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Abstract Background Fruit crops, including tropical and subtropical fruits like Avocado (Persea americana), Fig (Ficus carica), Date Palm (Phoenix dactylifera), Mango (Mangifera indica), Guava (Psidium guajava), Papaya (Carica papaya), Pineapple (Ananas comosus), and Banana (Musa acuminata) are economically vital, contributing significantly to global agricultural output, as classified by the FAO’s World Programme for the Census of Agriculture. Advancements in next-generation sequencing, have transformed fruit crop breeding by providing in-depth genomic and transcriptomic data. RNA sequencing enables high-throughput analysis of gene expression, and functional genomics, crucial for addressing horticultural challenges and enhancing fruit production. The genomic and expression data for key tropical and sub-tropical fruit crops is currently lacking a comprehensive expression atlas, revealing a significant gap in resources for horticulturists who require a unified platform with diverse datasets across various conditions and cultivars. Results The Fruit Expression Atlas (FEAtl), available at http://backlin.cabgrid.res.in/FEAtl/ , is a first-ever extensive and unified expression atlas for tropical and subtropical fruit crops developed using 3-tier architecture. The expressivity of coding and non-coding genes, encompassing 2,060 RNA-Seq samples across 91 tissue types and 177 BioProjects, it provides a comprehensive view of gene expression patterns for different tissues under various conditions. FEAtl features multiple tabs that cater to different aspects of the dataset, namely, Home, About, Analyze, Statistics, and Team and contains seven central functional modules: Transcript Information,Sample Information, Expression Profiles in FPKM and TPM, Functional Analysis, Genes Based on Tau Score, and Search for Specific Gene. The expression of a transcript of interest can be easily queried by searching by tissue ID and transcript type. Expression data can be displayed as a heat map, along with functional descriptions as well as Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. Conclusions This atlas represents a groundbreaking compilation of a wide array of information pertaining to eight distinct fruit crops and serves as a fundamental resource for comparative analysis among different fruit species and is a catalyst for functional genomic studies. Database availability: http://backlin.cabgrid.res.in/FEAtl/ .

Abstract 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.

Wheat, a highly versatile staple crop cultivated extensively for its grains on a global scale, is poised to experience increased demand to sustain the burgeoning population, owing to its superior nutritional potential. Modern wheat, a hexaploid species, has evolved through the introgression of numerous preceding ploidies, including Einkorn, Emmer, Aegilops, and others, each possessing distinct qualitative and quantitative traits. Scientometric and topical analyses serve as effective tools to quantitatively evaluate scientific research by measuring the knowledge expressed in scientific publications and keywords. Thus, comprehending the research status regarding wheat domestication events within primary, secondary, and tertiary gene pools is paramount for enhancing wheat production. In this study, we analyze data retrieved from PubMed to elucidate the research status and identify bottlenecks across different ploidy of genomic pools of wheat. The publication trends on wheat have experienced exponential growth over the past three decades, with China emerging as a leading center for publications. In contrast to the publication frequency observed in hexaploid common wheat, scholarly output concerning Einkorn and Aegilops is approximately tenfold lesser, with emmer trailing behind at three times fewer publications. This discrepancy underscores the prioritization of expedited research initiatives targeting these species, aimed at elucidating latent biological characteristics and optimizing their breeding capabilities. Keywords such as “stress,” “GWAS,” and “gene” are prominent, reflecting the challenges posed by climatic factors on wheat production and their mitigation through molecular breeding and gene manipulation. Notably, the keyword “einkorn” highlights its potential as a donor for fine-tuning traits related to wheat adaptation processes and quality, crucial for modern wheat’s survivability under adverse climates. Conversely, higher publication rates on emmer are primarily associated with Italy, possibly due to its favorable Mediterranean climate for tetraploid wheat. Keywords like “Pasta” and “Ochratoxin, DON” are prevalent, with the former being derived from durum wheat and the latter being reported in higher amounts in durum compared to other wheat species, rendering it less suitable for consumption. Enriched keywords such as “genome” and “resistance” underscore the critical characteristics of Aegilops. Other significant keywords like “Aceria tosichella” possibly indicate multiple stages of resistance conferred by Aegilops, while the presence of the grain softness protein “puroindoline” enhances its acceptability for donation by Aegilops. Spelt, a close relative of common wheat, exhibits a research trend with thousands of annual publications and enriched keywords such as “stress” and “yield” reflect the current scientific emphasis on wheat research. Furthermore, hierarchical keywords like “bio-control” and “celiac disease” merit consideration for future research on hexaploid wheat.

Abstract 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.

