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Abstract Background Despite great advances in genomic technology observed in several crop species, the availability of molecular tools such as microsatellite markers has been limited in tea (Camellia sinensis L.). The development of microsatellite markers will have a major impact on genetic analysis, gene mapping and marker assisted breeding. Unigene derived microsatellite (UGMS) markers identified from publicly available sequence database have the advantage of assaying variation in the expressed component of the genome with unique identity and position. Therefore, they can serve as efficient and cost effective alternative markers in such species. Results Considering the multiple advantages of UGMS markers, 1,223 unigenes were predicted from 2,181 expressed sequence tags (ESTs) of tea (Camellia sinensis L.). A total of 109 (8.9%) unigenes containing 120 SSRs were identified. SSR abundance was one in every 3.55 kb of EST sequences. The microsatellites mainly comprised of di (50.8%), tri (30.8%), tetra (6.6%), penta (7.5%) and few hexa (4.1%) nucleotide repeats. Among the dinucleotide repeats, (GA)n.(TC)n were most abundant (83.6%). Ninety six primer pairs could be designed form 83.5% of SSR containing unigenes. Of these, 61 (63.5%) primer pairs were experimentally validated and used to investigate the genetic diversity among the 34 accessions of different Camellia spp. Fifty one primer pairs (83.6%) were successfully cross transferred to the related species at various levels. Functional annotation of the unigenes containing SSRs was done through gene ontology (GO) characterization. Thirty six (60%) of them revealed significant sequence similarity with the known/putative proteins of Arabidopsis thaliana. Polymorphism information content (PIC) ranged from 0.018 to 0.972 with a mean value of 0.497. The average heterozygosity expected (HE) and observed (Ho) obtained was 0.654 and 0.413 respectively, thereby suggesting highly heterogeneous nature of tea. Further, test for IAM and SMM models for the UGMS loci showed excess heterozygosity and did not show any bottleneck operating in the tea population. Conclusion UGMS markers identified and characterized in this study provided insight about the abundance and distribution of SSR in the expressed genome of C. sinensis. The identification and validation of 61 new UGMS markers will not only help in intra and inter specific genetic diversity assessment but also be enriching limited microsatellite markers resource in tea. Further, the use of these markers would reduce the cost and facilitate the gene mapping and marker-aided selection in tea. Since, 36 of these UGMS markers correspond to the Arabidopsis protein sequence data with known functions will offer the opportunity to investigate the consequences of SSR polymorphism on gene functions.

Abstract Background Completely sequenced plant genomes provide scope for designing a large number of microsatellite markers, which are useful in various aspects of crop breeding and genetic analysis. With the objective of developing genic but non-coding microsatellite (GNMS) markers for the rice (Oryza sativa L.) genome, we characterized the frequency and relative distribution of microsatellite repeat-motifs in 18,935 predicted protein coding genes including 14,308 putative promoter sequences. Results We identified 19,555 perfect GNMS repeats with densities ranging from 306.7/Mb in chromosome 1 to 450/Mb in chromosome 12 with an average of 357.5 GNMS per Mb. The average microsatellite density was maximum in the 5' untranslated regions (UTRs) followed by those in introns, promoters, 3'UTRs and minimum in the coding sequences (CDS). Primers were designed for 17,966 (92%) GNMS repeats, including 4,288 (94%) hypervariable class I types, which were bin-mapped on the rice genome. The GNMS markers were most polymorphic in the intronic region (73.3%) followed by markers in the promoter region (53.3%) and least in the CDS (26.6%). The robust polymerase chain reaction (PCR) amplification efficiency and high polymorphic potential of GNMS markers over genic coding and random genomic microsatellite markers suggest their immediate use in efficient genotyping applications in rice. A set of these markers could assess genetic diversity and establish phylogenetic relationships among domesticated rice cultivar groups. We also demonstrated the usefulness of orthologous and paralogous conserved non-coding microsatellite (CNMS) markers, identified in the putative rice promoter sequences, for comparative physical mapping and understanding of evolutionary and gene regulatory complexities among rice and other members of the grass family. The divergence between long-grained aromatics and subspecies japonica was estimated to be more recent (0.004 Mya) compared to short-grained aromatics from japonica (0.006 Mya) and long-grained aromatics from subspecies indica (0.014 Mya). Conclusion Our analyses showed that GNMS markers with their high polymorphic potential would be preferred candidate functional markers in various marker-based applications in rice genetics, genomics and breeding. The CNMS markers provided encouraging implications for their use in comparative genome mapping and understanding of evolutionary complexities in rice and other members of grass family.

Abstract Background Protozoan infections are the most serious among all the superimposed infections in HIV patients and claim a number of lives every year. The line of treatment being different for diverse parasites necessitates a definitive diagnosis of the etiological agents to avoid empirical treatment. Thus, the present study has been aimed to elucidate the associations between diarrhoea and CD4 counts and to study the effect of HAART along with management of diarrhoea in HIV positive patients. This study is the first of its kind in this area where an attempt was made to correlate seasonal variation and intestinal protozoan infestations. Methods The study period was from January 2006 to October 2007 wherein stool samples were collected from 366 HIV positive patients with diarrhea attending the ART centre, inpatient department and ICTC of S.S. hospital, I.M.S., B.H.U., Varanasi. Simultaneously, CD4 counts were recorded to assess the status of HIV infection vis-à-vis parasitic infection. The identification of pathogens was done on the basis of direct microscopy and different staining techniques. Results Of the 366 patients, 112 had acute and 254 had chronic diarrhea. The percentages of intestinal protozoa detected were 78.5% in acute and 50.7% in chronic cases respectively. Immune restoration was observed in 36.6% patients after treatment on the basis of clinical observation and CD4 counts. In 39.8% of HIV positive cases Cryptosporidium spp. was detected followed by Microsporidia spp. (26.7%). The highest incidence of intestinal infection was in the rainy season. However, infection with Cyclospora spp. was at its peak in the summer. Patients with chronic diarrhea had lower CD4 cell counts. The maximum parasitic isolation was in the patients whose CD4 cell counts were below 200 cells/μl. Conclusion There was an inverse relation between the CD4 counts and duration of diarrhea. Cryptosporidium spp. was isolated maximum among all the parasites in the HIV patients. The highest incidence of infection was seen in the rainy season.

Presents information on a study which concluded that genomic DNA can be easily extracted from plants by fixing leaves or other soft tissues without impairing its quality for routine molecular biological work. Materials and methods; Results and discussion.

Tree species in the arid and semi-arid regions use various strategies to combat drought stress. Ziziphus nummularia (Burm. f.) Wight et Arn. native to the Thar Desert in India, is highly drought-tolerant. To identify the most drought-tolerant ecotype of Z. nummularia , one ecotype each from semi-arid (Godhra, annual rainfall >750 mm), arid (Bikaner, 250–350 mm) and hyper-arid (Jaisalmer, <150 mm) regions was selected along with two other Ziziphus species, Ziziphus mauritiana Lamk. and Ziziphus rotundifolia Lamk. and screened for parameters contributing to drought tolerance. Among these, Z. nummularia (Jaisalmer) (CIAHZN-J) was the most drought - tolerant. The tolerance nature of CIAHZN-J was associated with increased membrane stability, root length and number, length of hairs and thorns, root dry/fresh weight ratio, seed germination (at −0.5 MPa), proline content (31-fold), catalase and sugar content (two- to three-fold). Apart from these characteristics, it also exhibited the longest duration to reach highest cumulative drought stress rating, maintained higher relative water content for a longer period of time with reduced leaf size, leaf rolling and falling of older leaves, and displayed sustained shoot growth during drought stress. To determine drought tolerance in Ziziphus , we developed a morphological symptom-based screening technique in this study. Additionally, transcriptome profiling of CIAHZN-J in response to drought revealed the up-regulation of genes involved in sugar metabolism and transport, abscisic acid biosynthesis, osmoregulation, reactive oxygen species homeostasis and maintaining water potential. Expression profiles and semi-quantitative reverse transcription PCR results further correlated with the physiological and biochemical mechanisms. In conclusion, CIAHZN-J is an excellent genetic stock for the identification of drought-responsive genes and can also be deployed in crop improvement programs for drought tolerance. [ABSTRACT FROM AUTHOR]

Weather and climate play a key role in agricultural production. In recent past, the increased frequency of extreme climatic events has caused enormous damage to agriculture subsectors particularly in the Indian subcontinent. The Government of India through Indian Council of Agricultural Research (ICAR) and State Agricultural Universities (SAUs) has initiated documentation of climate resilient agricultural technologies for each district in the country. These documents titled as "District Agriculture Contingency Plans (DACP)" were developed to cope with weather aberrations and minimize their impact on agricultural sector. So far, the DACPs have been prepared for 623 out of 651 targeted districts in the country and are made available to different stakeholders for implementation. Implementation of DACPs during 2014-2016 with extensive planning and collective actions among stakeholders showed positive results in off-setting of sowing area reduction under deficient monsoon rainfall in India. Weather forecasting at subdistrict level with effective linkages with India Meteorological Department and ICAR/SAUs for developing farm level climate advisories is critical for further strengthening implementation process. The United Nations Framework Convention on Climate Change (UNFCCC) at Bonn, Germany, 2015 based on in-session workshop recommendation, have proposed agriculture contingency plans along early-warning-systems toward coping climate change impacts. Further, these experiences of India helped the South Asian Association for Regional Cooperation (SAARC) countries to develop a contingency template considering the vulnerability of each country. Thus, agriculture contingency plan is evolving as a future strategy to manage aberrant weather situations for ensuring food security and livelihoods in different parts of the world. [ABSTRACT FROM AUTHOR]

