analyze the stability, binding mechanism and energy requirements. MD simulation studies indicated energetically favorable complex formation between MTase and the selected antiviral compounds. Furthermore, the structural effects on these substitutions were analyzed using the principles of each trajectories, which validated the interaction studies. Our analysis suggests that there is a very high probability that these compounds may have a good potential to inhibit Methyltransferase (MTase) of SARS-CoV-2 and to be used in the treatment of COVID-19. Further studies on these natural compounds may offer a quick therapeutic choice to treat COVID-19. Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2021.1886174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7885726PMC
February 2021

Identification and characterization of MADS box gene family in pigeonpea for their role during floral transition.

3 Biotech 2021 Feb 1;11(2):108. Epub 2021 Feb 1.

ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 India.

MADS box genes are class of transcription factors involved in various physiological and developmental processes in plants. To understand their role in floral transition-related pathways, a genome-wide identification was done in , identifying 102 members which were classified into two different groups based on their gene structure. The status of all these genes was further analyzed in three wild species i.e. , and which revealed absence of 31-34 MADS box genes in them hinting towards their role in domestication and evolution. We could locate only a single copy of both FLOWERING LOCUS C () and SHORT VEGETATIVE PHASE () genes, while three paralogs of SUPPRESSOR OF ACTIVATION OF CONSTANS 1 () were found in genome. One of those paralogs i.e. CcMADS1.5 was found to be missing in all three wild relatives, also forming separate clade in phylogeny. This gene was also lacking the characteristic MADS box domain in it. Expression profiling of major MADS box genes involved in flowering was done in different tissues viz shoot apical meristem, vegetative leaf, reproductive meristem, and reproductive bud. Gene-based time tree of and gene dictates their divergence from before 71 and 23 million year ago (mya), respectively. This study provides valuable insights into the functional characteristics, expression pattern, and evolution of MADS box proteins in grain legumes with emphasis on , which may help in further characterizing these genes.

Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-020-02605-7.
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http://dx.doi.org/10.1007/s13205-020-02605-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7851294PMC
February 2021

Cdk5rap3 is essential for intestinal Paneth cell development and maintenance.

Cell Death Dis 2021 Jan 27;12(1):131. Epub 2021 Jan 27.

Department of Biochemistry & Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.

Intestinal Paneth cells are professional exocrine cells that play crucial roles in maintenance of homeostatic microbiome, modulation of mucosal immunity, and support for stem cell self-renewal. Dysfunction of these cells may lead to the pathogenesis of human diseases such as inflammatory bowel disease (IBD). Cdk5 activator binding protein Cdk5rap3 (also known as C53 and LZAP) was originally identified as a binding protein of Cdk5 activator p35. Although previous studies have indicated its involvement in a wide range of signaling pathways, the physiological function of Cdk5rap3 remains largely undefined. In this study, we found that Cdk5rap3 deficiency resulted in very early embryonic lethality, indicating its indispensable role in embryogenesis. To further investigate its function in the adult tissues and organs, we generated intestinal epithelial cell (IEC)-specific knockout mouse model to examine its role in intestinal development and tissue homeostasis. IEC-specific deletion of Cdk5rap3 led to nearly complete loss of Paneth cells and increased susceptibility to experimentally induced colitis. Interestingly, Cdk5rap3 deficiency resulted in downregulation of key transcription factors Gfi1 and Sox9, indicating its crucial role in Paneth cell fate specification. Furthermore, Cdk5rap3 is highly expressed in mature Paneth cells. Paneth cell-specific knockout of Cdk5rap3 caused partial loss of Paneth cells, while inducible acute deletion of Cdk5rap3 resulted in disassembly of the rough endoplasmic reticulum (RER) and abnormal zymogen granules in the mature Paneth cells, as well as loss of Paneth cells. Together, our results provide definitive evidence for the essential role of Cdk5rap3 in Paneth cell development and maintenance.
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http://dx.doi.org/10.1038/s41419-021-03401-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7841144PMC
January 2021

Exploring potential inhibitor of SARS-CoV2 replicase from FDA approved drugs using insilico drug discovery methods.

J Biomol Struct Dyn 2021 Jan 25:1-8. Epub 2021 Jan 25.

School of Biotechnology, Gautam Buddha University, Greater Noida, India.

Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV2) is responsible for fetal pneumonia called COVID19. SARS-CoV2 emerged in Wuhan, Hubei Province of China in December 2019. The COVID19 pandemic has now gripped the entire world with more than 70 million cases and over 1.5 million deaths so far. There no treatment option for COVID19 is in term of a drug or vaccine is currently available. Therefore drug repurposing may only provide a quick method for utilizing existing drugs for a therapeutic option. The virus genome contains several non-structural proteins (NSP) which serve as target for designing of antiviral agents. NSP9 of SARS-CoV2 encodes for a replicase enzyme which is essential for the virus replication in the host cell. In search of potent inhibitors, we have screened FDA approved drugs against NSP9 using methods. Five drugs fluspirilene, troglitazone, alvesco, dihydroergotoxine and avodart were found to have highest affinities with the replicase. The molecular dynamics simulation (MDS) studies demonstrated strong drugs binding and stable NSP9-drugs complexes formation. The findings are also strongly supported by root-mean-square deviation, root-mean-square fluctuation, radius of gyration, and hydrogen bond analysis of the complexes. Principal component analysis showed the stable conformation of NSP9 upon drug binding. It could be inferred that these five drugs individually or in combinations may be used as potential inhibitors of NSP9 of SARS-CoV-2 after exploring their antiviral potential. Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2020.1871416DOI Listing
January 2021

Comparative analysis of chloroplast genomes indicated different origin for Indian tea (Camellia assamica cv TV1) as compared to Chinese tea.