Air pollution which negatively impacts both human health and the environment is a mountainous challenge before policymakers and city planners in urban areas. Urban landscaping with effective pollution-combating tree species is one of the soundest strategies to mitigate pollution adversaries. However, not all tree species are equally suitable for urban environments due to varying levels of tolerance to air pollution. This study has been designed to evaluate the physiological and biochemical responses of seven commonly occurring tree species in the Talkatora garden (TG) and Income Tax Office (ITO) representing non-polluted and polluted locations in Delhi, respectively applying Air Pollution Tolerance Index (APTI). The current research study was carried out during 2021–22 at the Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute, New Delhi. In tree species understudy, it was recorded that the pH of leaf extract, total chlorophyll, and relative water content was lower in the winter season than summer season except for the ascorbic acid. Ficus religiosa with the highest APTI value (23.23) followed by Pongamia pinnata (20.85) were found most tolerant tree species to air pollution in Delhi during the winter season at the polluted (ITO) and non-polluted (TG) location respectively with a reverse trend for the summer season. Polyalthia longifolia was found most sensitive (bioindicator plant) to air pollution among the seven trees under study owing to the lowest APTI values (11.14 and 12.58) across the seasons at non-polluted (TG) and polluted (ITO) locations respectively. Furthermore, Ficus religiosa with the highest APTI across the locations and seasons was assessed as the best performer, hence, could be the most efficient option for landscaping in polluted and non-polluted areas.

IntroductionMomordica 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.MethodsThe 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.ResultsA 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.ConclusionGenome 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.

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.

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.

Background: To study the genetic basis of the impact of genotypes and morpho-physio-biochemical traits under different organic and inorganic fertilizer doses on the shelf life attribute of tomatoes, field experiments were conducted in randomized block designs during the rabi seasons of 2018–2019 and 2019–2020. The experiment comprised three diverse nutrient environments [T1—organic; T2—inorganic; T3—control (without any fertilizers)] and five tomato genotypes with variable growth habits, specifically Angoorlata (Indeterminate), Avinash-3 (semi-determinate), Swaraksha (semi-determinate), Pusa Sheetal (semi-determinate), and Pusa Rohini (determinate).Results: The different tomato genotypes behaved apparently differently from each other in terms of shelf life. All the genotypes had maximum shelf life when grown in organic environments. However, the Pusa Sheetal had a maximum shelf life of 8.35 days when grown in an organic environment and showed an increase of 12% over the control. The genotype Pusa Sheetal, organic environment and biochemical trait Anthocyanin provides a promise as potential contributor to improve the keeping quality of tomatoes.Conclusion: The genotype Pusa Sheetal a novel source for shelf life, organic environment, and anthocyanin have shown promises for extended shelf life in tomatoes. Thus, the identified trait and genotype can be utilized in tomato improvement programs. Furthermore, this identified trait can also be targeted for its quantitative enhancement in order to increase tomato shelf life through a genome editing approach. A generalized genome editing mechanism is consequently suggested.

Copy number variants (CNVs) have dynamic potential and evolutionary significance like other genetic variants, namely, single nucleotide polymorphisms, InDels, short tandem repeat polymorphisms, inversion variants, etc. Discovering CNVs leads to further speculation that the genomic DNA contains more changes than previously thought and contributes to the phenotypic variation. CNVs are big DNA fragments (> 1 kb) being duplicated or deleted. A bridge between CNVs and phenotypic variations supports CNVs to be utilized in GWAS, which are currently mostly based on SNPs. CNV, which refers to the structural differences, influence gene expression and can be an indicator of numerous traits for improvement. There is a severe dearth of research on CNVs in animals, especially equine. The present study investigates the genomes of the Bhutia Equine breed for genome-wide discovery of CNVs using the Axiom™ Equine Genotyping Array chip for a better understanding of its traits which had been unexplored till date. A total of 619 CNVs from 20 Bhutia equines were identified with the median and average size as 49.394 kb and 114.955 kb, respectively. Total 225 frequent CNVRs with > 1% CNV frequency were identified among them along with singleton type. These CNVRs contained 361 genes in all. The information obtained on genomic variation could be utilized to identify economically advantageous genetic features in Bhutia equine breed.

IntroductionMango (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.MethodsFor 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 discussionInitially, 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.

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.

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.

The impact of climate change has been alarming for the crop growth. The extreme weather conditions can stress the crops and reduce the yield of major crops belonging to Poaceae family too, that sustains 50% of the world’s food calorie and 20% of protein intake. Computational approaches, such as artificial intelligence-based techniques have become the forefront of prediction-based data interpretation and plant stress responses. In this study, we proposed a novel activation function, namely, Gaussian Error Linear Unit with Sigmoid (SIELU) which was implemented in the development of a Deep Learning (DL) model along with other hyper parameters for classification of unknown abiotic stress protein sequences from crops of Poaceae family. To develop this models, data pertaining to four different abiotic stress (namely, cold, drought, heat and salinity) responsive proteins of the crops belonging to poaceae family were retrieved from public domain. It was observed that efficiency of the DL models with our proposed novel SIELU activation function outperformed the models as compared to GeLU activation function, SVM and RF with 95.11%, 80.78%, 94.97%, and 81.69% accuracy for cold, drought, heat and salinity, respectively. Also, a web-based tool, named DeepAProt (http://login1.cabgrid.res.in:5500/) was developed using flask API, along with its mobile app. This server/App will provide researchers a convenient tool, which is rapid and economical in identification of proteins for abiotic stress management in crops Poaceae family, in endeavour of higher production for food security and combating hunger, ensuring UN SDG goal 2.0.

