RESUMO
Genetic diversity in Sclerotium rolfsii is useful for understanding its population structure, identifying different mycelial compatibility groups (MCGs), and developing targeted strategies for disease management in affected crops. In our study, a comprehensive genetic analysis was conducted on 50 isolates of S. rolfsii, collected from various geographic regions and host plants. Two specific genes, TEF1α and RPB2, were utilized to assess the genetic diversity and relationships among these isolates. Notably, out of 1225 pairings examined, only 154 exhibited a compatible reaction, while the majority displayed antagonistic reactions, resulting in the formation of a barrier zone. The isolates were grouped into 10 distinct MCGs. These MCGs were further characterized using genetic sequencing. TEF1α sequences distinguished the isolates into 17 distinct clusters, and RPB2 sequences classified them into 20 clusters. Some MCGs shared identical gene sequences within each gene, while others exhibited unique sequences. Intriguingly, when both TEF1α and RPB2 sequences were combined, all 10 MCGs were effectively differentiated, even those that appeared identical with single-gene analysis. This combined approach provided a comprehensive understanding of the genetic diversity and relationships among the S. rolfsii isolates, allowing for precise discrimination between different MCGs. The results shed light on the population structure and genetic variability within this plant pathogenic fungus, providing valuable insights for disease management and control strategies. This study highlights the significance of comprehending the varied virulence characteristics within S. rolfsii isolates, categorizing them into specific virulence groups based on disease severity index (DSI) values. The association with MCGs provides additional insights into the genetic underpinnings of virulence in this pathogen. Furthermore, the identification of geographical patterns in virulence implies the influence of region-specific factors, with potential implications for disease control and crop protection strategies.Please confirm if the author names are presented accurately and in the correct sequence (given name, middle name/initial, family name). Author 1 Given name: [G. M. Sandeep] Last name [Kumar]. Author 2 Given name: [Praveen Kumar] Last name [Singh]. Also, kindly confirm the details in the metadata are correct.I confirm that the given names are accurate and presented in the correct sequence.
Assuntos
Basidiomycota , Variação Genética , Tipagem de Sequências Multilocus , Filogenia , Doenças das Plantas , Doenças das Plantas/microbiologia , Basidiomycota/genética , Basidiomycota/isolamento & purificação , Basidiomycota/classificação , Micélio/genética , Proteínas Fúngicas/genética , DNA Fúngico/genética , Produtos Agrícolas/microbiologiaRESUMO
Pukzing cave, the largest cave of Mizoram, India was explored for bacterial diversity. Culture dependent method revealed 235 bacterial isolates using three different treatments. Identity of the microbial species was confirmed by 16S rDNA sequencing. The highest bacterial population was recovered from heat treatment (n = 97;41.2%) followed by normal (n = 79;33.6%) and cold treatment (n = 59;25.1%) indicating dominance of moderate thermophiles. Antimicrobial potential of isolates showed 20.4% isolates having antimicrobial ability against tested pathogens. Amplicon sequencing of PKSI, PKSII and NRP specific genes revealed presence of AMP genes in the microbial population. Six microbial pathogens were selected for screening as they are well known for different disease cause organism in various fields such as agriculture and human health. Cave environment harbors unique microbial flora and hypervariable region V4 is more informative. Higher activity of AMP assay against these microbes indicates that cave microbial communities could be potential source of future genomic resources.
Assuntos
Microbiota , Animais , Antibacterianos , Bactérias , DNA Ribossômico , RNA Ribossômico 16S/genéticaRESUMO
A massive bovine, Bos frontalis, also known as Mithun or Gayal, found at higher altitude is very promising meat and milk animal. For candidate gene and marker discovery, RNA-seq data was generated from longissimus dorsi muscle tissues with Illumina-HiSeq. Such markers can be used in future for genetic gain of traits like feed conversion efficiency (FCE) and average daily gain (ADG). Analysis revealed 297differentially expressed genes (DEGs) having 173 up and 124 down-regulated unigenes. Extensive conservation was found in genic region while comparing with Bos taurus. Analysis revealed 57 pathways having 112 enzymes, 72 transcriptional factors and cofactors, 212 miRNAs regulating 71 DEGs, 25,855 SSRs, mithun-specific 104,822 variants and 7288 indels, gene regulatory network (GRN) having 24 hub-genes and transcriptional factors regulating cell proliferation, immune tolerance and myogenesis. This is first report of muscle transcriptome depicting candidate genes with GRN controlling FCE and ADG. Reported putative molecular markers, candidate genes and hub proteins can be valuable genomic resources for association studies in genetic improvement programme.