Sci Rep 2021 Jan 8;11(1):110. Epub 2021 Jan 8.

ICAR-National Institute for Plant Biotechnology, LBS Centre, IARI, New Delhi, 110012, India.

Based upon the morphological characteristics, tea is classified botanically into 2 main types i.e. Assam and China, which are morphologically very distinct. Further, they are so easily pollinated among themselves, that a third category, Cambod type is also described. Although the general consensus of origin of tea is India, Burma and China adjoining area, yet specific origin of China and Assam type tea are not yet clear. Thus, we made an attempt to understand the origin of Indian tea through the comparative analysis of different chloroplast (cp) genomes under the Camellia genus by performing evolutionary study and comparing simple sequence repeats (SSRs) and codon usage distribution patterns among them. The Cp genome based phylogenetic analysis indicated that Indian Tea, TV1 formed a different group from that of China tea, indicating that TV1 might have undergone different domestications and hence owe different origins. The simple sequence repeats (SSRs) analysis and codon usage distribution patterns also supported the clustering order in the cp genome based phylogenetic tree.
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http://dx.doi.org/10.1038/s41598-020-80431-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7794434PMC
January 2021

Identification of a novel and potent small molecule inhibitor of SRPK1: mechanism of dual inhibition of SRPK1 for the inhibition of cancer progression.

Aging (Albany NY) 2020 12 3;13(1):163-180. Epub 2020 Dec 3.

School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India.

Protein kinases are the family of attractive enzyme targets for drug design with relevance to cancer biology. Serine arginine protein kinase 1 (SRPK1) is responsible for the phosphorylation of serine/arginine (SR)-rich proteins. Alternative Splicing Factor/Splicing Factor 2 (ASF/SF2) involved in mRNA editing. ASF/SF2 is over expressed in many cancers and plays crucial roles in the cell survival. Phosphorylation of ASF/SF2 is decisive for its functions in cancer. In search of potential anticancer therapeutic agents for attenuating phosphorylation of ASF/SF2, we have explored specific and potential inhibitors of SRPK1 from natural and drug like compounds databases using methods. Compound ZINC02154892 (C02) was found to be the most potent inhibitor for SRPK1. molecular and cell biology studies have shown C02 as a potent and specific inhibitor of phosphorylation of ASF/SF2 and cell survival in leukemic cell line. Structural analysis of SRPK1 with compound C02 revealed a unique pattern of binding targeting ATP binding site along with inhibiting recruitment of ASF/SF2 by SRPK1. The possibilities of compound C02 to be used as a lead compound paving way for the development of potent and specific inhibitors of SRPK1 for designing of novel potential anticancer inhibitor is inferred from the current studies.
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http://dx.doi.org/10.18632/aging.202301DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7835025PMC
December 2020

Biological Nanofactories: Using Living Forms for Metal Nanoparticle Synthesis.

Mini Rev Med Chem 2021 ;21(2):245-265

Department of Botany, Mahatma Gandhi Central University, Motihari, Bihar, India.

Metal nanoparticles are nanosized entities with dimensions of 1-100 nm that are increasingly in demand due to applications in diverse fields like electronics, sensing, environmental remediation, oil recovery and drug delivery. Metal nanoparticles possess large surface energy and properties different from bulk materials due to their small size, large surface area with free dangling bonds and higher reactivity. High cost and pernicious effects associated with the chemical and physical methods of nanoparticle synthesis are gradually paving the way for biological methods due to their eco-friendly nature. Considering the vast potentiality of microbes and plants as sources, biological synthesis can serve as a green technique for the synthesis of nanoparticles as an alternative to conventional methods. A number of reviews are available on green synthesis of nanoparticles but few have focused on covering the entire biological agents in this process. Therefore present paper describes the use of various living organisms like bacteria, fungi, algae, bryophytes and tracheophytes in the biological synthesis of metal nanoparticles, the mechanisms involved and the advantages associated therein.
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http://dx.doi.org/10.2174/1389557520999201116163012DOI Listing
January 2021

Genetic Architecture and Anthocyanin Profiling of Aromatic Rice From Manipur Reveals Divergence of Landraces.

Front Genet 2020 15;11:570731. Epub 2020 Oct 15.

Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India.

Aromatic rice of Manipur popularly known as is a speciality glutinous rice, for which protection under geographical indication in India has been granted recently. The agronomic and nutraceutical variability of the rice germplasm is yet to be genetically characterized. To address this gap, characterization of ninety-three landraces for agro-morphological traits, grain pigmentation, antioxidant properties, and molecular genetic variation was carried out to unravel their population genetic structure. Two major groups were identified based on pericarp color, namely, purple and non-purple, which showed a significant variation for plant height, panicle length, and grain yield. Molecular marker analysis revealed three subpopulations that could be associated with pericarp pigmentation. Deep purple genotypes formed POP3, genotypes adapted to hill environment formed POP1, while POP2 comprised of both and types. Liquid chromatography-mass spectrometry (LC-MS) analysis revealed two major anthocyanin compounds in pigmented rices, namely, cyanidin-3-O-glucoside (C3G) and peonidin-3-O-glucoside (P3G). The total anthocyanin content among pigmented genotypes ranged from 29.8 to 275.8 mg.100g DW. Total phenolics ranged from 66.5 to 700.3 mg GAE.100g DW with radical scavenging activity (RSA) varying between 17.7 and 65.7%. Anthocyanins and phenolics showed a direct relationship with RSA implying the nutraceutical benefits of deep pigmented rice such as Manipur black rice. Aromatic rices from Manipur were found to be genetically diverse. Therefore, efforts need to be made for maintaining the geographic identity of these rice and utilization in breeding for region-specific cultivar improvement.
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http://dx.doi.org/10.3389/fgene.2020.570731DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7593561PMC
October 2020

An Resistance Gene-Breaking Indian Strain of the Rice Bacterial Blight Pathogen pv. oryzae Is Nearly Identical to a Thai Strain.