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 ∼3.19%. 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.

Parthenocarpy is an extremely important trait that revolutionized the worldwide cultivation of cucumber under protected conditions. Pusa Parthenocarpic Cucumber-6 (PPC-6) is one of the important commercially cultivated varieties under protected conditions in India. Understanding the genetics of parthenocarpy, molecular mapping and the development of molecular markers closely associated with the trait will facilitate the introgression of parthenocarpic traits into non-conventional germplasm and elite varieties. The F1, F2 and back-crosses progenies with a non-parthenocarpic genotype, Pusa Uday indicated a single incomplete dominant gene controlling parthenocarpy in PPC-6. QTL-seq comprising of the early parthenocarpy and non-parthenocarpic bulks along with the parental lines identified two major genomic regions, one each in chromosome 3 and chromosome 6 spanning over a region of 2.7 Mb and 7.8 Mb, respectively. Conventional mapping using F2:3 population also identified two QTLs, Parth6.1 and Parth6.2 in chromosome 6 which indicated the presence of a major effect QTL in chromosome 6 determining parthenocarpy in PPC-6. The flanking markers, SSR01148 and SSR 01012 for Parth6.1 locus and SSR10476 and SSR 19174 for Parth6.2 locus were identified and can be used for introgression of parthenocarpy through the marker-assisted back-crossing programme. Functional annotation of the QTL-region identified two major genes, Csa_6G396640 and Csa_6G405890 designated as probable indole-3-pyruvate monooxygenase YUCCA11 and Auxin response factor 16, respectively associated with auxin biosynthesis as potential candidate genes. Csa_6G396640 showed only one insertion at position 2179 in the non-parthenocarpic parent. In the case of Csa_6G405890, more variations were observed between the two parents in the form of SNPs and InDels. The study provides insight about genomic regions, closely associated markers and possible candidate genes associated with parthenocarpy in PPC-6 which will be instrumental for functional genomics study and better understanding of parthenocarpy in cucumber.

ABSTRACT 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.

Abstract Background Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., post-spawning resting and initiation of gonadal activity appropriate for revealing the associated candidate genes. It can be deciphered by RNA sequencing of tissues involved in BPGL (Brain-Pituitary-Gonad-Liver) axis controlling seasonality. How far such BCGs of this fish are evolutionarily conserved across different phyla is unknown. Such study can be of further use to enhance fish productivity as seasonality restricts seed production beyond monsoon season. Result A total of ~ 150 Gb of transcriptomic data of four tissues viz., BPGL were generated using Illumina TruSeq. De-novo assembled BPGL tissues revealed 75,554 differentially expressed transcripts, 115,534 SSRs, 65,584 SNPs, 514 pathways, 5379 transcription factors, 187 mature miRNA which regulates candidate genes represented by 1576 differentially expressed transcripts are available in the form of web-genomic resources. Findings were validated by qPCR. This is the first report in carp fish having 32 BCGs, found widely conserved in fish, amphibian, reptile, birds, prototheria, marsupials and placental mammals. This is due to universal mechanism of rhythmicity in response to environment and earth rotation having adaptive and reproductive significance. Conclusion This study elucidates evolutionary conserved mechanism of photo-periodism sensing, neuroendocrine secretion, metabolism and yolk synthesis in liver, gonadal maturation, muscular growth with sensory and auditory perception in this fish. Study reveals fish as a good model for research on biological clock besides its relevance in reproductive efficiency enhancement.

Cucumber is an extremely perishable vegetable; however, under room conditions, the fruits become unfit for consumption 2–3 days after harvesting. One natural variant, DC-48 with an extended shelf-life was identified, fruits of which can be stored up to 10–15 days under room temperature. The genes involved in this economically important trait are regulated by non-coding RNAs. The study aims to identify the long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) by taking two contrasting genotypes, DC-48 and DC-83, at two different fruit developmental stages. The upper epidermis of the fruits was collected at 5 days and 10 days after pollination (DAP) for high throughput RNA sequencing. The differential expression analysis was performed to identify differentially expressed (DE) lncRNAs and circRNAs along with the network analysis of lncRNA, miRNA, circRNA, and mRNA interactions. A total of 97 DElncRNAs were identified where 18 were common under both the developmental stages (8 down regulated and 10 upregulated). Based on the back-spliced reads, 238 circRNAs were found to be distributed uniformly throughout the cucumber genomes with the highest numbers (71) in chromosome 4. The majority of the circRNAs (49%) were exonic in origin followed by inter-genic (47%) and intronic (4%) origin. The genes related to fruit firmness, namely, polygalacturonase, expansin, pectate lyase, and xyloglucan glycosyltransferase were present in the target sites and co-localized networks indicating the role of the lncRNA and circRNAs in their regulation. Genes related to fruit ripening, namely, trehalose-6-phosphate synthase, squamosa promoter binding protein, WRKY domain transcription factors, MADS box proteins, abscisic stress ripening inhibitors, and different classes of heat shock proteins (HSPs) were also found to be regulated by the identified lncRNA and circRNAs. Besides, ethylene biosynthesis and chlorophyll metabolisms were also found to be regulated by DElncRNAs and circRNAs. A total of 17 transcripts were also successfully validated through RT PCR data. These results would help the breeders to identify the complex molecular network and regulatory role of the lncRNAs and circRNAs in determining the shelf-life of cucumbers.

