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DNA methylation is an epigenetic alteration that impacts gene expression without changing the DNA sequence affecting an organism's phenotype. This study utilized a reduced representation bisulfite sequencing (RRBS) approach to investigate the patterns of DNA methylation in genetically selected Clarias magur stocks. RRBS generated 249.22 million reads, with an average of 490,120 methylation sites detected in various parts of genes, including exons, introns, and intergenic regions. A total of 896 differentially methylated regions (DMRs) were identified; 356 and 540 were detected as hyper-methylated and hypo-methylated regions, respectively. The DMRs and their association with overlapping genes were explored using whole genome data of magur, which revealed 205 genes in exonic, 210 in intronic, and 480 in intergenic regions. The analysis identified the maximum number of genes enriched in biological processes such as RNA biosynthetic process, response to growth factors, nervous system development, neurogenesis, and anatomical structure morphogenesis. Differentially methylated genes (DMGs) such as myrip, mylk3, mafb, egr3, ndnf, meis2a, foxn3, bmp1a, plxna3, fgf6, sipa1l1, mcu, cnot8, trim55b, and myof were associated with growth and development. The selected DMGs were analyzed using real-time PCR, which showed altered mRNA expression levels. This work offers insights into the epigenetic mechanisms governing growth performance regulation in magur stocks. This work provides a valuable resource of epigenetic data that could be integrated into breeding programs to select high-performing individuals.
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Metilación de ADN , Epigénesis Genética , AnimalesRESUMEN
Tilletia indica Mitra causes Karnal bunt (KB) in wheat by pathogenic dikaryophase. The present study is the first to provide the draft genomes of the dikaryon (PSWKBGD-3) and its two monosporidial lines (PSWKBGH-1 and 2) using Illumina and PacBio reads, their annotation and the comparative analyses among the three genomes by extracting polymorphic SSR markers. The trancriptome from infected wheat grains of the susceptible wheat cultivar WL711 at 24 h, 48h, and 7d after inoculation of PSWKBGH-1, 2 and PSWKBGD-3 were also isolated. Further, two transcriptome analyses were performed utilizing T. indica transcriptome to extract dikaryon genes responsible for pathogenesis, and wheat transcriptome to extract wheat genes affected by dikaryon involved in plant-pathogen interaction during progression of KB in wheat. A total of 54, 529, and 87 genes at 24hai, 48hai, and 7dai, respectively were upregulated in dikaryon stage while 21, 35, and 134 genes of T. indica at 24hai, 48hai, and 7dai, respectively, were activated only in dikaryon stage. While, a total of 23, 17, and 52 wheat genes at 24hai, 48hai, and 7dai, respectively were upregulated due to the presence of dikaryon stage only. The results obtained during this study have been compiled in a web resource called TiGeR ( http://backlin.cabgrid.res.in/tiger/ ), which is the first genomic resource for T. indica cataloguing genes, genomic and polymorphic SSRs of the three T. indica lines, wheat and T. indica DEGs as well as wheat genes affected by T. indica dikaryon along with the pathogenecity related proteins of T. indica dikaryon during incidence of KB at different time points. The present study would be helpful to understand the role of dikaryon in plant-pathogen interaction during progression of KB, which would be helpful to manage KB in wheat, and to develop KB-resistant wheat varieties.
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Basidiomycota , Enfermedades de las Plantas , Transcriptoma , Triticum , Triticum/genética , Triticum/microbiología , Enfermedades de las Plantas/genética , Enfermedades de las Plantas/microbiología , Basidiomycota/patogenicidad , Basidiomycota/fisiología , Perfilación de la Expresión Génica , Genoma Fúngico , Interacciones Huésped-Patógeno/genéticaRESUMEN
Black pepper (Piper nigrum L.), a crop of the genus Piper, is an important spice that has both economic and ecological significance. It is widely regarded as the "King of Spices" because of its pungency, attributed to the presence of piperine. BAHD acyl transferase, the crucial enzyme involved in the final step in piperine biosynthesis was the focus of our study and the aim was to identify the candidate isoform involved in biosynthesis of piperine. Reference genome-based analysis of black pepper identified six BAHD-AT isoforms and mapping of these sequences revealed that the isoforms were situated on six distinct chromosomes. By using specific primers for each of these transcripts, qPCR analysis was done in different tissues as well as berry stages to obtain detectable amplification products. Expression profiles of isoforms from chromosome 6 correlated well with piperine content compared to other five isoforms, across tissues and was therefore assumed to be involved in biosynthesis of piperine. In addition to this, we could also identify the binding sites of MYB transcription factor in the cis-regulatory regions of the isoforms. We also used in-silico docking and molecular dynamics simulation to calculate the binding free energy of the ligand and confirmed that among all the isoforms, BAHD-AT from chromosome 6 had the lowest free binding energy and highest affinity towards the ligand. Our findings are expected to aid the identification of new genes connecting enzymes involved in the biosynthetic pathway of piperine, which will have major implications for future research in metabolic engineering.Communicated by Ramaswamy H. Sarma.