Assuntos
Bovinos/genética , Redes Reguladoras de Genes , Músculos/metabolismo , Transcriptoma , Animais , Ontologia Genética , Mutação INDEL , MicroRNAs/metabolismo , Repetições de Microssatélites , Polimorfismo de Nucleotídeo ÚnicoRESUMO
Genetic diversity is crucial for successful adaptation and sustained improvement in crops. India is bestowed with diverse agro-climatic conditions which makes it rich in wheat germplasm adapted to various niches. Germplasm repository consists of local landraces, trait specific genetic stocks including introgressions from wild relatives, exotic collections, released varieties, and improved germplasm. Characterization of genetic diversity is done using morpho-physiological characters as well as by analyzing variations at DNA level. However, there are not many reports on array based high throughput SNP markers having characteristics of genome wide coverage employed in Indian spring wheat germplasm. Amongst wheat SNP arrays, 35K Axiom Wheat Breeder's Array has the highest SNP polymorphism efficiency suitable for genetic mapping and genetic diversity characterization. Therefore, genotyping was done using 35K in 483 wheat genotypes resulting in 14,650 quality filtered SNPs, that were distributed across the B (~ 50%), A (~ 39%), and D (~ 10%) genomes. The total genetic distance coverage was 4477.85 cM with 3.27 SNP/cM and 0.49 cM/SNP as average marker density and average inter-marker distance, respectively. The PIC ranged from 0.09 to 0.38 with an average of 0.29 across genomes. Population structure and Principal Coordinate Analysis resulted in two subpopulations (SP1 and SP2). The analysis of molecular variance revealed the genetic variation of 2% among and 98% within subpopulations indicating high gene flow between SP1 and SP2. The subpopulation SP2 showed high level of genetic diversity based on genetic diversity indices viz. Shannon's information index (I) = 0.648, expected heterozygosity (He) = 0.456 and unbiased expected heterozygosity (uHe) = 0.456. To the best of our knowledge, this study is the first to include the largest set of Indian wheat genotypes studied exclusively for genetic diversity. These findings may serve as a potential source for the identification of uncharacterized QTL/gene using genome wide association studies and marker assisted selection in wheat breeding programs.
Assuntos
Triticum/genética , Triticum/metabolismo , Mapeamento Cromossômico/métodos , Cromossomos de Plantas/genética , Grão Comestível/genética , Variação Genética/genética , Genoma de Planta/genética , Estudo de Associação Genômica Ampla/métodos , Genótipo , Fenótipo , Melhoramento Vegetal/métodos , Poaceae/genética , Polimorfismo de Nucleotídeo Único/genéticaRESUMO
Molecular markers, viz. microsatellites and single nucleotide polymorphisms, have revolutionized breed identification through the use of small samples of biological tissue or germplasm, such as blood, carcass samples, embryos, ova and semen, that show no evident phenotype. Classical tools of molecular data analysis for breed identification have limitations, such as the unavailability of referral breed data, causing increased cost of collection each time, compromised computational accuracy and complexity of the methodology used. We report here the successful use of an artificial neural network (ANN) in background to decrease the cost of genotyping by locus minimization. The webserver is freely accessible (http://nabg.iasri.res.in/bisgoat) to the research community. We demonstrate that the machine learning (ANN) approach for breed identification is capable of multifold advantages such as locus minimization, leading to a drastic reduction in cost, and web availability of reference breed data, alleviating the need for repeated genotyping each time one investigates the identity of an unknown breed. To develop this model web implementation based on ANN, we used 51,850 samples of allelic data of microsatellite-marker-based DNA fingerprinting on 25 loci covering 22 registered goat breeds of India for training. Minimizing loci to up to nine loci through the use of a multilayer perceptron model, we achieved 96.63% training accuracy. This server can be an indispensable tool for identification of existing breeds and new synthetic commercial breeds, leading to protection of intellectual property in case of sovereignty and bio-piracy disputes. This server can be widely used as a model for cost reduction by locus minimization for various other flora and fauna in terms of variety, breed and/or line identification, especially in conservation and improvement programs.