Cucumber is a model plant for studying parthenocarpy with abundant slicing- and pickling-type germplasm. This study was undertaken to understand the role of the important cytokines (CKs), auxin (AUX) and gibberellin (GA) biosynthesis and degradation genes for the induction of parthenocarpy in slicing and pickling germplasm. Two genotypes of gynoecious parthenocarpic cucumber, PPC-6 and DG-8, along with an MABC-derived gynoecious non-parthenocarpic line, IMPU-1, were evaluated in this study. The slicing and pickling cucumber genotypes PPC-6 and DG-8 were strongly parthenocarpic in nature and set fruit normally without pollination. Endogenous auxin and gibberellin were significantly higher in parthenocarpic than non-parthenocarpic genotypes, whereas the concentration of cytokinins varied among the genotypes at different developmental stages. However, the exogenous application of Zeatin and IAA + Zeatin was effective in inducing parthenocarpic fruit in IMPU-1. Expression analysis with important CK, AUX, and GA biosynthesis-related genes was conducted in IMPU-1, PPC-6, and DG-8. The expression of the CK synthase, IPT, IPT3, PaO, LOG1, LOG2, CYP735A1, and CYP735A2 was up-regulated in the parthenocarpic genotypes. Among the transcription factor response regulators (RRs), positive regulation of CSRR8/9b, CSRR8/9d, CSRR8/9e, and CSRR16/17 and negative feedback of the CK signalling genes, such as CsRR3/4a, CsRR3/4b, CsRR8/9a, and CsRR8/9c, were recorded in the parthenocarpic lines. Homeostasis between cytokinin biosynthesis and degradation genes such as CK oxidases (CKXs) and CK dehydrogenase resulted in a non-significant difference in the endogenous CK concentration in the parthenocarpic and non-parthenocarpic genotypes. In addition, up-regulation of the key auxin-inducing proteins and GA biosynthesis genes indicated their crucial role in the parthenocarpic fruit set of cucumber. This study establishes the critical role of the CKs, AUX, and GA regulatory networks and their cross-talk in determining parthenocarpy in slicing and pickling cucumber genotypes.

Cytokinin dehydrogenase (CKX; EC.1.5.99.12) regulates the level of cytokinin (CK) in plants and is involved in CK regulatory activities. In different plants, a small gene family encodes CKX proteins with varied numbers of members. These genes are expanded in the genome mainly due to segmental duplication events. Despite their biological importance, CKX genes in Triticum aestivum have yet to be studied in depth. A total of 11 CKX subfamilies were identified with similar gene structures, motifs, domains, cis-acting elements, and an average signal peptide of 25 amino acid length was found. Introns, ranging from one to four, were present in the coding regions at a similar interval in major CKX genes. Putative cis-elements such as abscisic acid, auxin, salicylic acid, and low-temperature-, drought-, and light-responsive cis-regulatory elements were found in the promoter region of majority CKX genes. Variation in the expression pattern of CKX genes were identified across different tissues in Triticum. Phylogenetic analysis shows that the same subfamily of CKX clustered into a similar clade that reflects their evolutionary relationship. We performed a genome-wide identification of CKX family members in the Triticum aestivum genome to get their chromosomal location, gene structure, cis-element, phylogeny, synteny, and tissue- and stage-specific expression along with gene ontology. This study has also elaborately described the tissue- and stage-specific expression and is the resource for further analysis of CKX in the regulation of biotic and abiotic stress resistance, growth, and development in Triticum and other cereals to endeavor for higher production and proper management.

Heat stress is one of the significant constraints affecting wheat production worldwide. To ensure food security for ever-increasing world population, improving wheat for heat stress tolerance is needed in the presently drifting climatic conditions. At the molecular level, heat stress tolerance in wheat is governed by a complex interplay of various heat stress-associated genes. We used a comparative transcriptome sequencing approach to study the effect of heat stress (5°C above ambient threshold temperature of 20°C) during grain filling stages in wheat genotype K7903 (Halna). At 7 DPA (days post-anthesis), heat stress treatment was given at four stages: 0, 24, 48, and 120 h. In total, 115,656 wheat genes were identified, including 309 differentially expressed genes (DEGs) involved in many critical processes, such as signal transduction, starch synthetic pathway, antioxidant pathway, and heat stress-responsive conserved and uncharacterized putative genes that play an essential role in maintaining the grain filling rate at the high temperature. A total of 98,412 Simple Sequences Repeats (SSR) were identified from de novo transcriptome assembly of wheat and validated. The miRNA target prediction from differential expressed genes was performed by psRNATarget server against 119 mature miRNA. Further, 107,107 variants including 80,936 Single nucleotide polymorphism (SNPs) and 26,171 insertion/deletion (Indels) were also identified in de novo transcriptome assembly of wheat and wheat genome Ensembl version 31. The present study enriches our understanding of known heat response mechanisms during the grain filling stage supported by discovery of novel transcripts, microsatellite markers, putative miRNA targets, and genetic variant. This enhances gene functions and regulators, paving the way for improved heat tolerance in wheat varieties, making them more suitable for production in the current climate change scenario.