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Cyprinus carpio is regarded as a substitute vertebrate fish model for zebrafish. A varied category of non-coding RNAs is comprised of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). These ncRNAs were once considered non-functional "junk DNA" but research now shows they play important roles in gene expression regulation, chromatin modification, and epigenetic regulation. The systemic tissue-specific research of the lncRNAs and circRNAs of C. carpio is yet unexplored. A total of 468 raw RNA-Seq dataset across 28 distinct tissues from different varieties of common carp retrieved from public domain were pre-processing, mapped and assembled for lncRNA identification/ classification using various bioinformatics tools. A total of 33,990 lncRNAs were identified along with revelation of 9 miRNAs having 19 unique lncRNAs acting as their precursors. Additionally, 2,837 miRNAs were found to target 4,782 distinct lncRNAs in the lncRNA-miRNA-mRNA interaction network analysis, which resulted in the involvement of 3,718 mRNAs in common carp. A total of 22,854 circRNAs were identified tissue-wise across all the 28 tissues. Moreover, the examination of the circRNA-miRNA-mRNA interaction network revealed that 15,731 circRNAs were targeted by 5,906 distinct miRNAs, which in turn targeted 4,524 mRNAs in common carp. Significant signaling pathways like necroptosis, NOD-like receptor signaling pathway, hypertrophic cardiomyopathy, small cell lung cancer, MAPK signaling pathway, etc. were identified using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. The web resource of common carp ncRNAs, named CCncRNAdb and available at http://backlin.cabgrid.res.in/ccncrnadb/ gives a comprehensive information about common carp lncRNAs, circRNAs, and ceRNAs interactions, which can aid in investigating their functional roles for its management.
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BACKGROUND: Drought is one of the important abiotic stresses that can significantly reduce crop yields. In India, about 24% of Brassica juncea (Indian mustard) cultivation is taken up under rainfed conditions, leading to low yields due to moisture deficit stress. Hence, there is an urgent need to improve the productivity of mustard under drought conditions. In the present study, a set of 87 B. carinata-derived B. juncea introgression lines (ILs) was developed with the goal of creating drought-tolerant genotypes. METHOD: The experiment followed the augmented randomized complete block design with four blocks and three checks. ILs were evaluated for seed yield and its contributing traits under both rainfed and irrigated conditions in three different environments created by manipulating locations and years. To identify novel genes and alleles imparting drought tolerance, Quantitative Trait Loci (QTL) analysis was carried out. Genotyping-by-Sequencing (GBS) approach was used to construct the linkage map. RESULTS: The linkage map consisted of 5,165 SNP markers distributed across 18 chromosomes and spanning a distance of 1,671.87 cM. On average, there was a 3.09 cM gap between adjoining markers. A total of 29 additive QTLs were identified for drought tolerance; among these, 17 (58.6% of total QTLs detected) were contributed by B. carinata (BC 4), suggesting a greater contribution of B. carinata towards improving drought tolerance in the ILs. Out of 17 QTLs, 11 (64.7%) were located on the B genome, indicating more introgression segments on the B genome of B. juncea. Eight QTL hotspots, containing two or more QTLs, governing seed yield contributing traits, water use efficiency, and drought tolerance under moisture deficit stress conditions were identified. Seventeen candidate genes related to biotic and abiotic stresses, viz., SOS2, SOS2 like, NPR1, FAE1-KCS, HOT5, DNAJA1, NIA1, BRI1, RF21, ycf2, WRKY33, PAL, SAMS2, orf147, MAPK3, WRR1 and SUS, were reported in the genomic regions of identified QTLs. CONCLUSIONS: The significance of B. carinata in improving drought tolerance and WUE by introducing genomic segments in Indian mustard is well demonstrated. The findings also provide valuable insights into the genetic basis of drought tolerance in mustard and pave the way for the development of drought-tolerant varieties.