Front Microbiol 2020 21;11:579504. Epub 2020 Oct 21.

Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India.

The rice bacterial blight pathogen pv. oryzae () constrains production in major rice growing countries of Asia. injects transcription activator-like effectors (TALEs) that bind to and activate host "susceptibility" () genes that are important for disease. The bacterial blight resistance gene 5, which reduces TALE activity generally, has been widely deployed. However, strains defeating 5 have been reported in India and recently also in Thailand. We completely sequenced and compared the genomes of one such strain from each country and examined the encoded TALEs. The two genomes are nearly identical, including the TALE genes, and belong to a previously identified, highly clonal lineage. Each strain harbors a TALE known to activate the major gene strongly enough to be effective even when diminished by 5. The findings suggest international migration of the -compatible pathotype and highlight the utility of whole genome sequencing and TALE analysis for understanding and responding to breakdown of resistance.
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http://dx.doi.org/10.3389/fmicb.2020.579504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7610140PMC
October 2020

Assembly and Annotation of the Nuclear and Organellar Genomes of a Dwarf Coconut (Chowghat Green Dwarf) Possessing Enhanced Disease Resistance.

OMICS 2020 12 10;24(12):726-742. Epub 2020 Nov 10.

Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India.

Coconut ( L.), an important source of vegetable oil, nutraceuticals, functional foods, and housing materials, provides raw materials for a repertoire of industries engaged in the manufacture of cosmetics, soaps, detergents, paints, varnishes, and emulsifiers, among other products. The palm plays a vital role in maintaining and promoting the sustainability of farming systems of the fragile ecosystems of islands and coastal regions of the tropics. In this study, we present the genome of a dwarf coconut variety "Chowghat Green Dwarf" (CGD) from India, possessing enhanced resistance to root (wilt) disease. Utilizing short reads from the Illumina HiSeq 4000 platform and long reads from the Pacific Biosciences RSII platform, we have assembled the draft genome assembly of 1.93 Gb. The genome is distributed over 26,855 scaffolds, with ∼81.56% of the assembled genome present in scaffolds of lengths longer than 50 kb. About 77.29% of the genome was composed of transposable elements and repeats. Gene prediction yielded 51,953 genes, which upon stringent filtering, based on Annotation Edit Distance, resulted in 13,707 genes, which coded for 11,181 proteins. Among these, we gathered transcript level evidence for a total of 6828 predicted genes based on the RNA-Seq data from different coconut tissues, since they presented assembled transcripts within the genome annotation coordinates. A total of 112 nucleotide-binding and leucine-rich repeat loci, belonging to six classes, were detected. We have also undertaken the assembly and annotation of the CGD chloroplast and mitochondrial genomes. The availability of the dwarf coconut genome shall prove invaluable for deducing the origin of dwarf coconut cultivars, dissection of genes controlling plant habit and fruit color, and accelerated breeding for improved agronomic traits.
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http://dx.doi.org/10.1089/omi.2020.0147DOI Listing
December 2020

Traditional Nutritional and Health Practices Targeting Lifestyle Behavioral Changes in Humans.

J Lifestyle Med 2020 Jul;10(2):67-73

School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, India.

In this 21st century who isn't enticed by the glamorous and appealing life in the fast lane? We are surrounded by wonders, something we could never have imagined erstwhile. We have everything just a click or a call away. This alluring lifestyle comes with its own perils, the biggest one being concerned with health which is often compromised with check ins and home delivered food but the problem doesn't just lie with the outside food but also with all those chemical enriched engineered expensive food items. The industry often tempers with our food to make it "More Attractive" to the consumer. However, in modern era, availability of drugs and fancy powders has led to imbalance of health and nutrition, contrary to the previous era when home gardening was very common and people preferred fresh-foods which didn't contain added chemicals. They even used to treat some of the health problems with the natural ways that we nowadays refer to DIYs (Do-it-yourselves). Since Ayurveda used natural herbs and plant extracts for treatment, the earth was fresher and less-polluted which led to greater life expectancy. The modern era also has its own benefits like excellences in allopathy medicine has brought a cure to many untreatable diseases of the ancient times, and have even eradicated certain diseases like smallpox and polio. To summarize, both the time had their own pros and cons, so it would be better if we take both of their advantages into consideration and work ahead to live a healthy life.
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http://dx.doi.org/10.15280/jlm.2020.10.2.67DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7502895PMC
July 2020

A genome-wide association study in Indian wild rice accessions for resistance to the root-knot nematode Meloidogyne graminicola.

PLoS One 2020 22;15(9):e0239085. Epub 2020 Sep 22.

Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India.

Rice root-knot nematode (RRKN), Meloidogyne graminicola is one of the major biotic constraints in rice-growing countries of Southeast Asia. Host plant resistance is an environmentally-friendly and cost-effective mean to mitigate RRKN damage to rice. Considering the limited availability of genetic resources in the Asian rice (Oryza sativa) cultivars, exploration of novel sources and genetic basis of RRKN resistance is necessary. We screened 272 diverse wild rice accessions (O. nivara, O. rufipogon, O. sativa f. spontanea) to identify genotypes resistant to RRKN. We dissected the genetic basis of RRKN resistance using a genome-wide association study with SNPs (single nucleotide polymorphism) genotyped by 50K "OsSNPnks" genic Affymetrix chip. Population structure analysis revealed that these accessions were stratified into three major sub-populations. Overall, 40 resistant accessions (nematode gall number and multiplication factor/MF < 2) were identified, with 17 novel SNPs being significantly associated with phenotypic traits such as number of galls, egg masses, eggs/egg mass and MF per plant. SNPs were localized to the quantitative trait loci (QTL) on chromosome 1, 2, 3, 4, 6, 10 and 11 harboring the candidate genes including NBS-LRR, Cf2/Cf5 resistance protein, MYB, bZIP, ARF, SCARECROW and WRKY transcription factors. Expression of these identified genes was significantly (P < 0.01) upregulated in RRKN-infected plants compared to mock-inoculated plants at 7 days after inoculation. The identified SNPs enrich the repository of candidate genes for future marker-assisted breeding program to alleviate the damage of RRKN in rice.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0239085PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7508375PMC
November 2020

Genome wide annotation and characterization of young, intact long terminal repeat retrotransposons (In-LTR-RTs) of seven legume species.