Agricultural productivity is highly influenced by its associated microbial community. With advancements in omics technology, metagenomics is known to play a vital role in microbial world studies by unlocking the uncultured microbial populations present in the environment. Metagenomics is a diagnostic tool to target unique signature loci of plant and animal pathogens as well as beneficial microorganisms from samples. Here, we reviewed various aspects of metagenomics from experimental methods to techniques used for sequencing, as well as diversified computational resources, including databases and software tools. Exhaustive focus and study are conducted on the application of metagenomics in agriculture, deciphering various areas, including pathogen and plant disease identification, disease resistance breeding, plant pest control, weed management, abiotic stress management, post-harvest management, discoveries in agriculture, source of novel molecules/compounds, biosurfactants and natural product, identification of biosynthetic molecules, use in genetically modified crops, and antibiotic-resistant genes. Metagenomics-wide association studies study in agriculture on crop productivity rates, intercropping analysis, and agronomic field is analyzed. This article is the first of its comprehensive study and prospects from an agriculture perspective, focusing on a wider range of applications of metagenomics and its association studies.

Black pepper (Piper nigrum), the “King of Spices,” is an economically important spice in India and is known for its medicinal and cultural values. SSRs, the tandem repeats of small DNA sequences, are often polymorphic in nature with diverse applications. For population structure, QTL/gene discovery, MAS, and diversity analysis, it is imperative to have their location specificity. The existing PinigSSRdb catalogs ~70K putative SSR markers but these are anonymous (unknown chromosomal location), based on 916 scaffolds rather than 26 chromosomes. Under this study, we generated ddRAD sequence data of 29 black pepper genotypes from all over India, being low-cost and most efficient technique for the identification of polymorphic markers. The major limitation of ddRAD with compromised/non-uniform coverage has been successfully overcome by taking advantage of chromosome-wise data availability. The latest black pepper genome assembly was used to extract genome-wide SSRs. A total of 276,230 genomic SSRs were mined distributed over 26 chromosomes, with relative density of 362.88 SSRs/Mb and average distance of 2.76 Kb between two SSRs. This assembly was also used to find the polymorphic SSRs in the generated GBS data of 29 black pepper genotypes utilizing rapid and cost-effective method giving 3,176 polymorphic SSRs, out of which 2015 were found to be hypervariable. The developed web-genomic resource, BlackP2MSATdb (http://webtom.cabgrid.res.in/blackp2msatdb/), is the largest and first reported web resource for genomic and polymorphic SSRs of black pepper, which is useful to develop varietal signature, coreset, physical map, QTL/gene identification, and MAS in endeavor of black pepper production.

Bemisia tabaci (Hemiptera: Aleyrodidae) is a highly efficient vector in the spread of chilli leaf curl virus (ChiLCV, Begomovirus) which is a major constraint in the production of chilli in South Asia. Transcriptome analysis of B. tabaci post-6 h acquisition of ChiLCV showed differential expression of 80 (29 upregulated and 51 downregulated) genes. The maximum number of DEGs are categorized under the biological processes category followed by cellular components and molecular functions. KEGG analysis of DEGs showed that the genes are involved in the functions like metabolism, signaling pathways, cellular processes, and organismal systems. The expression of highly expressed 20 genes post-ChiLCV acquisition was validated in RT-qPCR. DEGs such as cytosolic carboxypeptidase 3, dual-specificity protein phosphatase 10, 15, dynein axonemal heavy chain 17, fasciclin 2, inhibin beta chain, replication factor A protein 1, and Tob1 were found enriched and favored the virus infection and circulation in B. tabaci. The present study provides an improved understanding of the networks of molecular interactions between B. tabaci and ChiLCV. The candidate genes of B. tabaci involved in ChiLCV transmission would be novel targets for the management of the B. tabaci-begomovirus complex.