Weather and climate play a key role in agricultural production. In recent past, the increased frequency of extreme climatic events has caused enormous damage to agriculture subsectors particularly in the Indian subcontinent. The Government of India through Indian Council of Agricultural Research (ICAR) and State Agricultural Universities (SAUs) has initiated documentation of climate resilient agricultural technologies for each district in the country. These documents titled as "District Agriculture Contingency Plans (DACP)" were developed to cope with weather aberrations and minimize their impact on agricultural sector. So far, the DACPs have been prepared for 623 out of 651 targeted districts in the country and are made available to different stakeholders for implementation. Implementation of DACPs during 2014-2016 with extensive planning and collective actions among stakeholders showed positive results in off-setting of sowing area reduction under deficient monsoon rainfall in India. Weather forecasting at subdistrict level with effective linkages with India Meteorological Department and ICAR/SAUs for developing farm level climate advisories is critical for further strengthening implementation process. The United Nations Framework Convention on Climate Change (UNFCCC) at Bonn, Germany, 2015 based on in-session workshop recommendation, have proposed agriculture contingency plans along early-warning-systems toward coping climate change impacts. Further, these experiences of India helped the South Asian Association for Regional Cooperation (SAARC) countries to develop a contingency template considering the vulnerability of each country. Thus, agriculture contingency plan is evolving as a future strategy to manage aberrant weather situations for ensuring food security and livelihoods in different parts of the world. [ABSTRACT FROM AUTHOR]

The term ‘Green Revolution’ (GR) is used to highlight an unprecedented increase in wheat production in India during 1968–72. The critics of GR allege that there is technology fatigue, especially after 1980s. The present study was undertaken to analyse the trends in productivity of major cereals and compare yield gains during the GR era and post-GR era. The period of 68 years since 1950 was divided in four phases: pre-GR era (1950–66) referred to as phase I, GR era (1967–83) as phase II, post-GR era of 1984–2000 as phase III and post-GR era of 2001–17 as phase IV. The annual rate of gain in productivity (kg/ha/yr) in each phase was estimated by linear regression. The annual gain in wheat productivity in phase III (53.1 kg/ha) was 30% higher than that in the GR era (41.0 kg/ha). In rice, the productivity gains increased consistently: annual gain in phase III (32.3 kg/ha) and phase IV (41.6 kg/ha) was 68% to 117% respectively, higher than that in the GR era (19.2 kg/ha). The rate of gain in productivity of maize and pearl millet in phases III and IV was 188–530% higher in comparison to the GR phase. The progress can largely be attributed to development and adoption of improved cultivars with higher yield potential and crop management technologies. The analysis provided conclusive evidence of India experiencing evergreen revolution in major cereals. [ABSTRACT FROM AUTHOR]

Abstract Methane (CH 4) is predominantly produced in lowland rice soil, but its emission from soil to atmosphere primarily depends on passage/conduit or capillary pore spaces present in rice plants. The gas transport mechanism through aerenchyma pore spaces of rice cultivars was studied to explore the plant mediated CH 4 emission. Seven rice cultivars, based on the life cycle duration (LCD), were tested in tropical eastern India. Three LCD groups were, (a) Kalinga 1 and CR Dhan 204 (LCD: 110–120 days); (b) Lalat, Pooja and CR 1014 (LCD: 130–150 days); and (c) Durga and Varshadhan (LCD: 160–170 days). Rate of CH 4 emission, root exudates, root oxidase activities and shoot aerenchyma pore spaces were analyzed to study the mechanism of plant mediated emission from rice. Aerenchyma pore space was quantified in the hypothesis that it regulates the CH 4 transportation from soil to atmosphere. The ratio of pore space area to total space was lowest in Kalinga 1 cultivar (0.29) and highest was in Varshadhan (0.43). Significant variations in the methane emission were observed among the cultivars with an average emission rate ranged from 0.86 mg m−2 h−1 to 4.96 mg m−2 h−1. The CH4 emission rates were lowest in short duration cultivars followed by medium and long duration ones. The greenhouse gas intensity considering average CH 4 emission rate per unit grain yield was also lowest (0.35) in Kalinga 1 and relatively less in short and medium duration cultivars. Root exudation was higher at panicle initiation (PI) than maximum tillering (MT) stage. Lowest exudation was noticed in (197.2 mg C plant−1 day−1) Kalinga 1 and highest in Varsadhan (231.7 mg C plant−1 day−1). So we can say, the rate of CH 4 emission was controlled by aerenchyma orientation, root exudation and biomass production rate which are the key specific traits of a cultivar. Identified traits were closely associated with duration and adaptability to cultivars grown in specific ecology. Therefore, there is possibility to breed rice cultivars depending on ecology, duration and having less CH 4 emission potential, which could be effectively used in greenhouse gas mitigation strategies. Graphical abstract Unlabelled Image Highlights • Seven rice cultivars, based on the life cycle duration tested in tropical eastern India. • Aerenchyma pore space was quantified with regulation of CH 4 ransportation • Rate of CH 4 emission was controlled by aerenchyma orientation, rhizosphere-enzymatic • Significant variations in the methane emission was observed among the cultivars [ABSTRACT FROM AUTHOR]

Biochemical pathways of methanogenesis and methanotrophy coupled with carbon (C)-nitrogen (N) metabolism were studied in long term (13 years) manured systems in lowland rice paddy through metagenomics approach. Manured systems included in this study were, control (exclusion of application of any manure), farm yard manure (FYM, @5 Mg ha − 1 yr − 1 ) and green manuring (GM with Sesbania aculeata ). Metagenomic sequence data revealed the dominance of C decomposing bacterial communities' like Proteobacteria, Planctomycetes, Actinobacteria, Firmicutes, Acidobacteria, in manure amended soils as compared to control. Diversities for assimilatory and dissimilatory N-fixing microorganisms at phylum level were found higher under GM as compared to rest. Two genera responsible for methanogenesis, viz . Methanolobus and Methanotorris were absent in manured systems as compared to control. The acetoclastic and serine pathway was found as the predominant pathway for methanogenesis and methanotrophy, respectively, in tropical lowland rice paddy. Abundance reads of enzymes were in the range of 254–445 in the acetoclastic methanogenesis pathway. On the other hand, these were varied from 165 to 216 in serine pathway of methanotrophy. Lowland paddy soil exhibited higher functional and structural diversities in manured systems as compared to unamended control in respect to labile C pools and CH 4 production. Methane (CH 4 ) emission was 31% higher in FYM system than GM. However, nitrous oxide (N 2 O) emission was found 25% higher in GM as compared to FYM. As a whole, bacterial diversities were higher under FYM system in tropical lowland rice paddy as compared to GM and unamended systems. [ABSTRACT FROM AUTHOR]

Background: Increased water and labour scarcity in major rice growing areas warrants a shift towards direct seeded rice cultivation under which management of weeds is a major issue. Use of broad spectrum non-selective herbicides is an efficient means to manage weeds. Availability of rice genotypes with complete tolerance against broad-spectrum non-selective herbicides is a pre-requisite for advocating use of such herbicides. In the present study, we developed an EMS induced rice mutant, 'HTM-N22', exhibiting tolerance to a broad spectrum herbicide, 'Imazethapyr', and identified the mutations imparting tolerance to the herbicide. Results: We identified a stable and true breeding rice mutant, HTM-N22 (HTM), tolerant to herbicide, Imazethapyr, from an EMS-mutagenized population of approximately 100,000 M plants of an upland rice variety, Nagina 22 (N22). Analysis of inheritance of herbicide tolerance in a cross between Pusa 1656-10-61/HTM showed that this trait is governed by a single dominant gene. To identify the causal gene for Imazethapyr tolerance, bulked segregant analysis (BSA) was followed using microsatellite markers flanking the three putative candidate genes viz., an Acetolactate Synthase (ALS) on chromosome 6 and two Acetohydroxy Acid Synthase (AHAS) genes, one on chromosomes 2 and another on chromosome 4. RM 6844 on chromosome 2 located 0.16 Mbp upstream of AHAS (LOC_Os02g30630) was found to co-segregate with herbicide tolerance. Cloning and sequencing of AHAS (LOC_Os02g30630) from the wild type, N22 and the mutant HTM and their comparison with reference Nipponbare sequence revealed several Single Nucleotide Polymorphisms (SNPs) in the mutant, of which eight resulted in non-synonymous mutations. Three of the eight amino acid substitutions were identical to Nipponbare and hence were not considered as causal changes. Of the five putative candidate SNPs, four were novel (at positions 30, 50, 81 and 152) while the remaining one, S627D was a previously reported mutant, known to result in Imidazolinone tolerance in rice. Of the novel ones, G152E was found to alter the hydrophobicty and abolish an N myristoylation site in the HTM compared to the WT, from reference based modeling and motif prediction studies. Conclusions: A novel mutant tolerant to the herbicide 'Imazethapyr' was developed and characterized for genetic, sequence and protein level variations. This is a HTM in rice without any IPR (Intellectual Property Rights) infringements and hence can be used in rice breeding as a novel genetic stock by the public funded organizations in the country and elsewhere. [ABSTRACT FROM AUTHOR]