Genetica 2020 Dec 19;148(5-6):253-268. Epub 2020 Sep 19.

National Institute for Plant Biotechnology, New Delhi, 110012, India.

Availability of genome sequence of different legume species has provided an opportunity to characterize the abundance, distribution, and divergence of canonical intact long terminal retrotransposons (In-LTR-RT) superfamilies. Among seven legume species, Arachis ipaensis (Aip) showed the highest number of full-length canonical In-LTR-RTs (3325), followed by Glycine max (Gma, 2328), Vigna angularis (Van, 1625), Arachis durensis (Adu, 1348), Lotus japonicus (Lja, 1294), Medicago truncatula (Mtr, 788), and Circer arietinum (Car, 124). Divergence time analysis demonstrated that the amplification timeframe of LTR-RTs dramatically varied in different families. The average insertion time of Copia element varied from 0.51 (Van) to 1.37 million years ago (Mya) (Adu, and Aip), whereas that of Gypsy was between 0.22 (Mtr) and 1.82 Mya (Adu). Bayesian phylogenetic tree analysis suggested that the 1397 and 1917 reverse transcriptase (RT) domains of Copia and Gypsy families of the seven legume species were clustered into 7 and 14 major groups, respectively. The highest proportion (approximately 94.79-100%) of transposable element (TE)-associated genes assigned to pathways was mapped to metabolism-related pathways in all species. The results enabled the structural understanding of full-length In-LTR-RTs and will be valuable resource for the further study of the impact of TEs on gene structure and expression in legume species.
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http://dx.doi.org/10.1007/s10709-020-00103-5DOI Listing
December 2020

Cysteine-rich antimicrobial peptides from plants: The future of antimicrobial therapy.

Phytother Res 2021 Jan 17;35(1):256-277. Epub 2020 Sep 17.

Department of Botany, Mahatma Gandhi Central University, Motihari, India.

There has been a spurt in the spread of microbial resistance to antibiotics due to indiscriminate use of antimicrobial agents in human medicine, agriculture, and animal husbandry. It has been realized that conventional antibiotic therapy would be less effective in the coming decades and more emphasis should be given for the development of novel antiinfective therapies. Cysteine rich peptides (CRPs) are broad-spectrum antimicrobial agents that modulate the innate immune system of different life forms such as bacteria, protozoans, fungi, plants, insects, and animals. These are also expressed in several plant tissues in response to invasion by pathogens, and play a crucial role in the regulation of plant growth and development. The present work explores the importance of CRPs as potent antimicrobial agents, which can supplement and/or replace the conventional antibiotics. Different plant parts of diverse plant species showed the presence of antimicrobial peptides (AMPs), which had significant structural and functional diversity. The plant-derived AMPs exhibited potent activity toward a range of plant and animal pathogens, protozoans, insects, and even against cancer cells. The cysteine-rich AMPs have opened new avenues for the use of plants as biofactories for the production of antimicrobials and can be considered as promising antimicrobial drugs in biotherapeutics.
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http://dx.doi.org/10.1002/ptr.6823DOI Listing
January 2021

Marker Assisted Development and Characterization of Herbicide Tolerant Near Isogenic Lines of a Mega Basmati Rice Variety, "Pusa Basmati 1121".

Rice (N Y) 2020 Sep 15;13(1):68. Epub 2020 Sep 15.

Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.

Background: Direct-seeded rice (DSR) is a potential technology for sustainable rice farming as it saves water and labor. However, higher incidence of weed under DSR limits productivity. Therefore, there is a need to develop herbicide tolerant (HT) rice varieties.

Results: We used marker assisted backcross breeding (MABB) to transfer a mutant allele of Acetohydroxy acid synthase (AHAS) gene, which confers tolerance to imidazolinone group of herbicides from the donor parent (DP) "Robin" into the genetic background of an elite popular Basmati rice variety, Pusa Basmati 1121 (PB 1121). Foreground selection was done using the AHAS gene linked Simple Sequence Repeat (SSR) marker RM6844 and background selection was performed using 112 genome-wide SSR markers polymorphic between PB 1121 and Robin. Phenotypic selection for agronomic, Basmati grain and cooking quality traits in each generation was carried out to improve the recovery of recurrent parent phenome (RPP). Finally, a set of 12 BCF near isogenic lines (NILs), with recurrent parent genome (RPG) recovery ranging from 98.66 to 99.55% were developed and evaluated. PB 1121-HT NILs namely 1979-14-7-33-99-10, 1979-14-7-33-99-15 and 1979-14-7-33-99-66 were found superior to PB 1121 in yield with comparable grain and cooking quality traits and herbicide tolerance similar to Robin.

Conclusion: Overall, the present study reports successful development of HT NILs in the genetic background of popular Basmati rice variety, PB 1121 by introgression of mutated AHAS allele. This is the first report on the development of HT Basmati rice. Superior NILs are being evaluated in the national Basmati trials, the release of which is likely to provide a viable option for the adoption of DSR technology in Basmati rice cultivation.
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http://dx.doi.org/10.1186/s12284-020-00423-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7492307PMC
September 2020

Intestinal microbiota-derived short-chain fatty acids regulation of immune cell IL-22 production and gut immunity.