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Resistencia a la Sequía , Sitios de Carácter Cuantitativo , Sitios de Carácter Cuantitativo/genética , Mapeo Cromosómico , Fenotipo , Genotipo , Planta de la Mostaza/genéticaRESUMEN
Upland cotton (Gossypium hirsutum L.) is a major fiber crop that is cultivated worldwide and has significant economic importance. India harbors the largest area for cotton cultivation, but its fiber yield is still compromised and ranks 22nd in terms of productivity. Genetic improvement of cotton fiber yield traits is one of the major goals of cotton breeding, but the understanding of the genetic architecture underlying cotton fiber yield traits remains limited and unclear. To better decipher the genetic variation associated with fiber yield traits, we conducted a comprehensive genome-wide association mapping study using 117 Indian cotton germplasm for six yield-related traits. To accomplish this, we generated 2,41,086 high-quality single nucleotide polymorphism (SNP) markers using genotyping-by-sequencing (GBS) methods. Population structure, PCA, kinship, and phylogenetic analyses divided the germplasm into two sub-populations, showing weak relatedness among the germplasms. Through association analysis, 205 SNPs and 134 QTLs were identified to be significantly associated with the six fiber yield traits. In total, 39 novel QTLs were identified in the current study, whereas 95 QTLs overlapped with existing public domain data in a comparative analysis. Eight QTLs, qGhBN_SCY_D6-1, qGhBN_SCY_D6-2, qGhBN_SCY_D6-3, qGhSI_LI_A5, qGhLI_SI_A13, qGhLI_SI_D9, qGhBW_SCY_A10, and qGhLP_BN_A8 were identified. Gene annotation of these fiber yield QTLs revealed 2,509 unique genes. These genes were predominantly enriched for different biological processes, such as plant cell wall synthesis, nutrient metabolism, and vegetative growth development in the gene ontology (GO) enrichment study. Furthermore, gene expression analysis using RNAseq data from 12 diverse cotton tissues identified 40 candidate genes (23 stable and 17 novel genes) to be transcriptionally active in different stages of fiber, ovule, and seed development. These findings have revealed a rich tapestry of genetic elements, including SNPs, QTLs, and candidate genes, and may have a high potential for improving fiber yield in future breeding programs for Indian cotton.
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Millets are becoming more popular as a healthy substitute for people with lifestyle disorders. They offer dietary fiber, polyphenols, fatty acids, minerals, vitamins, protein, and antioxidants. The nutritional importance of millets leads to the present in-silico study of selective bioactive compounds docked against the targets of lifestyle diseases, viz., diabetes, hypertension, and atherosclerosis using molecular docking and molecular simulations approach. Pharmacokinetic analysis was also carried out to analyse ADME properties and toxicity analysis, drug-likeliness, and finally target prediction for new targets for uncharacterized compounds or secondary targets for recognized molecules by Swiss Target Prediction was also done. The docking results revealed that the bioactive compound flavan-4-ol, among all the 50 compounds studied, best docked to all the four targets of lifestyle diseases, viz., Human dipeptidyl peptidase IV (-5.94 kcal mol-1 binding energy), Sodium-glucose cotransporter-2 (-6.49 kcal mol-1) diabetes-related enzyme, the Human angiotensin-converting enzyme (-6.31 kcal mol-1) which plays a significant role in hypertension, and Proprotein convertase subtilisin kexin type 9 (-4.67 kcal mol-1) for atherosclerosis. Molecular dynamics simulation analysis substantiates that the flavan-4-ol forms a better stability complex with all the targets. ADMET profiles further strengthened the candidature of the flavan-4-ol bioactive compound to be considered for trial as an inhibitor of targets DPPIV, SGLT2, PCSK9, and hACE. We suggest that more research be conducted, taking Flavon-4-ol into account where it can be used as standard treatment for lifestyle diseases.