Carbon (C) and nitrogen (N) mineralization is one of the key processes of biogeochemical cycling in terrestrial ecosystem in general and rice ecology in particular. Rice rhizosphere is a rich niche of microbial diversity influenced by change in atmospheric temperature and concentration of carbon dioxide (CO 2 ). Structural changes in microbial communities in rhizosphere influence the nutrient cycling. In the present study, the bacterial diversity and population dynamics were studied under ambient CO 2 (a-CO 2 ) and elevated CO 2 + temperature (e-CO 2 T) in lowland rice rhizosphere using whole genome metagenomic approach. The whole genome metagenomic sequence data of lowland rice exhibited the dominance of bacterial communities including Proteobacteria, Firmicutes, Acidobacteria, Actinobacteria and Planctomycetes. Interestingly, four genera related to methane production namely, Methanobacterium , Methanosphaera , Methanothermus and Methanothermococcus were absent in a-CO 2 but noticed under e-CO 2 T. The acetoclastic pathway was found as the predominant pathway for methanogenesis, whereas, the serine pathway was found as the principal metabolic pathway for CH 4 oxidation in lowland rice. The abundances of reads of enzymes in the acetoclastic methanogenesis pathway and serine pathways of methanotrophy were much higher in e-CO 2 T (328 and 182, respectively) as compared with a-CO 2 (118 and 98, respectively). Rice rhizosphere showed higher structural diversities and functional activities in relation to N metabolism involving nitrogen fixation, assimilatory and dissimilatory nitrate reduction and denitrification under e-CO 2 T than that of a-CO 2 . Among the three pathways of N metabolism, dissimilarity pathways were predominant in lowland rice rhizosphere and more so under e-CO 2 T. Consequently, under e-CO 2 T, CH 4 emission, microbial biomass nitrogen (MBN) and dehydrogenase activities were 45%, 20% and 35% higher than a-CO 2 , respectively. Holistically, a high bacterial diversity and abundances of C and N decomposing bacteria in lowland rice rhizosphere were found under e-CO 2 T, which could be explored further for their specific role in nutrient cycling, sustainable agriculture and environment management. [ABSTRACT FROM AUTHOR]

The article focuses on a study which aims to identify and analyze the key residues of super mitochondrial antioxidant manganese superoxide dismutase enzymes responsible for salt stress tolerance mechanism in species. Information about the materials and the methods used in the study is presented including DNA sequencing.

Genomic prediction is meant for estimating the breeding value using molecular marker data which has turned out to be a powerful tool for efficient utilization of germplasm resources and rapid improvement of cultivars. Model-based techniques have been widely used for prediction of breeding values of genotypes from genomewide association studies. However, application of the random forest (RF), a model-free ensemble learning method, is not widely used for prediction. In this study, the optimum values of tuning parameters of RF have been identified and applied to predict the breeding value of genotypes based on genomewide single-nucleotide polymorphisms (SNPs), where the number of SNPs ( P variables) is much higher than the number of genotypes ( n observations) ( P > > n). Further, a comparison was made with the model-based genomic prediction methods, namely, least absolute shrinkage and selection operator (LASSO), ridge regression (RR) and elastic net (EN) under P > > n. It was found that the correlations between the predicted and observed trait response were 0.591, 0.539, 0.431 and 0.587 for RF, LASSO, RR and EN, respectively, which implies superiority of the RF over the model-based techniques in genomic prediction. Hence, we suggest that the RF methodology can be used as an alternative to the model-based techniques for the prediction of breeding value at genome level with higher accuracy. [ABSTRACT FROM AUTHOR]

Highlights: [•] Tropical flooded rice ecosystem behaved as net C sink on annual basis. [•] Low land rice ecology revealed C storage potential in wet and dry seasons. [•] Annual cumulative net ecosystem CO2 exchange was negative. [•] Integrated annual net ecosystem CH4 exchange was positive. [•] Annual gross primary production was greater than ecosystem respiration. [ABSTRACT FROM AUTHOR]

Grain size is one of the three productivity related traits in rice and hence a major target for genetic improvement. Since understanding genetic variation in grain size between Basmati and indica genotypes is important for rice improvement, a recombinant inbred population was developed from a traditional aromatic cultivar 'Basmati 370' and a non-aromatic indica genotype 'IRBB60'. This population was phenotyped in two locations for grain length (GL), grain breadth (GB), GL/GB ratio (LBR) and grain weight (GW). Though the RIL population reported in the current study exhibited segregation distortion (SD) for 54 % of the markers, they were utilized in analysis using an appropriate statistical package, PROC QTL in the SAS environment. Interval mapping revealed a total of 15 QTLs for GL, seven for GB, 15 for LBR and two for GW. Among them 13 were not reported earlier and thus novel. For a known major QTL identified in the study, GW8 for GB, a PCR based functional marker was designed and validated. This is the first report wherein a very high proportion of markers (>50 %) exhibiting SD have been successfully used for QTL mapping. [ABSTRACT FROM AUTHOR]

Assessment of genetic diversity in a crop germplasm is a vital part of plant breeding. DNA markers such as microsatellite or simple sequence repeat markers have been widely used to estimate the genetic diversity in rice. The present study was carried out to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic variability, and to assess the efficiency of random vis-à-vis QTL linked/gene based simple sequence repeat markers in diversity estimation. A set of 88 rice accessions that included landraces, farmer's varieties and popular Basmati lines were evaluated for agronomic traits and molecular diversity. The random set of SSR markers included 50 diversity panel markers developed under IRRI's Generation Challenge Programme (GCP) and the trait-linked/gene based markers comprised of 50 SSR markers reportedly linked to yield and related components. For agronomic traits, significant variability was observed, ranging between the maximum for grains/panicle and the minimum for panicle length. The molecular diversity based grouping indicated that varieties from a common centre were genetically similar, with few exceptions. The trait-linked markers gave an average genetic dissimilarity of 0.45 as against that of 0.37 by random markers, along with an average polymorphic information constant value of 0.48 and 0.41 respectively. The correlation between the kinship matrix generated by trait-linked markers and the phenotype based distance matrix (0.29) was higher than that of random markers (0.19). This establishes the robustness of trait-linked markers over random markers in estimating genetic diversity of rice germplasm. [ABSTRACT FROM AUTHOR]

GW2, a grain weight quantitative trait locus (QTL) in rice encodes a ring type E-3 ubiquitin ligase. A single nucleotide deletion at the 346th nucleotide position in the ligase domain of GW2 was earlier reported to result in higher grain weight in rice. The present study aimed at validating the known functional polymorphism and identifying additional natural genetic variation if any, in the region that included the functional domain of GW2 in a set of indica and aromatic genotypes for which ninety three rice genotypes were phenotyped for grain length, grain width and 100 grain weight. A wide range of variation was observed for these traits. PCR amplification and sequencing of GW2 target region revealed absence of insertion/deletion (InDel) at the 346th position which suggested that the genetic variation in grain weight in Basmati and non-Basmati indica genotypes was not explained by this InDel. However, four new single nucleotide polymorphisms (SNPs) were discovered at nucleotide positions 406, 461, 466 and 501 in the fifth exon and one InDel each in second and fourth introns. Only two of these SNPs, at positions 461 and 501 led to amino acid substitutions. A total of 10 haplotypes were constructed based on these four SNPs which could be regrouped into four categories based on their amino acid substitutions. Association genetic analysis of these haplotypes with different grain traits revealed a moderate association with grain width (R = 0.18 at P < 0.05). Thirteen haplotypes constructed using both intronic and exonic polymorphisms did not have any association with grain traits. [ABSTRACT FROM AUTHOR]