Nat Commun 2020 09 8;11(1):4457. Epub 2020 Sep 8.

Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, 77555, USA.

Innate lymphoid cells (ILCs) and CD4 T cells produce IL-22, which is critical for intestinal immunity. The microbiota is central to IL-22 production in the intestines; however, the factors that regulate IL-22 production by CD4 T cells and ILCs are not clear. Here, we show that microbiota-derived short-chain fatty acids (SCFAs) promote IL-22 production by CD4 T cells and ILCs through G-protein receptor 41 (GPR41) and inhibiting histone deacetylase (HDAC). SCFAs upregulate IL-22 production by promoting aryl hydrocarbon receptor (AhR) and hypoxia-inducible factor 1α (HIF1α) expression, which are differentially regulated by mTOR and Stat3. HIF1α binds directly to the Il22 promoter, and SCFAs increase HIF1α binding to the Il22 promoter through histone modification. SCFA supplementation enhances IL-22 production, which protects intestines from inflammation. SCFAs promote human CD4 T cell IL-22 production. These findings establish the roles of SCFAs in inducing IL-22 production in CD4 T cells and ILCs to maintain intestinal homeostasis.
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http://dx.doi.org/10.1038/s41467-020-18262-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7478978PMC
September 2020

Protein and gene integration analysis through proteome and transcriptome brings new insight into salt stress tolerance in pigeonpea (Cajanus cajan L.).

Int J Biol Macromol 2020 Dec 31;164:3589-3602. Epub 2020 Aug 31.

Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India. Electronic address:

Salt stress is a major constrain to the productivity of nutritionally rich pigeonpea, an important legume of SE Asia and other parts of the world. The present study provides a comprehensive insight on integrated proteomic and transcriptomic analysis of root and shoot tissues of contrasting pigeonpea varieties (ICP1071- salt-sensitive; ICP7- salt-tolerant) to unravel salt stress induced pathways. Proteome analysis revealed 82 differentially expressed proteins (DEPs) with ≥±1.5 fold expression on 2-Dimensional (2D) gel. Of these, 25 DEPs identified through MALDI-TOF/TOF were classified using Uniprot software into functional categories. Pathways analyses using KAAS server showed the highest abundance of functional genes regulating metabolisms of carbohydrate followed by protein folding/degradation, amino acids and lipids. Expression studies on six genes (triosephosphate isomerase, oxygen evolving enhancer protein 1, phosphoribulokinase, cysteine synthase, oxygen evolving enhancer protein 2 and early nodulin like protein 2) with ≥±3 fold change were performed, and five of these showed consistency in transcript and protein expressions. Transcript analysis of root and shoot led to positive identification of 25 differentially expressed salt-responsive genes, with seven genes having ≥±5 fold change have diverse biological functions. Our combinatorial analysis suggests important role of these genes/proteins in providing salt tolerance in pigeonpea.
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http://dx.doi.org/10.1016/j.ijbiomac.2020.08.223DOI Listing
December 2020

Transgenic Cotton ( L.) to Combat Weed Vagaries: Utility of an Apical Meristem-Targeted Transformation Strategy to Introgress a Modified Gene for Glyphosate Tolerance.

Front Plant Sci 2020 7;11:768. Epub 2020 Jul 7.

ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India.

Weeds burden plant growth as they compete for space, sunlight, and soil nutrients leading to 25-80% yield losses. Glyphosate [-(phosphonomethyl)glycine] is a widely used broad spectrum non-selective herbicide that controls weeds by inhibiting 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) enzyme and interfering with the shikimate biosynthesis pathway. Cotton ( L.) is one of the most important commercial crops grown worldwide for its fiber. We have developed herbicide tolerant transgenic cotton (cv. P8-6) by introgression of a codon-optimized and modified gene () possessing an N-terminal chloroplast targeting peptide from . Because of the recalcitrant nature of cotton, a genotype-independent non-tissue culture-based apical meristem-targeted transformation approach was used to develop transformants. Although transformation methodologies are advantageous in developing a large number of transgenic plants, effective screening strategies are essential for initial identification of transformants. In the present study, the use of a two-level rigorous screening strategy identified 2.27% of T1 generation plants as tolerant to 800 and 1,500 mg/L of commercially available glyphosate (Roundup). Precise molecular characterization revealed stable integration, expression, and inheritance of in advanced generations of the promising transgenic events. Further, superiority of selected transgenic plants in tolerating increasing levels of glyphosate (500-4,000 mg/L) was ascertained through reduced accumulation of shikimate. This report is the first of its kind where cotton transformants tolerating high levels of glyphosate (up to 4,000 mg/L) and accumulating low levels of shikimate have been identified. This study not only reiterated the genotype-independent nature of the transformation strategy but also reiterated the translational utility of the gene in management of weeds.
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http://dx.doi.org/10.3389/fpls.2020.00768DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7358616PMC
July 2020

Deficiency Reduces Tumor Growth by Targeting Stem Cell Self-Renewal.

Cancer Res 2020 09 14;80(18):3855-3866. Epub 2020 Jul 14.

Department of Biochemistry and Molecular Biology, Augusta University, Augusta, Georgia.