Assuntos
Cruzamento , Técnicas de Genotipagem/métodos , Cabras/genética , Redes Neurais de Computação , Algoritmos , Alelos , Animais , Impressões Digitais de DNA , Loci Gênicos , Cabras/classificação , Índia , Internet , Repetições de Microssatélites , Modelos Genéticos , Polimorfismo de Nucleotídeo ÚnicoRESUMO
Biological control agents are preferred over chemicals for managing plant diseases, with Trichoderma species being particularly effective against soil-borne pathogens. This study examines the use of a highly antagonistic strain, Trichoderma asperellum A10, and a virulent strain, Sclerotium rolfsii Sr38, identified and confirmed through ITS, ß-tubulin (T. asperellum), TEF 1α, and RPB2 (S. rolfsii) sequences. In vitro and in planta experiments compared the antagonistic potential of A10 with other antagonistic fungi and fungicides against S. rolfsii. A10 achieved 94.66% inhibition of S. rolfsii in dual culture assays. In greenhouse trials with tomato variety Pusa Ruby, A10 showed significant pre- and post-inoculation effectiveness, with disease inhibition of 86.17 and 80.60%, respectively, outperforming T. harzianum, Propiconazole, and Carbendazim. Additionally, microbial priming with A10 was explored to enhance plant defense responses. Pre-treatment of tomato plants with T. asperellum A10 led to significant upregulation of several defense-related genes, including PR1, PR2, PR3, PR5, PR12, thioredoxin peroxidase, catalase, polyphenol oxidase, phenylalanine ammonia lyase, isochorismate synthase, laccase, prosystemin, multicystatin, WRKY31, MYC2, lipoxygenase A, lipoxygenase C, proteinase inhibitor I, proteinase inhibitor II, and ethylene response 1 associated with various signaling pathways such as salicylic acid (SA)-mediated and jasmonic acid/ethylene (JA/ET)-mediated responses. This upregulation was particularly evident at 48 h post-inoculation in A10-primed plants challenged with S. rolfsii, inducing resistance against collar rot disease. This study underscores the effectiveness of T. asperellum A10 in controlling collar rot and highlights its potential for inducing resistance in plants through microbial priming, providing valuable insights into sustainable disease management strategies. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-024-04040-4.
RESUMO
An elucidated genome of domestic livestock river buffalo will contribute enormously to economy and better understanding of genome evolution as well. An attempt is made to obtain genomic information on buffalo, based on total Expressed Sequence Tags (ESTs) of Bubalus bubalis available in public domain. These ESTs were annotated and classified into 15 different functional categories based on their homology to the known proteins. Interestingly, 41.79% of the contigs were found to be buffalo specific novel ESTs with respect to other species used in analysis which needs further studies. Also, 224 pSNPs (putative Single Nucleotide Polymorphism) were detected. This study will provide a home base for further genomic studies of buffalo and comparative studies enabling a starting point for the genome annotation of the organism. Supplementary materials are available for this article online.