Moth bean (Vigna aconitifolia (Jacq.) Maréchal) is an important grain legume crop grown in rain fed areas of hot desert regions of Thar, India, under scorching sun rays with very little supplementation of water. An SSH cDNA library was generated from leaf tissues of V. aconitifolia var. RMO-40 exposed to an elevated temperature of 42 °C for 5 min to identify early-induced genes. A total of 488 unigenes (114 contigs and 374 singletons) were derived by cluster assembly and sequence alignment of 738 ESTs; out of 206 ESTs (28%) of unknown proteins, 160 ESTs (14%) were found to be novel to moth bean. Only 578 ESTs (78%) showed significant BLASTX similarity (<1 X 10"6) in the NCBI nonredundant database. Gene ontology functional classification terms were retrieved for 479 (65%) sequences, and 339 sequences were annotated with 165 EC codes and mapped to 68 different KEGG pathways. Four hundred and fifty-two ESTs were further annotated with InterProScan (IPS), and no IPS was assigned to 153 ESTs. In addition, the expression level of 27 ESTs in response to heat stress was evaluated through semiquantitative RT-PCR assay. Approximately 20 different signaling genes and 16 different transcription factors have been shown to be associated with heat stress in moth bean for the first time. [ABSTRACT FROM AUTHOR]

Sugarcane ( Saccharum spp.) has a large complex polyploid genome. Assay of molecular variation in the expressed component of its genome has relevance to the analysis of genetic diversity, variety identification and introgression of agronomically useful genes present in different members of the Saccharum complex. The present study was designed to evaluate single-strand conformational polymorphism (SSCP) as a potential tool to detect genetic variation in the expressed sequence tag (EST) derived microsatellites. Twenty primer pairs obtained from EST libraries and one designed from soluble acid invertase gene sequence were used to characterise 21 clones belonging to four different Saccharum species and 22 sugarcane varieties/genotypes. All the markers, including the two, which were reported monomorphic even at the interspecific level in an automated fragment analysis system in a previous study, could be successfully converted into polymorphic ones using SSCP analysis. A broad range of variation could be revealed by this technique. The Saccharum spp. clones could be grouped into distinct clusters, confirming the species relationships postulated earlier using morphological, biochemical and molecular methods. The polymorphic markers could also differentiate all the 22 sugarcane varieties from each other. This is a first report that demonstrates the usefulness of SSCP technique, in obtaining polymorphic microsatellite markers developed from EST sequences for various genetic and breeding applications, in this polyploid species. [ABSTRACT FROM AUTHOR]

Pusa RH10, the widely cultivated superfine grain aromatic rice hybrid, and its parental lines Pusa6B and PRR78 are susceptible to bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae. Pusa1460, a Basmati rice variety, was utilized as the donor for introgressing BB resistance genes xa13 and Xa21 into Pusa6B and PRR78 using a marker-assisted backcross breeding program. The markers RG136 and pTA248 linked to BB resistance genes xa13 and Xa21, respectively, were used for foreground selection. Seventy-four STMS markers polymorphic between Pusa6B and Pusa1460, and 54 STMS markers polymorphic between PRR78 and Pusa1460, were utilized for background selection to recover the recurrent parent genome ranging from 85.14 to 97.30% and 87.04 to 92.81% in the 10 best BC2F5 families of Pusa6B and PRR78, respectively. RM6100, an STMS marker linked to fertility restorer gene ( Rf), was used for marker-assisted selection of Rf gene in an improved version of PRR78. The extent of donor segments in the improved version of Pusa6B was estimated to be <0.97 and <2.15 Mb in the genomic regions flanking xa13 and Xa21, respectively, whereas in improved PRR78, it was estimated to be <2.07 and <3.45 Mb in the corresponding genomic regions. Improved lines of Pusa6B and PRR78 showed yield advantages of up to 8.24 and 5.23%, respectively. The performance of the BB-resistant version of Pusa RH10 produced by intercrossing the improved parental lines was on a par with or superior to the original Pusa RH10. [ABSTRACT FROM AUTHOR]

Mangroves play a key role in ecosystem balancing and climate change mitigation. It acts as a source and sink of methane (CH 4), a major greenhouse gas responsible for climate change. Energy metabolic pathways of methane production (methanogenesis) and oxidation (methanotrophy) are directly driven by sulphur (S) and nitrogen (N) metabolism and salinity in coastal wetlands. To investigate, how mangrove-degradations, affect the source-sink behaviour of CH 4 ; the pathways of CH 4 , S and N were studied through whole-genome metagenomic approach. Soil samples were collected from degraded and undisturbed mangrove systems in Sundarban, India. Structural and functional microbial diversities (KEGG pathways) of CH 4 , S and N metabolism were analysed and correlated with labile carbon pools and physico-chemical properties of soil. Overall, the acetoclastic pathway of methanogenesis was dominant. However, the relative proportion of conversion of CO 2 to CH 4 was more in degraded mangroves. Methane oxidation was higher in undisturbed mangroves and the serine pathway was dominant. After serine, the ribulose monophosphate pathway of CH 4 oxidation was dominant in degraded mangrove, while the xylulose monophosphate pathway was dominant in undisturbed site as it is more tolerant to salinity and higher pH. The assimilatory pathway (AMP) of S-metabolism was dominant in both systems. But in AMP pathway, adenosine triphosphate sulfurylase enzyme reads were higher in degraded mangrove, while NADPH-sulfite reductase abundance was higher in undisturbed mangrove due to higher salinity, and pH. In N-metabolism, the denitrification pathway was predominant in degraded sites, whereas the dissimilatory nitrate reduction pathway was dominant in undisturbed mangroves. The relative ratios of sulphur reducing bacteria (SRB): methanogens were higher in degraded mangrove; however, methanotrophs:methanogens was higher in undisturbed mangrove indicated lower source and greater sink capacity of CH 4 in the system. Microbial manipulation in mangrove-rhizosphere for regulating major energy metabolic pathways of methane could open-up a new window of climate change mitigation in coastal wetlands. [Display omitted] • Acetoclastic pathway of methanogenesis was dominant bot in DM and UM. • Methane oxidation was higher in UM and serine pathway was dominant in both DM and UM. • The assimilatory pathway of S-metabolism was dominant in both the systems. • Denitrification pathway was predominant in DM, whereas DNRP was dominant in UM. [ABSTRACT FROM AUTHOR]

During the past five decades, a large number of tobacco varieties have been developed for different end uses in India through pure line selection from local land-races, mutation breeding and hybridization involving local selections and exotic introductions followed by pedigree selection. No systematic effort has been made to understand the existing diversity pattern in these varieties, which is crucial to define future breeding strategy in this important commercial crop. Amplified fragment length polymorphism (AFLP) analysis was used to determine genetic variation in 54 varieties of cultivated tobacco (Nicotiana tabacum and N. rustica) and three accessions of exotic germplasm. Nine oligonucleotide primer-pair combinations resolved a total of 967 AFLP fragments, of which 785 (81.2%) were polymorphic. The mean genetic distance among the 49 cultivars and three exotic accessions of N. tabacum was 15.35%; 22% among the five cultivars of rustica. Genetic polymorphism present among the cultivars of tobacco was low, as evidenced by the high degree of similarity in the AFLP profiles of different tobacco types. All the five cultivars of N. rustica can be readily identified using the primer pairs E-ACT/M-CAG and E-AAC/M-CTG. Two major clusters were formed on the basis of species and seven sub-clusters were formed on the basis of manufacturing quality traits in the cultivars of N. tabacum. Cultivated flue-cured varieties were clustered separately from other air cured types. Species-specific markers identified in this study would be useful in identification of the true hybrids and monitoring introgression of useful genes from the wild relatives. The markers found specific to the varieties can be used in correct identification of the carrier genotypes in trade and commerce. [ABSTRACT FROM AUTHOR]

Abstract: Ten inbred lines of ash gourd [Benincasa hispida (Thunb.) Cogn.] were crossed to produce 45 F1 hybrids (without reciprocal) which were evaluated along with the parents for 20 growth- and yield-related traits, in a replicated field trial. High level of heterosis was observed among the hybrids for most of the traits examined, including yield. These inbred lines were analysed by using 42 RAPD primers those produced 282 DNA marker bands. A total of 130 RAPD markers were obtained with a mean of 3.1 per primer, which in combination discriminated all the inbreds from each other. Pair-wise genetic distance measurements ranged from 0.07 to 0.31, suggesting a wide genetic diversity for these inbreds. These inberds were also analysed with five ISSR primers of which four were informative. Twenty-six ISSR marker bands were generated of which 11 were polymorphic with an average of 2.80 per primers. The percentage of polymorphic bands produced were higher in ISSR markers (>80%) than generated through RAPD markers (46%). Although the results indicated significant positive correlations of genetic distance with hybrid performance and heterosis, the RAPD based genetic distance measures and use of limited ISSR markers in this present study could not effectively predict hybrid performance in this crop. The genetic variation among ash gourd inbred lines examined, herein, defined a marker array (combined ISSR and RAPD) for the development of a standard reference for further genetic analyses, and the selection of potential parents for predicting hybrid performance and heterosis. [Copyright &y& Elsevier]