RAD51-associated protein 1 (RAD51AP1) plays an integral role in homologous recombination by activating RAD51 recombinase. Homologous recombination is essential for preserving genome integrity and RAD51AP1 is critical for D-loop formation, a key step in homologous recombination. Although RAD51AP1 is involved in maintaining genomic stability, recent studies have shown that RAD51AP1 expression is significantly upregulated in human cancers. However, the functional role of RAD51AP1 in tumor growth and the underlying molecular mechanism(s) by which RAD51AP1 regulates tumorigenesis have not been fully understood. Here, we use Rad51ap1-knockout mice in genetically engineered mouse models of breast cancer to unravel the role of RAD51AP1 in tumor growth and metastasis. RAD51AP1 gene transcript was increased in both luminal estrogen receptor-positive breast cancer and basal triple-negative breast cancer, which is associated with poor prognosis. Conversely, knockdown of RAD51AP1 (RADP51AP1 KD) in breast cancer cell lines reduced tumor growth. Rad51ap1-deficient mice were protected from oncogene-driven spontaneous mouse mammary tumor growth and associated lung metastasis. , limiting dilution studies provided evidence that Rad51ap1 plays a critical role in breast cancer stem cell (BCSC) self-renewal. RAD51AP1 KD improved chemotherapy and radiotherapy response by inhibiting BCSC self-renewal and associated pluripotency. Overall, our study provides genetic and biochemical evidences that RAD51AP1 is critical for tumor growth and metastasis by increasing BCSC self-renewal and may serve as a novel target for chemotherapy- and radiotherapy-resistant breast cancer. SIGNIFICANCE: This study provides evidence that RAD51AP1 plays a critical role in breast cancer growth and metastasis by regulating breast cancer stem cell self-renewal.
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http://dx.doi.org/10.1158/0008-5472.CAN-19-3713DOI Listing
September 2020

Introgressed Saltol QTL Lines Improves the Salinity Tolerance in Rice at Seedling Stage.

Front Plant Sci 2020 11;11:833. Epub 2020 Jun 11.

Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, India.

Rice is a staple food crop in Asia and plays a crucial role in the economy of this region. However, production of rice and its cultivating areas are under constant threat of soil salinity. A major QTL, , responsible for salinity tolerance at seedling stage has been mapped on chromosome 1 using Pokkali/IR29 Recombinant Inbred Lines (RIL) population. The present study was aimed to incorporate Quantitative Trait Loci (QTL) in two high yielding mega rice varieties i.e. Pusa44 and Sarjoo52 through Marker Assisted Backcross Breeding (MABB). To improve the seedling stage salinity tolerance in these cultivars, we introgressed the QTL from donor parent FL478 a derivative of Pokkali. A total of three backcrosses (BC) followed by selfing have led to successful introgression of QTL. Foreground selection at each breeding cycle was done using micro-satellite markers RM3412 and AP3206 to confirm QTL. The precise transfer of region was established using recombinant selection through flanking markers RM493 and G11a. Finally, 10 near isogenic lines (NILs) of Pusa44 and eight NILs of Sarjoo52 were successfully developed. These NILs (BCF) were evaluated for seedling stage salinity under hydroponic system. The NILs PU99, PU176, PU200, PU215, PU229, PU240, PU241, PU244, PU252, PU263 of Pusa44 and SAR17, SAR23, SAR35, SAR39, SAR77, SAR87, SAR123, SAR136 NILs of Sarjoo52 confirmed tolerance to salinity with low salt injury score of 3 or 5. Ratio of Na/K content of NILs ranged from 1.26 to 1.85 in Pusa44 and 1.08 to 1.69 in Sarjoo52. The successfully developed NILs were further phenotyped stringently for morphological traits to estimate Phenotypic Recovery. Background selection of NILs along with parents was carried out with 50K SNP chip and recovered 94.83-98.38% in Pusa44 NILs and 94.51 to 98.31% in Sarjoo52 NILs of recurrent genome. The present study of MAB has accelerated the development of salt tolerant lines in the genetic background of Pusa44 and Sarjoo52. These NILs could be used for commercial cultivation in saline affected area.
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http://dx.doi.org/10.3389/fpls.2020.00833DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7300257PMC
June 2020

Genome-wide association studies using 50 K rice genic SNP chip unveil genetic architecture for anaerobic germination of deep-water rice population of Assam, India.

Mol Genet Genomics 2020 Sep 6;295(5):1211-1226. Epub 2020 Jun 6.

ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, 110012, India.

North Eastern part of India such as Assam is inundated by flood every year where the farmers are forced to grow the traditional tall deep-water rice. Genetic improvement of this type of rice is slow because of insufficient knowledge about their genetic architecture and population structure. In the present investigation, the genetic diversity architecture of 94 deep-water rice genotypes of Assam and association mapping strategy was, for the first time, applied to determine the significant SNPs and genes for deep-water rice. These genotypes are known for their unique elongation ability under deep-water condition. The anaerobic germination (AG) related trait-associated genes identified here can provide affluent resources for rice breeding especially in flood-prone areas. We investigated the genome-wide association studies (GWAS) using 50 K rice genic SNP chip across 94 deep-water rice genotypes collected from different flood-prone districts/villages of Assam. Population structure and diversity analysis revealed that these genotypes were stratified into four sub-populations. Using GWAS approach, 20 significant genes were identified and found to be associated with AG-related traits. Of them, two most relevant genes (OsXDH1and SSXT) have been identified which explain phenotypic variability (R > 20%) in the population. These genes were located in Chr 3 (LOC_Os03g31550) which encodes for enzyme xanthine dehydrogenase 1(OsXDH1) and in Chr 12 (LOC_Os12g31350) which encodes for SSXT family protein. Both of these genes were found to be associated with anaerobic response index (increase in the coleoptile length under water in anaerobic condition with respect to control), respectively. Interestingly, OsXDH1is involved in purine catabolism pathway and acts as a scavenger of reactive oxygen species in plants, whereas SSXT is GRF1-interacting factor 3. These two candidate genes associated with AG of deep-water rice have been found to be reported for the first time. Thus, this study provides a greater resource for breeders not only for improvement of deep-water rice, but also for AG tolerant variety useful for direct-seeded rice in flood-affected areas.
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http://dx.doi.org/10.1007/s00438-020-01690-wDOI Listing
September 2020

Fréchet PDF based Matched Filter Approach for Retinal Blood Vessels Segmentation.