Assuntos
Búfalos/genética , Bases de Dados Genéticas , Etiquetas de Sequências Expressas , Marcadores Genéticos/genética , Animais , Frequência do Gene , Genoma , Genômica , Polimorfismo de Nucleotídeo Único , Especificidade da EspécieRESUMO
Spike fertility and associated traits are key factors in deciding the grain yield potential of wheat. Genome-wide association study (GWAS) interwoven with advanced post-GWAS analysis such as a genotype-phenotype network (geno-pheno network) for spike fertility, grain yield, and associated traits allow to identify of novel genomic regions and represents attractive targets for future marker-assisted wheat improvement programs. In this study, GWAS was performed on 200 diverse wheat genotypes using Breeders' 35K Axiom array that led to the identification of 255 significant marker-trait associations (MTAs) (-log10P ≥ 3) for 15 metric traits phenotyped over three consecutive years. MTAs detected on chromosomes 3A, 3D, 5B, and 6A were most promising for spike fertility, grain yield, and associated traits. Furthermore, the geno-pheno network prioritised 11 significant MTAs that can be utilised as a minimal marker system for improving spike fertility and yield traits. In total, 119 MTAs were linked to 81 candidate genes encoding different types of functional proteins involved in various key pathways that affect the studied traits either way. Twenty-two novel loci were identified in present GWAS, twelve of which overlapped by candidate genes. These results were further validated by the gene expression analysis, Knetminer, and protein modelling. MTAs identified from this study hold promise for improving yield and related traits in wheat for continued genetic gain and in rapidly evolving artificial intelligence (AI) tools to apply in the breeding program.
RESUMO
MicroRNA are 20-24 nt, non-coding, single stranded molecule regulating traits and stress response. Tissue and time specific expression limits its detection, thus is major challenge in their discovery. Wheat has limited 119 miRNAs in MiRBase due to limitation of conservation based methodology where old and new miRNA genes gets excluded. This is due to origin of hexaploid wheat by three successive hybridization, older AA, BB and younger DD subgenome. Species specific miRNA prediction (SMIRP concept) based on 152 thermodynamic features of training dataset using support vector machine learning approach has improved prediction accuracy to 97.7%. This has been implemented in TamiRPred ( http://webtom.cabgrid.res.in/tamirpred ). We also report highest number of putative miRNA genes (4464) of wheat from whole genome sequence populated in database developed in PHP and MySQL. TamiRPred has predicted 2092 (>45.10%) additional miRNA which was not predicted by miRLocator. Predicted miRNAs have been validated by miRBase, small RNA libraries, secondary structure, degradome dataset, star miRNA and binding sites in wheat coding region. This tool can accelerate miRNA polymorphism discovery to be used in wheat trait improvement. Since it predicts chromosome-wise miRNA genes with their respective physical location thus can be transferred using linked SSR markers. This prediction approach can be used as model even in other polyploid crops.
Assuntos
Biologia Computacional/métodos , MicroRNAs/genética , RNA de Plantas/genética , Software , Triticum/genética , Cromossomos de Plantas , Bases de Dados Genéticas , Genoma de Planta , Aprendizado de Máquina , MicroRNAs/química , Modelos Genéticos , Reprodutibilidade dos Testes , Máquina de Vetores de Suporte , Interface Usuário-ComputadorRESUMO
Half of the global human population is dependent on rice as a staple food crop and more than 25% increase in rice productivity is required to feed the global population by 2030. With increase in irrigation, global warming and rising sea level, rising salinity has become one of the major challenges to enhance the rice productivity. Since the loss on this account is to the tune of US$12 billion per annum, it necessitates the global attention. In the era of technological advancement, substantial progress has been made on phenomics and genomics data generation but reaping benefit of this in rice salinity variety development in terms of cost, time and precision requires their harmonization. There is hardly any comprehensive holistic review for such combined approach. Present review describes classical salinity phenotyping approaches having morphological, physiological and biochemical components. It also gives a detailed account of invasive and non-invasive approaches of phenomic data generation and utilization. Classical work of rice salinity QLTs mapping in the form of chromosomal atlas has been updated. This review describes how QTLs can be further dissected into QTN by GWAS and transcriptomic approaches. Opportunities and progress made by transgenic, genome editing, metagenomics approaches in combating rice salinity problems are discussed. Major aim of this review is to provide a comprehensive over-view of hitherto progress made in rice salinity tolerance research which is required to understand bridging of phenotype based breeding with molecular breeding. This review is expected to assist rice breeders in their endeavours by fetching greater harmonization of technological advances in phenomics and genomics for better pragmatic approach having practical perspective.