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In the global market, spices possess a high-value but low-volume commodities of commerce. The food industry depends largely on spices for taste, flavor, and therapeutic properties in replacement of cheap synthetic ones. The estimated growth rate for spices demand in the world is â¼3.19%. Since spices grow in limited geographical regions, India is one of the leading producer of spices, contributing 25-30 percent of total world trade. Hitherto, there has been no comprehensive review of the genomic resources of industrially important major medicinal spices to overcome major impediments in varietal improvement and management. This review focuses on currently available genomic resources of 24 commercially significant spices, namely, Ajwain, Allspice, Asafoetida, Black pepper, Cardamom large, Cardamom small, Celery, Chillies, Cinnamon, Clove, Coriander, Cumin, Curry leaf, Dill seed, Fennel, Fenugreek, Garlic, Ginger, Mint, Nutmeg, Saffron, Tamarind, Turmeric and Vanilla. The advent of low-cost sequencing machines has contributed immensely to the voluminous data generation of these spices, cracking the complex genomic architecture, marker discovery, and understanding comparative and functional genomics. This review of spice genomics resources concludes the perspective and way forward to provide footprints by uncovering genome assemblies, sequencing and re-sequencing projects, transcriptome-based studies, non-coding RNA-mediated regulation, organelles-based resources, developed molecular markers, web resources, databases and AI-directed resources in candidate spices for enhanced breeding potential in them. Further, their integration with molecular breeding could be of immense use in formulating a strategy to protect and expand the production of the spices due to increased global demand.
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One of the key enigmas in conventional and modern crop improvement programmes is how to introduce beneficial traits without any penalty impairment. Rice (Oryza sativa L.), among the essential staple food crops grown and utilized worldwide, needs to improve genotypes in multifaceted ways. With the global view to feed ten billion under the climatic perturbation, only a potent functional master regulator can withstand with hope for the next green revolution and food security. miRNAs are such, miniature, fine tuners for crop improvement and provide a value addition in emerging technologies, namely large-scale genotyping, phenotyping, genome editing, marker-assisted selection, and genomic selection, to make rice production feasible. There has been surplus research output generated since the last decade on miRNAs in rice, however, recent functional knowledge is limited to reaping the benefits for conventional and modern improvements in rice to avoid ambiguity and redundancy in the generated data. Here, we present the latest functional understanding of miRNAs in rice. In addition, their biogenesis, intra- and inter-kingdom signaling and communication, implication of amiRNAs, and consequences upon integration with CRISPR-Cas9. Further, highlights refer to the application of miRNAs for rice agronomical trait improvements, broadly classified into three functional domains. The majority of functionally established miRNAs are responsible for growth and development, followed by biotic and abiotic stresses. Tabular cataloguing reveals and highlights two multifaceted modules that were extensively studied. These belong to miRNA families 156 and 396, orchestrate multifarious aspects of advantageous agronomical traits. Moreover, updated and exhaustive functional aspects of different supplemental miRNA modules that would strengthen rice improvement are also being discussed.
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MicroARNs , Oryza , MicroARNs/genética , Oryza/genética , Edición Génica , Productos Agrícolas/genética , Sitios de Carácter CuantitativoRESUMEN
The horse, one of the most domesticated animals, has been used for several purposes, like transportation, hunting, in sport, or for agriculture-related works. Kathiawari, Marwari, Manipuri, Zanskari, Bhutia, Spiti, and Thoroughbred are the main breeds of horses, particularly due to their agroclimatic adaptation and role in any kind of strong physical activity, and these characteristics are majorly governed by genetic factors. The genetic diversity and phylogenetic relationship of these Indian equine breeds using microsatellite markers have been reported, but further studies exploring the SNP diversity and runs of homozygosity revealing the selection signature of breeds are still warranted. In our study, the identification of genes that play a vital role in muscle development is performed through SNP detection via the whole-genome sequencing approach. A total of 96 samples, categorized under seven breeds, and 620,721 SNPs were considered to ascertain the ROH patterns amongst all the seven breeds. Over 5444 ROH islands were mined, and the maximum number of ROHs was found to be present in Zanskari, while Thoroughbred was confined to the lowest number of ROHs. Gene enrichment of these ROH islands produced 6757 functional genes, with AGPAT1, CLEC4, and CFAP20 as important gene families. However, QTL annotation revealed that the maximum QTLs were associated with Wither's height trait ontology that falls under the growth trait in all seven breeds. An Equine SNP marker database (EqSNPDb) was developed to catalogue ROHs for all these equine breeds for the flexible and easy chromosome-wise retrieval of ROH along with the genotype details of all the SNPs. Such a study can reveal breed divergence in different climatic and ecological conditions.