Sugarcane (Saccharum spp.) is a tropical plant. In India, systematic breeding initiated early in the twentieth century led to the development of cultivars suitable for subtropical conditions. In spite of a long breeding history, no systematic effort has been made to understand the genetic constitution of these cultivars. The present study was performed to characterize 28 commercial sugarcane cultivars grown in the tropical and subtropical regions of India by means of amplified fragment length polymorphism (AFLP). Eleven of the 12 selective primer combinations used in the study could individually discriminate all the cultivars from each other, which suggested their usefulness in identification of sugarcane cultivars. Comparison of the AFLP profiles of the cultivars with that of their progenitor species revealed the presence of 78.8% of the 250 S. officinarum L. specific DNA fragments, whereas 28.85% of the 260 S. spontaneum L. specific fragments could be traced in the cultivars. Saccharum officinarum specific DNA fragments were found equally shared by the tropical and subtropical cultivars. The subtropical cultivars, however, retained significantly higher number of £ spontaneum specific DNA fragments than did the tropical cultivars, reflecting the breeding strategy followed in the development of these cultivars. The level of genetic diversity between the tropical and subtropical cultivars was much higher than most of the pair-wise diversity measures within each of these two adaptive groups. The AFLP-based clustering of the cultivars also corresponded well with their pedigree relationships. [ABSTRACT FROM AUTHOR]

Bacterial Blight (BB) caused by Xanthomonas oryzae pv. oryzae is a major disease of rice in tropical Asia. Since all the Basmati varieties are highly susceptible and the disease is prevalent in the entire Basmati growing region of India, BB is a severe constraint in Basmati rice production. The present study was undertaken with the objective of combining the important Basmati quality traits with resistance to BB by a combination of phenotypic and molecular marker-assisted selection (MAS). Screening of 13 near-isogenic lines of rice against four isolates of the pathogen from Basmati growing regions identified the Xa4, xa8, xa13 and Xa21 effective against all the isolates tested. Two or more of these genes in combination imparted enhanced resistance as expressed by reduced average lesion length in comparison to individual genes. The two-gene pyramid line IRBB55 carrying xa13 and Xa21 was found equally effective as three/four gene pyramid lines. The two BB resistance genes present in IRBB55 were combined with the Basmati quality traits of Pusa Basmati-1 (PB-1), the most popular high yielding Basmati rice variety used as recurrent parent. Phenotypic selection for disease resistance, agronomic and Basmati quality characteristics and marker-assisted selection for the two resistance genes were carried out in BC1F1, BC1F2 and BC1F3 generations. Background analysis using 252 polymorphic amplified fragment length polymorphism (AFLP) markers detected 80.4 to 86.7% recurrent parent alleles in BC1F3 selections. Recombinants having enhanced resistance to BB, Basmati quality and desirable agronomic traits were identified, which can either be directly developed into commercial varieties or used as immediate donors of BB resistance in Basmati breeding programs. [ABSTRACT FROM AUTHOR]

Microsatellite markers were used for fingerprinting of hybrids, assessing variation within parental lines and testing the genetic purity of hybrid seed lot in rice. Ten sequence tagged microsatellite sites (STMS) markers were employed for fingerprinting 11 rice hybrids and their parental lines. Nine STMS markers were found polymorphic across the hybrids and produced unique fingerprint for the 11 hybrids. A set of four markers (RM 206, RM 216, RM 258 and RM 263) differentiated all the hybrids from each other, which can be used as referral markers for unambiguous identification and protection of these hybrids. Cluster analysis based on Jaccard's similarity coefficient using UPGMA grouped the hybrids into three clusters. Within the cluster all the hybrids shared a common cytoplasmic male sterile line as female parent. The genetic similarity between the hybrids ranged from 0.33 to 0.92 with an average similarity index of 0.63. The analysis of plant-to-plant variation within the parental lines of the hybrid Pusa RH 10, using informative markers indicated residual heterozygosity at two marker loci. This highlights the importance of STMS markers in maintaining the genetic purity of the parental lines. The unique value of the restorer gene linked marker for testing the genetic purity of hybrid seeds is demonstrated for the first time. [ABSTRACT FROM AUTHOR]

Background Septic complications reported from stones and concretions lost in the peritoneal cavity following laparoscopic cholecystectomy reflect the infective potential of gallstones. Although bacteria have been demonstrated in the core of gallstones by scanning electron microscopy and molecular genetic techniques, gallstone culture is the only conclusive proof of whether such bacteria are viable and can cause infection. Methods Gallstones retrieved from patients undergoing cholecystectomy were decontaminated after surface cleaning with alcohol, and each core was scooped for culture. Results In this study organisms were cultured from the cores of gallstones in 81% of cases of cholelithiasis and 77% of cases of gallbladder carcinoma, irrespective of stone type and size. Both enteric (57.5%) and non-enteric (20%) organisms were isolated in cholelithiasis, whereas only enteric bacteria could be cultured from cases of gallbladder carcinoma. Long thought to be a causative agent, Salmonella organisms were detected in none of the 14 cases of gallbladder carcinoma. Conclusion Contrary to the popular belief that bacteria inside gallstones are dead, gallstones from most patients contain live bacteria with the potential to cause infective complications. [ABSTRACT FROM AUTHOR]

At present, testing for distinctness, uniformity and stability (DUS) of crop varieties relies on a set of morphological characters. These characters suffer from the limitations of number, interaction with the environment in which the variety grows and subjectivity in decision-making. The potential of DNA-based markers such as sequence tagged microsatellite site (STMS), for establishing DUS merits investigation. In the present study, a set of 55 mapped STMS markers, selected from 12 linkage groups of rice genome, was used to examine distinctness of 23 aromatic rice genotypes including the commercially important Basmati varieties. Forty-one of these markers (74.5%) showed polymorphism between the varieties. The number of alleles per locus ranged from 2–4 with an average of 2.3. The polymorphism information content (PIC) of the markers varied from 0.083 to 0.665 with an average of 0.338. All the varieties could be differentiated from each other at a low probability (0.07×10-13) of identical match by chance. The marker-based clustering of the varieties corresponded with the known phenotypic classification, thereby providing confidence in the distinctness established by the mapped STMS markers. The utility of these markers to study uniformity and stability was analysed using a commercially important crossbred Basmati rice variety Pusa Basmati 1 (IET-10364) that contributes about 40–50% of Basmati rice export from India. Genotyping of twenty individual plants, grown from the nucleus, breeder, foundation, certified and farmer's saved seed samples using all the 55 markers revealed no variation among the plants. These observations suggested that the set of mapped markers employed in this study could be further used for establishing distinctness of aromatic rice varieties and for studying DUS of the important commercial variety Pusa Basmati 1. [ABSTRACT FROM AUTHOR]

Lowland rice along with wetland sequesters one third of terrestrial carbon (C) which is responsible for both positive and negative feed-back to climate change. Labile C pools are sensitive to anticipated climate change condition (elevated CO 2 and temperature). Those may eventually affect the C-stock in soil-microbes-plant-atmospheric (SMPA) continuum through priming effect and could enhance positive climate change feedback. Therefore, the objectives of the study were to analysis the effect elevated CO 2 on C partitioning in rice-plant parts, soil labile C pools, and methane emission; along with identify related bacterial diversities and C-fixation pathways through whole genome metagenomic approach. The labile carbon flow in SMPA continuum was estimated for 3 years in lowland rice under elevated CO 2 and temperature in open top chambers (OTCs). Rice was grown under ambient CO 2 (a-CO 2 ; 390 ± 20 μmol mol−1) and elevated CO 2 and temperature (e-CO 2 T; 550 ± 20 μmol mol−1; 2 °C above ambient) under OTCs with replications. Soil labile C pools were increased by 25.4 to 38.9%, under e-CO 2 T over a-CO 2. In microbes, biomass C, C-fixation pathways (metagenomic analysis) and C related soil enzymes were assayed. In atmosphere, the methane emission was measured and in plant system, C in different plant- parts, photosynthetic rates, root exudates-C were estimated to quantify labile C flow. Root exudates C was increased by 31.9% and microbial biomass C was enhanced by 23.3% under e-CO 2 T. Primarily, 12 soil bacterial genera which were responsible for C-fixation were dominant with higher abundance reads under e-CO 2 T. In C-fixation, dicarboxylate hydroxybutyrate cycle pathway and reductive citric acid cycle pathway were predominant under a-CO 2 and e-CO 2 T, respectively. The methane emission was 26.0 and 26.8% higher under e-CO 2 T than a-CO 2 at vegetative and reproductive stage of crop, respectively. Further, we got higher biomass accumulation, photosynthetic rate and stomatal conductance of rice under e-CO 2 T. Therefore, these augmented labile C flows in SMPA continuum may trigger the priming of soil C stocks, and at the same time could affect the system as a whole and results a positive feedback to climate change. [ABSTRACT FROM AUTHOR]