RESUMO
Crop varieties or genotypes of a given species are pivotal for agricultural production and ownership, management and improvement of their germplasm is a great challenge. Its morphological identification requires time, cost and descriptors are often compromised statistically due to phenotypic plasticity. Development of DNA based signature of varieties can overcome these limitations. There is a global need to implement world trade organization (WTO) and intellectual property rights (IPR) guidelines of Plant Breeders Rights (PBR) where DUS (distinctness, uniformity and stability) testing can be supplemented by DNA profile. Universalization and minimization of SNP number without compromising identification accuracy is the major challenge in development of varietal profile by rapid genotype assay. Besides this, there is no server-based approach reducing computational skill with global accessibility of referral phenotypic and genotypic data. We report world's first model web server for crop variety identification using >350 Indian wheat varieties and Axiom 35 K SNP chip data. Standard filtering and linkage disequilibrium approach were used to develop varietal signature in Linux using HTML, Java, PHP and MySQL with provision of QR code generator to facilitate bar-coding. Phylogenetic tree constructed by selected SNPs confirms six major trait based clusters of varieties and their pedigree. Our user friendly server based tool, VISTa (Variety Identification System of Triticum aestivum) ( http://webtom.cabgrid.res.in/vista ) can be used in DUS testing having dispute resolution of sovereignty and access benefit sharing (ABS) issues. This model approach can be used in other crops with pan-global level management of crop germplasm in endeavour of crop productivity.
Assuntos
Bases de Dados de Ácidos Nucleicos , Genoma de Planta , Genótipo , Modelos Genéticos , Polimorfismo de Nucleotídeo Único , Software , Triticum/genéticaRESUMO
Wheat genetic improvement by integration of advanced genomic technologies is one way of improving productivity. To facilitate the breeding of economically important traits in wheat, SNP loci and underlying candidate genes associated with the 36 agro-morphological traits were studied in a diverse panel of 404 genotypes. By using Breeders' 35K Axiom array in a comprehensive genome-wide association study covering 4364.79 cM of the wheat genome and applying a compressed mixed linear model, a total of 146 SNPs (-log10 P ≥ 4) were found associated with 23 traits out of 36 traits studied explaining 3.7-47.0% of phenotypic variance. To reveal this a subset of 260 genotypes was characterized phenotypically for six quantitative traits [days to heading (DTH), days to maturity (DTM), plant height (PH), spike length (SL), awn length (Awn_L), and leaf length (Leaf_L)] under five environments. Gene annotations mined â¼38 putative candidate genes which were confirmed using tissue and stage specific gene expression data from RNA Seq. We observed strong co-localized loci for four traits (glume pubescence, SL, PH, and awn color) on chromosome 1B (24.64 cM) annotated five putative candidate genes. This study led to the discovery of hitherto unreported loci for some less explored traits (such as leaf sheath wax, awn attitude, and glume pubescence) besides the refined chromosomal regions of known loci associated with the traits. This study provides valuable information of the genetic loci and their potential genes underlying the traits such as awn characters which are being considered as important contributors toward yield enhancement.
RESUMO
Microsatellites are ubiquitously distributed, polymorphic repeat sequence valuable for association, selection, population structure and identification. They can be mined by genomic library, probe hybridization and sequencing of selected clones. Such approach has many limitations like biased hybridization and selection of larger repeats. In silico mining of polymorphic markers using data of various genotypes can be rapid and economical. Available tools lack in some or other aspects like: targeted user defined primer generation, polymorphism discovery using multiple sequence, size and number limits of input sequence, no option for primer generation and e-PCR evaluation, transferability, lack of complete automation and user-friendliness. They also lack the provision to evaluate published primers in e-PCR mode to generate additional allelic data using re-sequenced data of various genotypes for judicious utilization of previously generated data. We developed the tool (PolyMorphPredict) using Perl, R, Java and launched at Apache which is available at http://webtom.cabgrid.res.in/polypred/. It mines microsatellite loci and computes primers from genome/transcriptome data of any species. It can perform e-PCR using published primers for polymorphism discovery and across species transferability of microsatellite loci. Present tool has been evaluated using five species of different genome size having 21 genotypes. Though server is equipped with genomic data of three species for test run with gel simulation, but can be used for any species. Further, polymorphism predictability has been validated using in silico and in vitro PCR of four rice genotypes. This tool can accelerate the in silico microsatellite polymorphism discovery in re-sequencing projects of any species of plant and animal for their diversity estimation along with variety/breed identification, population structure, MAS, QTL and gene discovery, traceability, parentage testing, fungal diagnostics and genome finishing.