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Genómica , Polimorfismo de Nucleótido Simple , Animales , Caballos/genética , Polimorfismo de Nucleótido Simple/genética , Filogenia , Homocigoto , GenotipoRESUMEN
Introduction: Mango (Mangifera indica L.), acclaimed as the 'king of fruits' in the tropical world, has historical, religious, and economic values. It is grown commercially in more than 100 countries, and fresh mango world trade accounts for ~3,200 million US dollars for the year 2020. Mango is widely cultivated in sub-tropical and tropical regions of the world, with India, China, and Thailand being the top three producers. Mango fruit is adored for its taste, color, flavor, and aroma. Fruit color and firmness are important fruit quality traits for consumer acceptance, but their genetics is poorly understood. Methods: For mapping of fruit color and firmness, mango varieties Amrapali and Sensation, having contrasting fruit quality traits, were crossed for the development of a mapping population. Ninety-two bi-parental progenies obtained from this cross were used for the construction of a high-density linkage map and identification of QTLs. Genotyping was carried out using an 80K SNP chip array. Results and discussion: Initially, we constructed two high-density linkage maps based on the segregation of female and male parents. A female map with 3,213 SNPs and male map with 1,781 SNPs were distributed on 20 linkages groups covering map lengths of 2,844.39 and 2,684.22cM, respectively. Finally, the integrated map was constructed comprised of 4,361 SNP markers distributed on 20 linkage groups, which consisted of the chromosome haploid number in Mangifera indica (n =20). The integrated genetic map covered the entire genome of Mangifera indica cv. Dashehari, with a total genetic distance of 2,982.75 cM and an average distance between markers of 0.68 cM. The length of LGs varied from 85.78 to 218.28 cM, with a mean size of 149.14 cM. Phenotyping for fruit color and firmness traits was done for two consecutive seasons. We identified important consistent QTLs for 12 out of 20 traits, with integrated genetic linkages having significant LOD scores in at least one season. Important consistent QTLs for fruit peel color are located at Chr 3 and 18, and firmness on Chr 11 and 20. The QTLs mapped in this study would be useful in the marker-assisted breeding of mango for improved efficiency.
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Interspecific hybridization resulted in the creation of B. juncea introgression lines (ILs) generated from B. carinata with increased productivity and adaptability. Forty ILs were crossed with their respective B. juncea recipient parents to generate introgression line hybrids (ILHs) and the common tester (SEJ 8) was used to generate test hybrids (THs). Mid-parent heterosis in ILHs and standard heterosis in THs were calculated for eight yield and yield-related traits. Heterotic genomic regions were dissected using ten ILs with significant mid-parent heterosis in ILHs and standard heterosis in THs for seed yield. A high level of heterosis for seed yield was contributed by 1000 seed weight (13.48%) in D31_ILHs and by total siliquae/plant (14.01%) and siliqua length (10.56%) in PM30_ILHs. The heterotic ILs of DRMRIJ 31 and Pusa Mustard 30 were examined using polymorphic SNPs between the parents, and a total of 254 and 335 introgressed heterotic segments were identified, respectively. This investigation discovered potential genes, viz., PUB10, glutathione S transferase, TT4, SGT, FLA3, AP2/ERF, SANT4, MYB, and UDP-glucosyl transferase 73B3 that were previously reported to regulate yield-related traits. The heterozygosity of the FLA3 gene significantly improved siliqua length and seeds per siliqua in ILHs of Pusa Mustard 30. This research proved that interspecific hybridization is an effective means of increasing the diversity of cultivated species by introducing new genetic variants and improving the level of heterosis.