This study provides the first high-quality draft genome assembly (762.5 Mb) of Tenualosa ilisha that is highly contiguous and nearly complete. We observed a total of 2,864 contigs, with 96.4% completeness with N50 of 2.65 Mbp and the largest contig length of 17.4 Mbp, along with a complete mitochondrial genome of 16,745 bases. A total number of 33,042 protein coding genes were predicted, among these, 512 genes were classified under 61 Gene Ontology (GO) terms, associated with various homeostasis processes. Highest number of genes belongs to cellular calcium ion homeostasis, followed by tissue homeostasis. A total of 97 genes were identified, with 16 GO terms related to water homeostasis. Claudins, Aquaporins, Connexins/Gap junctions, Adenylate cyclase, Solute carriers and Voltage gated potassium channel genes were observed to be higher in number in T. ilisha, as compared to that in other teleost species. Seven novel gene variants, in addition to claudin gene (CLDZ), were found in T. ilisha. The present study also identified two putative novel genes, NKAIN3 and L4AM1, for the first time in fish, for which further studies are required for pinpointing their functions in fish. In addition, 1.6 million simple sequence repeats were mined from draft genome assembly. The study provides a valuable genomic resource for the anadromous Hilsa. It will form a basis for future studies, pertaining to its adaptation mechanisms to different salinity levels during migration, which in turn would facilitate in its domestication. [ABSTRACT FROM AUTHOR]

The FRG1(FSHD region gene 1) gene has emerged as a pivotal tumor suppressor in both breast and prostate cancer. HPF1 (Histone PARylation Factor 1), a gene crucial in the base excision repair (BER) mechanism for single-stranded DNA (ssDNA) lesions, showcases a robust correlation with FRG1. This implies that FRG1 might have the capacity to influence BER via HPF1, potentially playing a role in tumorigenesis. Using a comprehensive approach that integrates in-silico analyses involving differential gene expression, KEGG (Kyoto Encyclopedia of Genes and Genomes), GO (Gene Ontology), and STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) databases, we unravelled the intricate network of genes and pathways influenced by FRG1, which includes BER. Our linear regression analysis unveiled a positive relationship between FRG1 and key genes crucial for BER. Notably, breast cancer patients with low FRG1 expression exhibited a significantly higher frequency of mutation in TP53. To enhance the accuracy of our analysis, we conducted qRT-PCR assays, which demonstrated that FRG1 affects the transcription of DNA base excision repair genes, showing differential expression in breast cancer cells. Moreover, through the Alkaline Comet Assay, a technique that quantifies DNA damage at the single-cell level, we observed diminished DNA repair capabilities when FRG1 levels are low. Risk scores were calculated using the Cox regression coefficients, and we found notable differences in Overall Survival (OS) and mRNA expression of DEGs in the low and high-risk groups. In summary, our findings shed light on the pivotal role of FRG1 in maintaining DNA repair efficiency within breast cancer cells., (© 2024. The Author(s).)

Introduction: Arthritis is the cause of morbidity associated with Chikungunya virus (CHIKV) infection. It persists even after the virus has been cleared from the body. MBZM-NIBT was earlier shown to inhibit (CHIKV) infection in vitro and in vivo., Objective: The objective of this study is to determine the ability of MBZM-N-IBT to manage arthritis independent of CHIKV infection., Method: The acute toxicity of MBZM-N-IBT was determined to find a permissible oral dose. Effects against inflammation and arthritis were determined in relevant preclinical models. Network pharmacology was used to propose possible modes of action., Result: It showed no acute toxicity orally, with an estimated LD50 of more than 5000 mg/kg in rats. It significantly reduced inflammation. Its effect against Complete Freund's Adjuvant (CFA) induced arthritis was comparable to that of Diclofenac sodium. Network pharmacology analysis revealed that MBZM-N-IBT can potentially interfere with multiple targets and pathways. MMP12 and CTSD were found to be the most probable hub targets of MBZM-N-IBT for its effect against arthritis., Conclusion: In conclusion, MBZM-N-IBT is safe at 50 mg/kg and can manage arthritis independent of CHIKV infection through modulation of multiple pathways and arthritis-associated targets., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Main Conclusion: Differential expression of 128 known and 111 novel miRNAs in the panicle of Nagina 22 under terminal drought stress targeting transcription factors, stress-associated genes, etc., enhances drought tolerance and helps sustain agronomic performance under terminal drought stress. Drought tolerance is a complex multigenic trait, wherein the genes are fine-tuned by coding and non-coding components in mitigating deleterious effects. MicroRNA (miRNA) controls gene expression at post-transcriptional level either by cleaving mRNA (transcript) or by suppressing its translation. miRNAs are known to control developmental processes and abiotic stress tolerance in plants. To identify terminal drought-responsive novel miRNA in contrasting rice cultivars, we constructed small RNA (sRNA) libraries from immature panicles of drought-tolerant rice [Nagina 22 (N 22)] and drought-sensitive (IR 64) cultivars grown under control and terminal drought stress. Our analysis of sRNA-seq data resulted in the identification of 169 known and 148 novel miRNAs in the rice cultivars. Among the novel miRNAs, 68 were up-regulated while 43 were down-regulated in the panicle of N 22 under stress. Interestingly, 31 novel miRNAs up-regulated in N 22 were down-regulated in IR 64, whereas 4 miRNAs down-regulated in N 22 were up-regulated in IR 64 under stress. To detect the effects of miRNA on mRNA expression level, transcriptome analysis was performed, while differential expression of miRNAs and their target genes was validated by RT-qPCR. Targets of the differentially expressed miRNAs include transcription factors and stress-associated genes involved in cellular/metabolic/developmental processes, response to abiotic stress, programmed cell death, photosynthesis, panicle/seed development, and grain yield. Differential expression of the miRNAs could be validated in an independent set of the samples. The findings might be useful in genetic improvement of drought-tolerant rice., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Genetic information in eukaryotic organisms is stored, replicated, transcribed, and inherited through the nucleus of a cell. Epigenetic modifications in the genetic material, including DNA methylation, histone modification, changes in non-coding RNA (ncRNA) biogenesis, and chromatin architecture play important roles in determining the genomic landscape and regulating gene expression. Genome architecture (structural features of chromatin, affected by epigenetic modifications) is a major driver of genomic functions/activities. Segregation of euchromatin (transcriptionally active) from heterochromatin (transcriptionally repressed chromosome) and positioning of genes in specific nuclear space in eukaryotic cells emphasise non-randomness in the organization of the genetic information. Not only does the base sequence of a gene carry the genetic information but the covalent modifications of bases, three-dimensional positioning of the genome, and chromatin loops are vital for switching on/off the gene and regulating its expression during growth/environmental stress. The epigenetic dynamics depend on the activities of writers and erasers under changing environmental conditions. The discovery of non-coding RNAs (one of the players in de novo methylation of DNA), increased DNA methylation protein (guide for the DNA demethylase), and methylation monitoring sequence (that helps keep a balance between DNA demethylation and methylation) have been some of the new developments in the era of epigenomics. To respond to environmental stimuli, plants depend on modulating gene expression through different mechanisms including biochemical, molecular, genetic, and epigenetic alterations. Studies on plants might provide better insights into epigenetic stress memory and molecular bases of adaptability to enable (epi)genome editing of crops for climate resilience and sustainable agriculture in the present era of multifaceted climate change., Competing Interests: The authors declare no conflict of interest., (© 2024 The Author(s). Published by IMR Press.)

Traditionally, it has been believed that inheritance is driven as phenotypic variations resulting from changes in DNA sequence. However, this paradigm has been challenged and redefined in the contemporary era of epigenetics. The changes in DNA methylation, histone modification, non-coding RNA biogenesis, and chromatin remodeling play crucial roles in genomic functions and regulation of gene expression. More importantly, some of these changes are inherited to the next generations as a part of epigenetic memory and play significant roles in gene expression. The sum total of all changes in DNA bases, histone proteins, and ncRNA biogenesis constitutes the epigenome. Continuous progress in deciphering epigenetic regulations and the existence of heritable epigenetic/epiallelic variations associated with trait of interest enables to deploy epigenome editing tools to modulate gene expression. DNA methylation marks can be utilized in epigenome editing for the manipulation of gene expression. Initially, genome/epigenome editing technologies relied on zinc-finger protein or transcriptional activator-like effector protein. However, the discovery of clustered regulatory interspaced short palindromic repeats CRISPR)/deadCRISPR-associated protein 9 (dCas9) enabled epigenome editing to be more specific/efficient for targeted DNA (de)methylation. One of the major concerns has been the off-target effects, wherein epigenome editing may unintentionally modify gene/regulatory element which may cause unintended change/harmful effects. Moreover, epigenome editing of germline cell raises several ethical/safety issues. This review focuses on the recent developments in epigenome editing tools/techniques, technological limitations, and future perspectives of this emerging technology in therapeutics for human diseases as well as plant improvement to achieve sustainable developmental goals.