Water buffalo (Bubalus bubalis), belonging to the Bovidae family, is an economically important animal as it is the major source of milk, meat, and drought in numerous countries. It is mainly distributed in tropical and subtropical regions with a global population of approximately 202 million. The advent of low cost and rapid sequencing technologies has opened a new vista for global buffalo researchers. In this study, we utilized the genomic data of five commercially important buffalo breeds, distributed globally, namely, Mediterranean, Egyptian, Bangladesh, Jaffrarabadi, and Murrah. Since there is no whole-genome sequence analysis of these five distinct buffalo breeds, which represent a highly diverse ecosystem, we made an attempt for the same. We report the first comprehensive, holistic, and user-friendly web genomic resource of buffalo (BuffGR) accessible at http://backlin.cabgrid.res.in/buffgr/, that catalogues 6028881 SNPs and 613403 InDels extracted from a set of 31 buffalo tissues. We found a total of 7727122 SNPs and 634124 InDels distributed in four breeds of buffalo (Murrah, Bangladesh, Jaffarabadi, and Egyptian) with reference to the Mediterranean breed. It also houses 4504691 SSR markers from all the breeds along with 1458 unique circRNAs, 37712 lncRNAs, and 938 miRNAs. This comprehensive web resource can be widely used by buffalo researchers across the globe for use of markers in marker trait association, genetic diversity among the different breeds of buffalo, use of ncRNAs as regulatory molecules, post-transcriptional regulations, and role in various diseases/stresses. These SNPs and InDelscan also be used as biomarkers to address adulteration and traceability. This resource can also be useful in buffalo improvement programs and disease/breed management.

Water-soluble carbohydrates (WSCs) play a vital role in water stress avoidance and buffering wheat grain yield. However, the genetic architecture of stem WSCs’ accumulation is partially understood, and few candidate genes are known. This study utilizes the compressed mixed linear model-based genome wide association study (GWAS) and heuristic post GWAS analyses to identify causative quantitative trait nucleotides (QTNs) and candidate genes for stem WSCs’ content at 15 days after anthesis under different water regimes (irrigated, rainfed, and drought). Glucose, fructose, sucrose, fructans, total non-structural carbohydrates (the sum of individual sugars), total WSCs (anthrone based) quantified in the peduncle of 301 bread wheat genotypes under multiple environments (E01-E08) pertaining different water regimes, and 14,571 SNPs from “35K Axiom Wheat Breeders” Array were used for analysis. As a result, 570 significant nucleotide trait associations were identified on all chromosomes except for 4D, of which 163 were considered stable. A total of 112 quantitative trait nucleotide regions (QNRs) were identified of which 47 were presumable novel. QNRs qWSC-3B.2 and qWSC-7A.2 were identified as the hotspots. Post GWAS integration of multiple data resources prioritized 208 putative candidate genes delimited into 64 QNRs, which can be critical in understanding the genetic architecture of stem WSCs accumulation in wheat under optimum and water-stressed environments. At least 19 stable QTNs were found associated with 24 prioritized candidate genes. Clusters of fructans metabolic genes reported in the QNRs qWSC-4A.2 and qWSC-7A.2. These genes can be utilized to bring an optimum combination of various fructans metabolic genes to improve the accumulation and remobilization of stem WSCs and water stress tolerance. These results will further strengthen wheat breeding programs targeting sustainable wheat production under limited water conditions.

Thrips palmi (Thysanoptera: Thripidae) is the predominant tospovirus vector in Asia-Pacific region. It transmits economically damaging groundnut bud necrosis virus (GBNV, family Tospoviridae) in a persistent propagative manner. Thrips serve as the alternate host, and virus reservoirs making tospovirus management very challenging. Insecticides and host plant resistance remain ineffective in managing thrips–tospoviruses. Recent genomic approaches have led to understanding the molecular interactions of thrips–tospoviruses and identifying novel genetic targets. However, most of the studies are limited to Frankliniella species and tomato spotted wilt virus (TSWV). Amidst the limited information available on T. palmi–tospovirus relationships, the present study is the first report of the transcriptome-wide response of T. palmi associated with GBNV infection. The differential expression analyses of the triplicate transcriptome of viruliferous vs. nonviruliferous adult T. palmi identified a total of 2,363 (1,383 upregulated and 980 downregulated) significant transcripts. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses showed the abundance of differentially expressed genes (DEGs) involved in innate immune response, endocytosis, cuticle development, and receptor binding and signaling that mediate the virus invasion and multiplication in the vector system. Also, the gene regulatory network (GRN) of most significant DEGs showed the genes like ABC transporter, cytochrome P450, endocuticle structural glycoprotein, gamma-aminobutyric acid (GABA) receptor, heat shock protein 70, larval and pupal cuticle proteins, nephrin, proline-rich protein, sperm-associated antigen, UHRF1-binding protein, serpin, tyrosine–protein kinase receptor, etc., were enriched with higher degrees of interactions. Further, the expression of the candidate genes in response to GBNV infection was validated in reverse transcriptase-quantitative real-time PCR (RT-qPCR). This study leads to an understanding of molecular interactions between T. palmi and GBNV and suggests potential genetic targets for generic pest control.