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Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are the two classes of non-coding RNAs (ncRNAs) present predominantly in plant cells and have various gene regulatory functions at pre- and post-transcriptional levels. Previously deemed as "junk", these ncRNAs have now been reported to be an important player in gene expression regulation, especially in stress conditions in many plant species. Black pepper, scientifically known as Piper nigrum L., despite being one of the most economically important spice crops, lacks studies related to these ncRNAs. From a panel of 53 RNA-Seq datasets of black pepper from six tissues, namely, flower, fruit, leaf, panicle, root, and stem of six black pepper cultivars, covering eight BioProjects across four countries, we identified and characterized a total of 6406 lncRNAs. Further downstream analysis inferred that these lncRNAs regulated 781 black pepper genes/gene products via miRNA-lncRNA-mRNA network interactions, thus working as competitive endogenous RNAs (ceRNAs). The interactions may be various mechanisms like miRNA-mediated gene silencing or lncRNAs acting as endogenous target mimics (eTMs) of the miRNAs. A total of 35 lncRNAs were also identified to be potential precursors of 94 miRNAs after being acted upon by endonucleases like Drosha and Dicer. Tissue-wise transcriptome analysis revealed 4621 circRNAs. Further, miRNA-circRNA-mRNA network analysis showed 432 circRNAs combining with 619 miRNAs and competing for the binding sites on 744 mRNAs in different black pepper tissues. These findings can help researchers to get a better insight to the yield regulation and responses to stress in black pepper in endeavor of higher production and improved breeding programs in black pepper varieties.
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Introduction: Prevalence of obesity is high in diabetes mellitus (DM) and is associated with hyperuricemia (HU), hypertension, metabolic syndrome, cardiovascular disease and dyslipidemia. In obesity, elevated serum uric acid (SUA) has been shown to be associated in many studies from different countries, but data from India are lacking. The aim of the present study is to know the prevalence of obesity and to know the relationship between obesity and SUA in newly onset DM. Methods: In this cross-sectional study from India, 402 consecutive newly onset diabetic patients (male: 284; female: 118) were enrolled. All patients were grouped into four based on BMI (body mass index): underweight (<18.5 kg/m2), normal weight (18.5-23 kg/m2), overweight (>23-27.5 kg/m2), and obese (>27.5 kg/m2). All participants were grouped into four quartiles based on SUA (Q1: <4.23; Q2: ≥4.24-5.19; Q3: ≥5.20-6.16; Q4: >6.16). Results: The mean age, BMI and SUA of the participants were 46.20±0.52 years, 26.35±0.21 kg/m2 and 5.24±0.007 mg/dl, respectively. Overall prevalence of generalized obesity, central obesity and hyperuricemia (HU) were 35.07%, 85.82% and 13.43%, respectively. The prevalence of generalized obesity increased across the SUA quartile. A multinomial logistic regression analysis showed that serum uric acid level was independently associated with generalized obesity (p<0.001). Conclusion: This first report from India shows a significant positive association between SUA and generalized obesity among newly onset DM. Therefore, routine estimation of SUA is recommended in newly onset DM to prevent and treat HU and its related complications.
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Bitter gourd is an important vegetable crop grown throughout the tropics mainly because of its high nutritional value. Sex expression and identification of gynoecious trait in cucurbitaceous vegetable crops has facilitated the hybrid breeding programme in a great way to improve productivity. In bitter gourd, gynoecious sex expression is poorly reported and detailed molecular pathways involve yet to be studied. The present experiment was conducted to study the inheritance, identify the genomic regions associated with gynoecious sex expression and to reveal possible candidate genes through QTL-seq. Segregation for the gynoecious and monoecious sex forms in the F2 progenies indicated single recessive gene controlling gynoecious sex expression in the genotype, PVGy-201. Gynoecious parent, PVGy-201, Monoecious parent, Pusa Do Mausami (PDM), and two contrasting bulks were constituted for deep-sequencing. A total of 10.56, 23.11, 15.07, and 19.38 Gb of clean reads from PVGy-201, PDM, gynoecious bulk and monoecious bulks were generated. Based on the ΔSNP index, 1.31 Mb regions on the chromosome 1 was identified to be associated with gynoecious sex expression in bitter gourd. In the QTL region 293,467 PVGy-201 unique variants, including SNPs and indels, were identified. In the identified QTL region, a total of 1019 homozygous variants were identified between PVGy1 and PDM genomes and 71 among them were non-synonymous variants (SNPS and INDELs), out of which 11 variants (7 INDELs, 4 SNPs) were classified as high impact variants with frame shift/stop gain effect. In total twelve genes associated with male and female gametophyte development were identified in the QTL-region. Ethylene-responsive transcription factor 12, Auxin response factor 6, Copper-transporting ATPase RAN1, CBL-interacting serine/threonine-protein kinase 23, ABC transporter C family member 2, DEAD-box ATP-dependent RNA helicase 1 isoform X2, Polygalacturonase QRT3-like isoform X2, Protein CHROMATIN REMODELING 4 were identified with possible role in gynoecious sex expression. Promoter region variation in 8 among the 12 genes indicated their role in determining gynoecious sex expression in bitter gourd genotype, DBGy-1. The findings in the study provides insight about sex expression in bitter gourd and will facilitate fine mapping and more precise identification of candidate genes through their functional validation.