Rice is a major staple food, and, hence, doubling its productivity is critical to sustain future food security. Improving photosynthesis, source-sink relationships and grain-filling mechanisms are promising traits for improvement in grain yield. To understand the source-sink relationship and grain yield, a set of contrasting rice genotypes differing in yield and biomass were studied for physiological, biochemical and gene-expression differences. The physiological and yield component traits of selected rice genotypes were analyzed in 2016 and 2017 under field conditions. This led to the categorization of genotypes as high yielding (HY) and high biomass, viz., Dular, Gontra Bidhan 3, Way Rarem, Patchai Perumal, Sahbhagi Dhan, Indira Barani Dhan-1, MTU1010, and Maudamani; while, low yielding (LY) and low biomass, viz. Anjali, Ghanteswari, Parijat, Khao Daw Tai, RKVY-104, Ghati Kamma Nangarhar, BAM4510 and BAM5850. The HY genotypes in general had relatively better values of yield component traits, higher photosynthetic rate (Pn) and chlorophyll (Chl) content. The study revealed that leaf area per plant and whole plant photosynthesis are the key traits contributing to high biomass production. We selected two good-performing (Sahbhagi Dhan and Maudamani) and two poor-performing (Ghanteswari and Parijat) rice genotypes for a detailed expression analysis of selected genes involved in photosynthesis, sucrose synthesis, transport, and starch synthesis in the leaf and starch metabolism in grain. Some of the HY genotypes had a relatively high level of expression of key photosynthesis genes, such as RbcS , RCA , FBPase , and ZEP over LY genotypes. This study suggests that traits, such as leaf area, photosynthesis and grain number, contribute to high grain yield in rice. These good-performing genotypes can be used as a donor in a breeding program aimed at high yields in rice.

Main Conclusion: Roots play an important role in adaptive plasticity of rice under dry/direct-sown conditions. However, hypomethylation of genes in leaves (resulting in up-regulated expression) complements the adaptive plasticity of Nagina-22 under DSR conditions. Rice is generally cultivated by transplanting which requires plenty of water for irrigation. Such a practice makes rice cultivation a challenging task under global climate change and reducing water availability. However, dry-seeded/direct-sown rice (DSR) has emerged as a resource-saving alternative to transplanted rice (TPR). Though some of the well-adapted local cultivars are used for DSR, only limited success has been achieved in developing DSR varieties mainly because of a limited knowledge of adaptability of rice under fluctuating environmental conditions. Based on better morpho-physiological and agronomic performance of Nagina-22 (N-22) under DSR conditions, N-22 and IR-64 were grown by transplanting and direct-sowing and used for whole genome methylome analysis to unravel the epigenetic basis of adaptive plasticity of rice. Comparative methylome and transcriptome analyses indicated a large number (4078) of genes regulated through DNA methylation/demethylation in N-22 under DSR conditions. Gene × environment interactions play important roles in adaptive plasticity of rice under direct-sown conditions. While genes for pectinesterase, LRK10, C2H2 zinc-finger protein, splicing factor, transposable elements, and some of the unannotated proteins were hypermethylated, the genes for regulation of transcription, protein phosphorylation, etc. were hypomethylated in CG context in the root of N-22, which played important roles in providing adaptive plasticity to N-22 under DSR conditions. Hypomethylation leading to up-regulation of gene expression in the leaf complements the adaptive plasticity of N-22 under DSR conditions. Moreover, differential post-translational modification of proteins and chromatin assembly/disassembly through DNA methylation in CHG context modulate adaptive plasticity of N-22. These findings would help developing DSR cultivars for increased water-productivity and ecological efficiency., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Recurrent occurrence of drought stress in varying intensity has become a common phenomenon in the present era of global climate change, which not only causes severe yield losses but also challenges the cultivation of rice. This raises serious concerns for sustainable food production and global food security. The root of a plant is primarily responsible to perceive drought stress and acquire sufficient water for the survival/optimal growth of the plant under extreme climatic conditions. Earlier studies reported the involvement/important roles of microRNAs (miRNAs) in plants' responses to environmental/abiotic stresses. A number (738) of miRNAs is known to be expressed in different tissues under varying environmental conditions in rice, but our understanding of the role, mode of action, and target genes of the miRNAs are still elusive. Using contrasting rice [IR-64 (reproductive-stage drought sensitive) and N-22 (drought-tolerant)] cultivars, imposed with terminal (reproductive-stage) drought stress, we demonstrate differential expression of 270 known and 91 novel miRNAs in roots of the contrasting rice cultivars in response to the stress. Among the known miRNAs, osamiR812, osamiR166, osamiR156, osamiR167, and osamiR396 were the most differentially expressed miRNAs between the rice cultivars. In the root of N-22, 18 known and 12 novel miRNAs were observed to be exclusively expressed, while only two known (zero novels) miRNAs were exclusively expressed in the roots of IR-64. The majority of the target gene(s) of the miRNAs were drought-responsive transcription factors playing important roles in flower, grain development, auxin signaling, root development, and phytohormone-crosstalk. The novel miRNAs identified in this study may serve as good candidates for the genetic improvement of rice for terminal drought stress towards developing climate-smart rice for sustainable food production.

A plant, being a sessile organism, needs to modulate biochemical, physiological, and molecular responses to the environment in a quick and efficient manner to be protected. Drought stress is a frequently occurring abiotic stress that severely affects plant growth, development, and productivity. Short- and long-term memories are well-known phenomena in animals; however, the existence of such remembrance in plants is still being discovered. In this investigation, different rice genotypes were imposed with drought stress just before flowering and the plants were re-watered for recovery from the stress. Seeds collected from the stress-treated (stress-primed) plants were used to raise plants for the subsequent two generations under a similar experimental setup. Modulations in physio-biochemical (chlorophyll, total phenolics and proline contents, antioxidant potential, lipid peroxidation) and epigenetic [5-methylcytosine (5-mC)] parameters were analyzed in the leaves of the plants grown under stress as well as after recovery. There was an increase in proline (>25%) and total phenolic (>19%) contents, antioxidant activity (>7%), and genome-wide 5-mC level (>56%), while a decrease (>9%) in chlorophyll content was recorded to be significant under the stress. Interestingly, a part of the increased proline content, total phenolics content, antioxidant activity, and 5-mC level was retained even after the withdrawal of the stress. Moreover, the increased levels of biochemical and epigenetic parameters were observed to be transmitted/inherited to the subsequent generations. These might help in developing stress-tolerant crops and improving crop productivity under the changing global climate for sustainable food production and global food security.

Identifying novel targets that control both tumorigenesis and angiogenesis can aid in developing a more potent anti-angiogenic therapeutic strategy. We previously reported that reduction of FRG1 is associated with increased p38-MAPK signaling in prostate cancer and with elevated MEK-ERK signaling in breast cancer. Here, we reveal the role of FRG1 in tumor angiogenesis. Our findings demonstrate that depleted FRG1 levels enhance the proliferation, migration, and tubule formation of HUVECs in a paracrine manner, and this was further substantiated in multiple animal models. Mechanistically, FRG1 depletion activated the expression of FGF2 in breast cancer cells, which triggered the ERK/AKT cascade in endothelial cells. As FRG1 affects multiple tumorigenic properties and it is upstream of FGF2, it can be explored as a therapeutic target that is less prone to resistance., (© 2023 The Authors. FEBS Open Bio published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.)

In the current global warming scenario, it is imperative to develop crops with improved heat tolerance or acclimation, for which knowledge of major heat stress-tolerant genes or genomic regions is a prerequisite. Though several quantitative trait loci (QTLs) for heat tolerance have been mapped in rice, candidate genes from these QTLs have not been reported yet. The meta-analysis of microarray datasets for heat stress in rice can give us a better genomic resource for the dissection of QTLs and the identification of major candidate genes for heat stress tolerance. In the present study, a database, RiceMetaSys-H, comprising 4227 heat stress-responsive genes (HRGs), was created using seven publicly available microarray datasets. This included in-house-generated microarray datasets of Nagina 22 (N22) and IR64 subjected to 8 days of heat stress. The database has provisions for searching the HRGs through genotypes, growth stages, tissues, and physical intervals in the genome, as well as Locus IDs, which provide complete information on the HRGs with their annotations and fold changes, along with the experimental material used for the analysis. The up-regulation of genes involved in hormone biosynthesis and signalling, sugar metabolism, carbon fixation, and the ROS pathway were found to be the key mechanisms of enhanced heat tolerance. Integrating variant and expression analysis, the database was used for the dissection of the major effect of QTLs on chromosomes 4, 5, and 9 from the IR64/N22 mapping population. Out of the 18, 54, and 62 genes in these three QTLs, 5, 15, and 12 genes harboured non-synonymous substitutions. Fifty-seven interacting genes of the selected QTLs were identified by a network analysis of the HRGs in the QTL regions. Variant analysis revealed that the proportion of unique amino acid substitutions (between N22/IR64) in the QTL-specific genes was much higher than the common substitutions, i.e., 2.58:0.88 (2.93-fold), compared to the network genes at a 0.88:0.67 (1.313-fold) ratio. An expression analysis of these 89 genes showed 43 DEGs between IR64/N22. By integrating the expression profiles, allelic variations, and the database, four robust candidates (LOC&#95;Os05g43870, LOC&#95;Os09g27830, LOC&#95;Os09g27650, andLOC&#95;Os09g28000) for enhanced heat stress tolerance were identified. The database thus developed in rice can be used in breeding to combat high-temperature stress.