Comput Methods Programs Biomed 2020 Oct 5;194:105490. Epub 2020 Jun 5.

Department of Computer Science and Engineering, National Institute of Technology, Hamirpur, India. Electronic address:

Background And Objective: Retinal pathology diseases such as glaucoma, obesity, diabetes, hypertension etc. have deadliest impact on life of human being today. Retinal blood vessels consist of various significant information which are helpful in detection and treatment of these diseases. Therefore, it is essential to segment these retinal vessels. Various matched filter approaches for segmentation of retinal blood vessels are reported in the literature but their kernel templates are not appropriate to vessel profile resulting poor performance. To overcome this, a novel matched filter approach based on Fréchet probability distribution function has been proposed.

Methods: Image processing operations which we have used in the proposed approach are basically divided into three major stages viz; pre processing, Fréchet matched filter and post processing. In pre processing, principle component analysis (PCA) method is used to convert color image into grayscale image thereafter contrast limited adaptive histogram equalization (CLAHE) is applied on obtained grayscale to get enhanced grayscale image. In Fréchet matched filter, exhaustive experimental tests are conducted to choose optimal values for both Fréchet function parameters and matched filter parameters to design new matched filter. In post processing, entropy based optimal thresholding technique is applied on obtained MFR image to get binary image followed by length filtering and masking methods are applied to generate to a clear and whole vascular tree.

Results: For evaluation of the proposed approach, quantitative performance metrics such as average specificity, average sensitivity and average accuracy and root mean square deviation (RMSD) are computed in the literature. We found the average specificity 97.24%, average sensitivity 72.78%, average accuracy 95.09% for STARE dataset while average specificity 97.61%, average sensitivity 73.07%, average accuracy 95.44% for DRIVE dataset. Average RMSD values are found 0.07 and 0.04 for STARE and DRIVE databases respectively.

Conclusions: From experimental results, it can be observed that our proposed approach outperforms over latest and prominent works reported in the literature. The cause of improved performance is due to better matching between vessel profile and Fréchet template.
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http://dx.doi.org/10.1016/j.cmpb.2020.105490DOI Listing
October 2020

Identification of potential inhibitors of SARS-COV-2 endoribonuclease (EndoU) from FDA approved drugs: a drug repurposing approach to find therapeutics for COVID-19.

J Biomol Struct Dyn 2020 Jun 9:1-11. Epub 2020 Jun 9.

School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, India.

SARS-CoV-2 is causative agent of COVID-19, which is responsible for severe social and economic disruption globally. Lack of vaccine or antiviral drug with clinical efficacy suggested that drug repurposing approach may provide a quick therapeutic solution to COVID-19. Nonstructural protein-15 (NSP15) encodes for an uridylate-specific endoribonuclease (EndoU) enzyme, essential for virus life cycle and an attractive target for drug development. We have performed based virtual screening of FDA approved compounds targeting EndoU in search of COVID-19 drugs from commercially available approved molecules. Two drugs Glisoxepide and Idarubicin used for treatment for diabetes and leukemia, respectively, were selected as stronger binder of EndoU. Both the drugs bound to the active site of the viral endonuclease by forming attractive intermolecular interactions with catalytically essential amino acid residues, His235, His250, and Lys290. Molecular dynamics simulation studies showed stable conformation dynamics upon drugs binding to endoU. The binding free energies for Glisoxepide and Idarubicin were calculated to be -141±11 and -136±16kJ/mol, respectively. The IC were predicted to be 9.2µM and 30µM for Glisoxepide and Idarubicin, respectively. Comparative structural analysis showed the stronger binding of EndoU to Glisoxepide and Idarubicin than to uridine monophosphate (UMP). Surface area calculations showed buried are of 361.8Å by Glisoxepide which is almost double of the area occupied by UMP suggesting stronger binding of the drug than the ribonucleotide. However, further studies on these drugs for evaluation of their clinical efficacy and dose formulations may be required, which may provide a quick therapeutic option to treat COVID-19. Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2020.1775127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7298882PMC
June 2020

Allelic sequence variation in the Sub1A, Sub1B and Sub1C genes among diverse rice cultivars and its association with submergence tolerance.

Sci Rep 2020 05 25;10(1):8621. Epub 2020 May 25.

ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India.

Erratic rainfall leading to flash flooding causes huge yield losses in lowland rice. The traditional varieties and landraces of rice possess variable levels of tolerance to submergence stress, but gene discovery and utilization of these resources has been limited to the Sub1A-1 allele from variety FR13A. Therefore, we analysed the allelic sequence variation in three Sub1 genes in a panel of 179 rice genotypes and its association with submergence tolerance. Population structure and diversity analysis based on a 36-plex genome wide genic-SNP assay grouped these genotypes into two major categories representing Indica and Japonica cultivar groups with further sub-groupings into Indica, Aus, Deepwater and Aromatic-Japonica cultivars. Targetted re-sequencing of the Sub1A, Sub1B and Sub1C genes identfied 7, 7 and 38 SNPs making 8, 9 and 67 SNP haplotypes, respectively. Haplotype networks and phylogenic analysis revealed evolution of Sub1B and Sub1A genes by tandem duplication and divergence of the ancestral Sub1C gene in that order. The alleles of Sub1 genes in tolerant reference variety FR13A seem to have evolved most recently. However, no consistent association could be found between the Sub1 allelic variation and submergence tolerance probably due to low minor allele frequencies and presence of exceptions to the known Sub1A-1 association in the genotype panel. We identified 18 cultivars with non-Sub1A-1 source of submergence tolerance which after further mapping and validation in bi-parental populations will be useful for development of superior flood tolerant rice cultivars.
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http://dx.doi.org/10.1038/s41598-020-65588-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7248102PMC
May 2020

Comparative RNA sequencing based transcriptome profiling of regular bearing and alternate bearing mango (Mangifera indica L.) varieties reveals novel insights into the regulatory mechanisms underlying alternate bearing.