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The advent of advanced NGS technologies have led to the generation of enormous amount of sequence data which further aid in the discovery of the various type of markers such as SSRs, SNPs, InDels, etc. Among all these markers, microsatellite SSR markers can be mined from the ddRADseq data as certain properties of SSR markers make them ideal markers for study. These assist researchers and breeders in diversity analysis and producing new varieties with desired traits. To extract the markers, first, the ddRADseq data is assembled into consensus sequences using STACKS program which are further assembled for mining microsatellites using QDD along with MISA tool.
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Genoma de Planta , Polimorfismo de Nucleótido Simple , Etiquetas de Secuencia Expresada , Repeticiones de Microsatélite/genéticaRESUMEN
This current research set out to characterize Halari donkey milk by investigating its nutritional constituents, including its proximate analysis, water activity, titratable acidity, energy, and microbiological analysis. A comprehensive profiling of vitamins, minerals, and amino acids was also carried out. It was found that the composition of Halari donkey milk was consistent with previously published donkey milk literature and was comparable to that of human milk. Halari donkey milk has low 0.86 ± 0.04% fat content, 2.03 ± 0.03% protein content, 0.51 ± 0.05% ash content, and high 5.75 ± 0.15% lactose content making it sweet and palatable. The energy content of Halari donkey milk was 40.39 ± 0.31 kcal/100 g, and the water activity ranged from 0.973 to 0.975. Titratable acidity was 0.03 ± 0.01%. Halari donkey milk can be considered acceptable and microbiologically safe, having low total plate count and yeast and mould counts. Mineral testing revealed that Halari donkey milk included significant amounts of magnesium, sodium, calcium, potassium, phosphorus, and zinc. The concentration of different vitamins and amino acids such as isoleucine and valine also contribute to the nutritional value of Halari donkey milk.
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Introduction: Momordica balsamina is the closest wild species that can be crossed with an important fruit vegetable crop, Momordica charantia, has immense medicinal value, and placed under II subclass of primary gene pool of bitter gourd. M. balsamina is tolerant to major biotic and abiotic stresses. Genome characterization of Momordica balsamina as a wild relative of bitter gourd will contribute to the knowledge of the gene pool available for improvement in bitter gourd. There is potential to transfer gene/s related to biotic resistance and medicinal importance from M. balsamina to M. charantia to produce high-quality, better yielding and stress tolerant bitter gourd genotypes. Methods: The present study provides the first and high-quality chromosome-level genome assembly of M. balsamina with size 384.90 Mb and N50 30.96 Mb using sequence data from 10x Genomics, Nanopore, and Hi-C platforms. Results: A total of 6,32,098 transposons elements; 2,15,379 simple sequence repeats; 5,67,483 transcription factor binding sites; 3,376 noncoding RNA genes; and 41,652 protein-coding genes were identified, and 4,347 disease resistance, 67 heat stress-related, 05 carotenoid-related, 15 salt stress-related, 229 cucurbitacin-related, 19 terpenes-related, 37 antioxidant activity, and 06 sex determination-related genes were characterized. Conclusion: Genome sequencing of M. balsamina will facilitate interspecific introgression of desirable traits. This information is cataloged in the form of webgenomic resource available at http://webtom.cabgrid.res.in/mbger/. Our finding of comparative genome analysis will be useful to get insights into the patterns and processes associated with genome evolution and to uncover functional regions of cucurbit genomes.