Subclinical mastitis (SCM) in buffalo is one of the most challenging paradoxes for the dairy sector with very significant milk production losses and poses an imminent danger to milch animal’s milk-producing ability. We present here the genome-wide methylation specific to SCM in water buffalo and its consequential effect on the gene expression landscape for the first time. Whole-genome DNA methylation profiles from peripheral blood lymphocytes and gene expression profiles from milk somatic cells of healthy and SCM cases were catalogued from the MeDIP-Seq and RNA-Seq data. The average methylation in healthy buffaloes was found to be higher than that in the SCM-infected buffaloes. DNA methylation was abundant in the intergenic region followed by the intronic region in both healthy control and SCM groups. A total of 3,950 differentially methylated regions (DMRs) were identified and annotated to 370 differentially methylated genes (DMGs), most of which were enriched in the promoter region. Several important pathways were activated due to hypomethylation and belonged to the Staphylococcus aureus infection, Th17 cell differentiation, and antigen processing and presentation pathways along with others of defense responses. DNA methylome was compared with transcriptome to understand the regulatory role of DNA methylation on gene expression specific to SCM in buffaloes. A total of 4,778 significant differentially expressed genes (DEGs) were extracted in response to SCM, out of which 67 DMGs were also found to be differentially expressed, suggesting that during SCM, DNA methylation could be one of the epigenetic regulatory mechanisms of gene expression. Genes like CSF2RB, LOC102408349, C3 and PZP like, and CPAMD8 were found to be downregulated in our study, which are known to be involved in the immune response to SCM. Association of DNA methylation with transposable elements, miRNAs, and lncRNAs was also studied. The present study reports a buffalo SCM web resource (BSCM2TDb) available at http://webtom.cabgrid.res.in/BSCM2TDb that catalogues all the mastitis-related information of the analyses results of this study in a single place. This will be of immense use to buffalo researchers to understand the host–pathogen interaction involving SCM, which is required in endeavors of mastitis control and management.

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.

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.

Trihelix transcription factors play a crucial role in varied stress responses as well as in the growth and development of plants. The role of trihelix transcription factors in the non-shattering phenotype in domesticated rice is known. The Vigna group of crops has different degrees of shattering phenotypes in different species. To understand the evolutionary conservation or divergence of the trihelix gene family in important Vigna species here, the genome-wide identification and characterization of the trihelix gene family in four Vigna species including the cowpea (Vigna unguiculata), mung bean (V. radiata), adzuki bean (V. angularis) and rice bean (V. umbellata) was performed. A total of 39, 35, 41 and 50 trihelix genes were identified in the cowpea, mung bean, adzuki bean and rice bean, respectively. The trihelix genes in each of the four Vigna species were classified into five subgroups: GT, GTγ, SH4, S1P1 and GTδ. The members of each subgroup shared similar patterns of gene structure and motif across the four species. The cross-species positional relationships of the cowpea, adzuki bean and mung bean vis-a-vis rice trihelix genes were studied. Further, the Ka/Ks ratio for the trihelix genes in the four Vigna species indicated the purifying or stabilizing selection of the family. The gene expression analysis of the trihelix gene family in the cowpea showed that most of the genes express in at least some of the seed and/or pod developmental stages, although at varying degrees. Based on detailed bioinformatic analysis, a potential target for gene editing towards a possible non-shattering phenotype in the four important Vigna crops was discussed.

PolyGalacturonase Inhibiting Proteins (PGIPs) are leucine rich repeat pathogenesis-related (PR) cell wall proteins, which interact and inhibit the PolyGalacturonase (PG), an enzyme secreted by the pathogen to degrade pectin. Interaction of PGIP with PG limits the vulnerability of PG by the activation of host defense response against pathogenic attack. Erwinia is gram-negative soft rot bacteria responsible for rhizome rot disease in banana and many other crop plants. The interaction of PG with PGIP is one of the crucial steps for plant-pathogen interaction. To study the molecular mechanism of PR proteins, we employed molecular modelling, protein-protein docking and molecular dynamics simulations of banana PGIP (bPGIP) with Erwinia carotovora PG (ecPG). Further, insilico site-directed mutagenesis was performed in Phaseolus vulgaris PGIP (pvPGIP2) to elucidate the interaction with ecPG. Docking and simulation studies divulge that binding of bPGIP and PvPGIP2 with active site residues of EcPG induces structural changes and thereby inhibit the enzyme. This study provides a unique insight into PG-PGIP interaction, which may help in the development of bacterial soft-rot resistant banana cultivars.

Abstract 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.

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.