RESUMO
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
RESUMO
Pearl millet, (Pennisetum glaucum L.), an efficient (C4) crop of arid/semi-arid regions is known for hardiness. Crop is valuable for bio-fortification combating malnutrition and diabetes, higher caloric value and wider climatic resilience. Limited studies are done in pot-based experiments for drought response at gene-expression level, but field-based experiment mimicking drought by withdrawal of irrigation is still warranted. We report de novo assembly-based transcriptomic signature of drought response induced by irrigation withdrawal in pearl millet. We found 19983 differentially expressed genes, 7595 transcription factors, gene regulatory network having 45 hub genes controlling drought response. We report 34652 putative markers (4192 simple sequence repeats, 12111 SNPs and 6249 InDels). Study reveals role of purine and tryptophan metabolism in ABA accumulation mediating abiotic response in which MAPK acts as major intracellular signal sensing drought. Results were validated by qPCR of 13 randomly selected genes. We report the first web-based genomic resource ( http://webtom.cabgrid.res.in/pmdtdb/ ) which can be used for candidate genes-based SNP discovery programs and trait-based association studies. Looking at climatic change, nutritional and pharmaceutical importance of this crop, present investigation has immense value in understanding drought response in field condition. This is important in germplasm management and improvement in endeavour of pearl millet productivity.
Assuntos
Genoma de Planta/genética , Pennisetum/genética , Estresse Fisiológico/genética , Transcriptoma/genética , Secas , Regulação da Expressão Gênica de Plantas/genética , Genômica/métodos , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética , Fatores de Transcrição/genéticaRESUMO
Tomato (Solanum lycopersicum) is one of the major vegetable plant and a model system for fruit development. Its global importance is due to its lycopene pigment which has anti-oxidative and anti-cancerous properties. Though > 1.5 M biotic stress associated ESTs of tomato are available but cumulative analysis to predict genes is warranted. Availability of whole genome de novo assembly can advantageously be used to map them over different chromosome. Further, available 0.14 M catalogued markers can be used to introgress specific desirable genes in varietal improvement program. We report here 57 novel genes associated with biotic stress of tomato along with 50 genes having physical location over different chromosomes. We also report 52 cis-regulating elements and 69 putative miRNAs which are involved in regulation of these biotic stresses associated genes. These putative candidate genes associated with biotic stress can be used in molecular breeding in the endeavor of tomato productivity along with its sustainable germplasm management.
RESUMO
Groundnut (Arachis hypogaea L.) is an important oil seed crop having major biotic constraint in production due to stem rot disease caused by fungus, Athelia rolfsii causing 25-80% loss in productivity. As chemical and biological combating strategies of this fungus are not very effective, thus genome sequencing can reveal virulence and pathogenicity related genes for better understanding of the host-parasite interaction. We report draft assembly of Athelia rolfsii genome of ~73 Mb having 8919 contigs. Annotation analysis revealed 16830 genes which are involved in fungicide resistance, virulence and pathogenicity along with putative effector and lethal genes. Secretome analysis revealed CAZY genes representing 1085 enzymatic genes, glycoside hydrolases, carbohydrate esterases, carbohydrate-binding modules, auxillary activities, glycosyl transferases and polysaccharide lyases. Repeat analysis revealed 11171 SSRs, LTR, GYPSY and COPIA elements. Comparative analysis with other existing ascomycotina genome predicted conserved domain family of WD40, CYP450, Pkinase and ABC transporter revealing insight of evolution of pathogenicity and virulence. This study would help in understanding pathogenicity and virulence at molecular level and development of new combating strategies. Such approach is imperative in endeavour of genome based solution in stem rot disease management leading to better productivity of groundnut crop in tropical region of world.