Bacteriophages are key viruses that can kill thousands of harmful microbes generally present at polluted sites. Such bacteriophages are abundantly present in the river Ganga, where millions of people in India and abroad drink its water and take baths every day for spiritual reasons. Besides bacteriophages, several pathogenic and zoonotic microbes are present in the river Ganga. It is interesting to study the diversity and abundance of bacteria and their respective phages present in polluted or non-polluted sites. Thus, the metagenomics study was carried out at the most polluted sites of river Ganga near Kanpur and non-polluted sites at Farakka, which harbors several harmful bacteria and their phages. The results revealed a significantly higher percentage of Microviridae phage family, ssDNA viruses, and Mimiviridae virus family near Kanpur than Farakka. In addition, compared to Kanpur, Farakka has a more significant percentage of Myoviridae, an unidentified phage family, and Retroviridae viral families. Despite heavy drainage of untreated and contaminated effluents from the leather industry, pesticide industry, paper mills, metropolitan cities, and other sources, the vast number of said phages kills several harmful pathogenic microbes in polluted sites to maintain the Ganga water's healing power or natural sterility. In a polluted aquatic environment, the varieties of bacteriophages were identified in the Ganga and their interaction with the microbial host. The taxonomic diversity of several bacteriophages found in pathogenic host systems was investigated to get exceptional knowledge of these small viruses in the aquatic environment., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Functional characterization of stress-responsive genes through the analysis of transgenic plants is a standard approach to comprehend their role in climate resilience and subsequently exploit them for sustainable crop improvement. In this study, we investigated the function of LOC&#95;Os04g59420 , a gene of DUF740 family ( OsSRDP - Oryza sativa Stress Responsive DUF740 Protein) from rice, which showed upregulation in response to abiotic stress in the available global expression data, but is yet to be functionally characterized. Transgenic plants of the rice OsSRDP gene, driven by a stress-inducible promoter AtRd29A , were developed in the background of cv. Pusa Sugandh 2 (PS2) and their transgene integration and copy number were confirmed by molecular analysis. The three independent homozygous transgenic plants (AtRd29A::OsSRDP rice transformants) showed better resilience to drought, salinity, and cold stresses, but not heat stress, as compared to the non-transformed PS2, which corresponded with their respective relative transcript abundance for OsSRDP . Transgenic plants maintained higher RWC, photosynthetic pigments, and proline accumulation under drought and salinity stresses. Furthermore, they exhibited less accumulation of reactive oxygen species (ROS) than PS2 under drought stress, as seen from the transcript abundance studies of the ROS genes. Under cold stress, OsSRDP transgenic lines illustrated minimal cell membrane injury compared to PS2. Additionally, the transgenic plants showed resistance to a virulent strain of rice blast fungus, Magnaporthe oryzae ( M. oryzae ). The promoter analysis of the gene in N22 and PS2 revealed the presence of multiple abiotic and biotic stress-specific motif elements supporting our observation on multiple stress tolerance. Based on bioinformatics studies, we identified four potential candidate interaction partners for LOC&#95;Os04g59420 , of which two genes ( LOC&#95;Os05g09640 and LOC&#95;Os06g50370 ) showed co-expression under biotic and drought stress along with OsSRDP . Altogether, our findings established that stress-inducible expression of OsSRDP can significantly enhance tolerance to multiple abiotic stresses and a biotic stress., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Jayaraman, Sevanthi, Raman, Jiwani, Solanke, Mandal and Mohapatra.)

Drought stress severely affects the growth and development of rice, especially at the reproductive stage, which results in disturbed metabolic processes, reduced seed-set/grain filling, deteriorated grain quality, declined productivity, and lower yield. Despite the recent advances in understanding the responses of rice to drought stress, there is a need to comprehensively integrate the morpho-physio-biochemical studies with the molecular responses/differential expression of genes and decipher the underlying pathways that regulate the adaptability of rice at various drought-sensitive growth stages. Our comparative analysis of immature panicle from a drought-tolerant (Nagina 22) and a drought-sensitive (IR 64) rice cultivar grown under control (well-watered) and water-deficit/drought stress (treatment, imposed at the reproductive stage) conditions unraveled some novel stress-responsive genes/pathways responsible for reproductive-stage drought stress tolerance. The results revealed a more important role of upregulated (6706) genes in the panicle of N 22 at reproductive-stage drought stress compared to that (5590) in IR 64. Functional enrichment and MapMan analyses revealed that majority of the DEGs were associated with the phytohormone, redox signalling/homeostasis, secondary metabolite, and transcription factor-mediated mitigation of the adverse effects of drought stress in N 22. The upregulated expression of the genes associated with starch/sucrose metabolism, secondary metabolites synthesis, transcription factors, glutathione, linoleic acid, and phenylalanine metabolism in N 22 was significantly more than that in the panicle of IR 64. Compared to IR 64, 2743 genes were upregulated in N 22 under control conditions, which further increased (4666) under drought stress in panicle of the tolerant cultivar. Interestingly, we observed 6706 genes to be upregulated in the panicle of N 22 over IR 64 under drought and 5814 genes get downregulated in the panicle of N 22 over IR 64 under the stress. In addition, RT-qPCR analysis confirmed differential expression patterns of the DEGs. These genes/pathways associated with the reproductive-stage drought tolerance might provide an important source of molecular markers for genetic manipulation of rice for enhanced drought tolerance.

The inheritance of the mitochondria genome and its diversity is unique for genetic and evolutionary studies relative to nuclear genomes. Northeast India and Himalayan regions are considered as one of the centres of indica rice origin. Also, rice diversity in northeast India is very distinct and highly suited for evolutionary studies. Although reports are available on the genetic diversity of indigenous northeast rice landraces, its relationship with the wild relatives is not yet properly explored and understood. In an attempt, mitochondrial markers were used to study the evolutionary relationship between the 68 landraces of northeast India and wild relatives ( O. rufipogon and O. nivara ) along with IR64 ( indica ) and Nipponbare ( japonica ) were taken as reference cultivars. Phylogenetically, the findings include two distinct clusters in the indigenous northeast India landraces representing indica and japonica groups. Further, the wild relatives and ~60% of northeast India landraces were identified to be closely related to the Nipponbare cluster. Besides, landraces of northeast India grouping with the indica group (IR64) are characterized by the absence of wild relatives. This indicates that there are two distinct evolutionary paths in the origin of northeast Indian rice landraces based on mitochondrial markers diversity and it is proposed that the inheritance of mitochondria, mitonuclear genome interactions, and bottleneck events could have genetically separated these two phylogenetically unique groups of northeast rice landraces.

MicroRNAs (miRNAs) are known to interact with specific mRNAs to regulate gene expression at the post-transcriptional level by cleaving/repressing the translation process. MiRNA-mediated regulation of gene expression has become an interesting area of research on biological processes like growth, development, and stress responses. Studies suggest that some of the noncoding RNAs possess short open reading frames (ORFs) that code for micropeptides (miPEPs) having a regulatory function. Dual functions of some MIR genes are being deciphered, wherein the gene is transcribed into a longer transcript having a stem-loop structure and a shorter alternatively spliced transcript with no stem-loop. While the longer transcript is processed into miRNA, the shorter one is translated into miPEP. The miPEP enhances the transcription/production of the pri-miRNA from which it originates. Regulatory action of miPEP being species-specific, synthetic miPEP being is tested for exogenous application on crop plant to improve stress tolerance/agronomic performance. Deployment of the miPEP-mediated regulatory function might be a promising strategy to modulated miRNA-facilitated regulation of gene/trait of interest towards developing climate-resilient crops. In this review, we describe the newly identified and verified function of the MIR gene in the coding of miPEPs along with the comparison of the features of miRNA and miPEP in plant. We also discuss about their potential role in crop improvement and some of the yet unanswered question about miPEP., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Scaffolding proteins colocalize interacting partners on their surface and facilitate complex formation. They have multiple domains and motifs, which provide binding sites for various molecules. This property of scaffolding proteins helps in the orderly transduction of signals. Abnormal signal transduction is frequently observed in cancers, which can also be attributed to the altered functionality of scaffolding proteins. IQ motif containing GTPase activating proteins (IQGAPs), kinase suppressor of Ras (KSR), and A-kinase anchoring proteins (AKAPs) tether oncogenic pathways RAS/RAF/MEK/ERK, PI3K/AKT, Hippo, Wnt, and CDC42/RAC to them. Scaffolding proteins are attractive drug targets as they are the controlling hub for multiple pathways and regulate crosstalk between them. The first part of this review describes the human scaffolding proteins known to play a role in oncogenesis, pathways altered by them, and the impact on oncogenic processes. The second part provides information on the therapeutic potential of scaffolding proteins and future possibilities. The information on the explored and unexplored areas of the therapeutic potential of scaffolding proteins will be equally helpful for biologists and chemists., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society.)