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Wheat being the important staple food crop plays a significant role in nutritional security. A wide variety of microbial communities beneficial to plants and contributing to plant health and production are found in the rhizosphere. The wheat microbiome encompasses an extensive variety of microbial species playing a key role in sustaining the physiology of the crop, nutrient uptake, and biotic/abiotic stress resilience. This report presents wheat microbiome analysis under six different farm practices, namely, organic (Org), timely sown (TS), wheat after pulse crop (WAPC), temperature-controlled phenotyping facility (TCPF), maize-wheat cropping system (MW), and residue burnt field (Bur), using 16S rRNA sequencing methodology. The soil samples collected from either side of the wheat row were mixed to get a final sample set for DNA extraction under each condition. After the data preprocessing, microbial community analysis was performed, followed by functional analysis and annotation. An abundance of the phylum Proteobacteria was observed, followed by Acidobacteria, Actinobacteria, and Gemmatimonadetes in the majority of the samples, while relative abundance was found to vary at the genus level. Analysis against the Carbohydrate-Active Enzymes (CAZy) database showed a high number of glycoside hydrolase genes in the TS, TCPF, and WAPC samples, while the Org, MW, and Bur samples predominantly had glycosyltransferase genes and carbohydrate esterase genes were in the lowest numbers. Also, the Org and TCPF samples showed lower diversity, while rare and abundant species ranged from 12 to 25% and 20 to 32% of the total bacterial species in all the sets, respectively. These variations indicate that the different cropping sequence had a significant impact on soil microbial diversity and community composition, which characterizes its economic and environmental value as a sustainable agricultural approach to maintaining food security and ecosystem health. IMPORTANCE This investigation examined the wheat microbiome under six different agricultural field conditions to understand the role of cropping pattern on soil microbial diversity. This study also elaborated the community composition, which has importance in economic (role of beneficial community leading to higher production) and environmental (role of microbial diversity/community in safeguarding the soil health, etc.) arenas. This could lead to a sustainable farming approach for food security and improved ecosystem health. Also, the majority of the microbes are unculturable; hence, technology-based microcultivation will be a potential approach for harnessing other cultured microorganisms, leading to unique species for commercial production. The outcome of this research-accelerated work can provide an idea to the scientists/breeders/agronomists/pathologists under the mentioned field conditions regarding their influence over their crops.
Asunto(s)
Microbiota , Triticum , Triticum/microbiología , ARN Ribosómico 16S/genética , Microbiota/genética , Suelo/química , Productos Agrícolas/microbiología , Bacterias/genética , Microbiología del SueloRESUMEN
Wheat is one of the most widely grown and consumed food crops in the world. Spot blotch and terminal heat stress are the two significant constraints mainly in the Indo-Gangetic plains of South Asia. The study was undertaken using 185 recombinant lines (RILs) derived from the interspecific hybridization of 'Triticum aestivum (HUW234) × T. spelta (H+26)' to reveal genomic regions associated with tolerance to combined stress to spot blotch and terminal heat. Different physiological (NDVI, canopy temperature, leaf chlorophyll) and grain traits (TGW, grain size) were observed under stressed (spot blotch, terminal heat) and non-stressed environments. The mean maturity duration of RILs under combined stress was reduced by 12 days, whereas the normalized difference vegetation index (NDVI) was 46.03%. Similarly, the grain size was depleted under combined stress by 32.23% and thousand kernel weight (TKW) by 27.56% due to spot blotch and terminal heat stress, respectively. The genetic analysis using 6734 SNP markers identified 37 significant loci for the area under the disease progress curve (AUDPC) and NDVI. The genome-wide functional annotation of the SNP markers revealed gene functions such as plant chitinases, NB-ARC and NBS-LRR, and the peroxidase superfamily Cytochrome P450 have a positive role in the resistance through a hypersensitive response. Zinc finger domains, cysteine protease coding gene, F-box protein, ubiquitin, and associated proteins, play a substantial role in the combined stress of spot blotch and terminal heat in bread wheat, according to genomic domains ascribed to them. The study also highlights T. speltoides as a source of resistance to spot blotch and terminal heat tolerance.