Assuntos
Basidiomycota/genética , Basidiomycota/patogenicidade , Genoma Fúngico , Anotação de Sequência Molecular , Análise de Sequência de DNA , Fatores de Virulência/genética , Arachis/microbiologia , Doenças das Plantas/microbiologia , VirulênciaRESUMO
Mango is one of the most important fruits of tropical ecological region of the world, well known for its nutritive value, aroma and taste. Its world production is >45MT worth >200 billion US dollars. Genomic resources are required for improvement in productivity and management of mango germplasm. There is no web-based genomic resources available for mango. Hence rapid and cost-effective high throughput putative marker discovery is required to develop such resources. RAD-based marker discovery can cater this urgent need till whole genome sequence of mango becomes available. Using a panel of 84 mango varieties, a total of 28.6 Gb data was generated by ddRAD-Seq approach on Illumina HiSeq 2000 platform. A total of 1.25 million SNPs were discovered. Phylogenetic tree using 749 common SNPs across these varieties revealed three major lineages which was compared with geographical locations. A web genomic resources MiSNPDb, available at http://webtom.cabgrid.res.in/mangosnps/ is based on 3-tier architecture, developed using PHP, MySQL and Javascript. This web genomic resources can be of immense use in the development of high density linkage map, QTL discovery, varietal differentiation, traceability, genome finishing and SNP chip development for future GWAS in genomic selection program. We report here world's first web-based genomic resources for genetic improvement and germplasm management of mango.
Assuntos
Mangifera/genética , Filogenia , Polimorfismo de Nucleotídeo Único , Bases de Dados Genéticas , Frutas/genética , Genoma de Planta , Genômica , Internet , FilogeografiaRESUMO
Microbial diseases in fish, plant, animal and human are rising constantly; thus, discovery of their antidote is imperative. The use of antibiotic in aquaculture further compounds the problem by development of resistance and consequent consumer health risk by bio-magnification. Antimicrobial peptides (AMPs) have been highly promising as natural alternative to chemical antibiotics. Though AMPs are molecules of innate immune defense of all advance eukaryotic organisms, fish being heavily dependent on their innate immune defense has been a good source of AMPs with much wider applicability. Machine learning-based prediction method using wet laboratory-validated fish AMP can accelerate the AMP discovery using available fish genomic and proteomic data. Earlier AMP prediction servers are based on multi-phyla/species data, and we report here the world's first AMP prediction server in fishes. It is freely accessible at http://webapp.cabgrid.res.in/fishamp/ . A total of 151 AMPs related to fish collected from various databases and published literature were taken for this study. For model development and prediction, N-terminus residues, C-terminus residues and full sequences were considered. Best models were with kernels polynomial-2, linear and radial basis function with accuracy of 97, 99 and 97 %, respectively. We found that performance of support vector machine-based models is superior to artificial neural network. This in silico approach can drastically reduce the time and cost of AMP discovery. This accelerated discovery of lead AMP molecules having potential wider applications in diverse area like fish and human health as substitute of antibiotics, immunomodulator, antitumor, vaccine adjuvant and inactivator, and also for packaged food can be of much importance for industries.
Assuntos
Algoritmos , Aquicultura/instrumentação , Aquicultura/métodos , Animais , Anti-Infecciosos/análise , Humanos , Aprendizado de Máquina , Modelos Teóricos , Peptídeos , ProteômicaRESUMO
Karnal bunt disease caused by the fungus Tilletia indica Mitra is a serious concern due to strict quarantines affecting international trade of wheat. We announce here the first draft assembly of two monosporidial lines, PSWKBGH-1 and -2, of this fungus, having approximate sizes of 37.46 and 37.21 Mbp, respectively.