Biotechnol Lett 2020 Jun 19;42(6):1035-1050. Epub 2020 Mar 19.

ICAR-National Institute for Plant Biotechnology, Pusa campus, New Delhi, 110012, India.

Objective: This study is to understand a comprehensive perspective on the molecular mechanisms underlying alternate bearing in mango (Mangifera indica L.) via transcriptome wide gene expression profiling of both regular and irregular mango varieties.

Results: Transcriptome data of regular (Neelam) and irregular (Dashehari) mango varieties revealed a total of 42,397 genes. Out of that 12,557 significantly differentially expressed genes were identified, of which 6453 were found to be up-regulated and 6104 were found to be down-regulated genes. Further, many of the common unigenes which were involved in hormonal regulation, metabolic processes, oxidative stress, ion homeostasis, alternate bearing etc. showed significant differences between these two different bearing habit varieties. Pathway analysis showed the highest numbers of differentially expressed genes were related with the metabolic processes (523). A total of 26 alternate bearing genes were identified and principally three genes viz; SPL-like gene (GBVX01015803.1), Rumani GA-20-oxidase-like gene (GBVX01019650.1) and LOC103420644 (GBVX01016070.1) were significantly differentially expressed (at log2FC and pval less than 0.05) while, only single gene (gbGBVW01004309.1) related with flowering was found to be differentially expressed. A total of 15 differentially expressed genes from three important pathways viz; alternate bearing, carbohydrate metabolism and hormone synthesis were validated using Real time PCR and results were at par with in silico analysis.

Conclusions: Deciphering the differentially expressed genes (DEGs) and potential candidate genes associated with alternate bearing, hormone and carbohydrate metabolism pathways will help for illustrating the molecular mechanisms underlying the bearing tendencies in mango.
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http://dx.doi.org/10.1007/s10529-020-02863-8DOI Listing
June 2020

A 62K genic-SNP chip array for genetic studies and breeding applications in pigeonpea (Cajanus cajan L. Millsp.).

Sci Rep 2020 03 18;10(1):4960. Epub 2020 Mar 18.

ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.

Pigeonpea is the second most important pulse legume crop for food and nutritional security of South Asia that requires accelerated breeding using high throughput genomic tools. Single nucleotide polymorphisms (SNPs) are highly suitable markers for this purpose because of their bi-allelic nature, reproducibility and high abundance in the genome. Here we report on development and use of a pigeonpea 62 K SNP chip array 'CcSNPnks' for Affymetrix GeneTitan platform. The array was designed after filtering 645,662 genic-SNPs identified by re-sequencing of 45 diverse genotypes and has 62,053 SNPs from 9629 genes belonging to five different categories, including 4314 single-copy genes unique to pigeonpea, 4328 single-copy genes conserved between soybean and pigeonpea, 156 homologs of agronomically important cloned genes, 746 disease resistance and defense response genes and 85 multi-copy genes of pigeonpea. This fully genic chip has 28.94% exonic, 33.04% intronic, 27.56% 5'UTR and 10.46% 3'UTR SNPs and incorporates multiple SNPs per gene allowing gene haplotype network analysis. It was used successfully for the analysis of genetic diversity and population structure of 95 pigeonpea varieties and high resolution mapping of 11 yield related QTLs for number of branches, pod bearing length and number of seeds per pod in a biparental RIL population. As an accurate high-density genotyping tool, 'CcSNPnks' chip array will be useful for high resolution fingerprinting, QTL mapping and genome wide as well as gene-based association studies in pigeonpea.
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http://dx.doi.org/10.1038/s41598-020-61889-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7080765PMC
March 2020

Root-specific expression of chickpea cytokinin oxidase/dehydrogenase 6 leads to enhanced root growth, drought tolerance and yield without compromising nodulation.

Plant Biotechnol J 2020 11 1;18(11):2225-2240. Epub 2020 Sep 1.

National Institute of Plant Genome Research, New Delhi, India.

Cytokinin group of phytohormones regulate root elongation and branching during post-embryonic development. Cytokinin-degrading enzymes cytokinin oxidases/dehydrogenases (CKXs) have been deployed to investigate biological activities of cytokinin and to engineer root growth. We expressed chickpea cytokinin oxidase 6 (CaCKX6) under the control of a chickpea root-specific promoter of CaWRKY31 in Arabidopsis thaliana and chickpea having determinate and indeterminate growth patterns, respectively, to study the effect of cytokinin depletion on root growth and drought tolerance. Root-specific expression of CaCKX6 led to a significant increase in lateral root number and root biomass in Arabidopsis and chickpea without any penalty to vegetative and reproductive growth of shoot. Transgenic chickpea lines showed increased CKX activity in root. Soil-grown advanced chickpea transgenic lines exhibited higher root-to-shoot biomass ratio and enhanced long-term drought tolerance. These chickpea lines were not compromised in root nodulation and nitrogen fixation. The seed yield in some lines was up to 25% higher with no penalty in protein content. Transgenic chickpea seeds possessed higher levels of zinc, iron, potassium and copper. Our results demonstrated the potential of cytokinin level manipulation in increasing lateral root number and root biomass for agronomic trait improvement in an edible legume crop with indeterminate growth habit.
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http://dx.doi.org/10.1111/pbi.13378DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7589355PMC
November 2020