Precise early pregnancy diagnosis in dairy animals is of utmost importance for an efficient dairy production system. Not detecting a dairy animal pregnant sufficiently early after the breeding results to extending the unproductive time of their milk production cycle and causes substantial economic loss for a dairy producer. At present, the most conventional and authentic pregnancy confirmation practice in cows and buffaloes is rectal palpation of the reproductive organs at Days 35–40 after insemination, which sometime leads to considering an animal as false pregnant. Other alternative methods available for early pregnancy diagnosis lack either accuracy or reproducibility or require elaborate instrumentation and laboratory setup not feasible to practice at farmers’ doorstep. The present study was aimed at establishment of the microRNA (miRNA) repertoire of the placentome in buffaloes, which could capture the event of the cross talk between a growing embryo and a dam, through fetal cotyledons and maternal caruncles, and thus could hint at the early pregnancy establishment event in ruminants. Total RNA was isolated from buffalo placentome tissues during early stages of pregnancy (at Day < 25 and Days 30–35), and global small RNA analysis was performed by using Illumina single-end read chemistry and Bubalus bubalis genome. A total of 2,199 miRNAs comprising 1,620 conserved and 579 non-conserved miRNAs were identified. Stringent functional miRNA selection criteria could predict 20 miRNAs worth evaluating for their abundance in the plasma of pregnant, non-pregnant, cyclic non-bred, and non-cyclic prepubertal animals. Eight of them (viz., miR-195-5p, miR-708-3p, miR-379-5p, miR-XX1, miR-XX2, miR-130a-3p, miR-200a-3p, and miR-27) displayed typical abundance patterns in the plasma samples of the animals on Day 19 as well as Day 25 post-insemination, thus making them ambiguous candidates for early pregnancy detection. Similarly, higher abundance of miR-200a-3p and miR130a-3p in non-pregnant animals was indicative of their utility for detecting the animals as not pregnant. Most interestingly, miR-XX1 and miR-XX2 were very characteristically abundant only in pregnant animals. In silico target prediction analysis confirmed that these two miRNAs are important regulators of cyclooxygenase-2 (COX-2) and cell adhesion molecule-2 (CADM-2), both of which play a significant role in the implantation process during feto-maternal cross talk. We interpret that circulatory miR-XX1 and miR-XX2 in blood plasma could be the potential biomarkers for early pregnancy detection in buffaloes.

For thousands of years, cereals which include rice, wheat, maize, sorghum and millets etc. have been playing major role in human civilization. These are the principal components of human diet and important staples for daily survival of billions of people globally. The cereal crops belong to poaceae family and rich in vitamins, minerals and fiber. They are reported to reduce the coronary heart disease and other serious diseases. These crops are adversely affected by biotic and abiotic stresses like cold, drought, heat and salinity. With the advent of modern NGS technologies, the plethora of molecular data leads to infer many unexplored facts of the cereal crops using in-silico approach. In the present work, computational techniques were applied to study thoroughly the classification of abiotic stresses (cold, drought, heat and salinity) responsive genes in cereals. The datasets of four stress responsive genes in poaceae family was retrieved from public domain. The machine learning based methodologies namely, Random forest, Support Vector Machines and Deep Learning-Long Short-Term Memory (DL-LSTM) were applied. A comparative analysis was carried out for classification of the retrieved data with k-fold cross validation applying the machine learning techniques at different parameters. It was observed that for all the four sets of data, accuracy was maximum, i.e. 95.11%, 76.88%, 94.31% and 82.04% for cold, drought, heat and salinity, respectively using DL-LSTM. Comparison of the methodologies obviates the outperformance of deep leaning. Such approach of computational studies will help researchers to study the complex biological problems of gene classification more efficiently.

Water buffalo (Bubalus bubalis) are an important animal resource that contributes milk, meat, leather, dairy products, and power for plowing and transport. However, mastitis, a bacterial disease affecting milk production and reproduction efficiency, is most prevalent in populations having intensive selection for higher milk yield, especially where the inbreeding level is also high. Climate change and poor hygiene management practices further complicate the issue. The management of this disease faces major challenges, like antibiotic resistance, maximum residue level, horizontal gene transfer, and limited success in resistance breeding. Bovine mastitis genome wide association studies have had limited success due to breed differences, sample sizes, and minor allele frequency, lowering the power to detect the diseases associated with SNPs. In this work, we focused on the application of targeted gene panels (TGPs) in screening for candidate gene association analysis, and how this approach overcomes the limitation of genome wide association studies. This work will facilitate the targeted sequencing of buffalo genomic regions with high depth coverage required to mine the extremely rare variants potentially associated with buffalo mastitis. Although the whole genome assembly of water buffalo is available, neither mastitis genes are predicted nor TGP in the form of web-genomic resources are available for future variant mining and association studies. Out of the 129 mastitis associated genes of cattle, 101 were completely mapped on the buffalo genome to make TGP. This further helped in identifying rare variants in water buffalo. Eighty-five genes were validated in the buffalo gene expression atlas, with the RNA-Seq data of 50 tissues. The functions of 97 genes were predicted, revealing 225 pathways. The mastitis proteins were used for protein-protein interaction network analysis to obtain additional cross-talking proteins. A total of 1,306 SNPs and 152 indels were identified from 101 genes. Water Buffalo-MSTdb was developed with 3-tier architecture to retrieve mastitis associated genes having genomic coordinates with chromosomal details for TGP sequencing for mining of minor alleles for further association studies. Lastly, a web-genomic resource was made available to mine variants of targeted gene panels in buffalo for mastitis resistance breeding in an endeavor to ensure improved productivity and the reproductive efficiency of water buffalo.

Pearl millet (Pennisetum glaucum L.) is affected by drought stress, affecting crop productivity and survival. Long non-coding RNAs (lncRNAs) are reported to play a vital role in the response to drought stress. LncRNAs represent a major part of non-protein coding RNAs and are present prevalently. These are involved in various biological processes, which may functionally act as RNA rather than getting transcribed as protein. We targeted genome-wide identification of lncRNAs in pearl millet from root and leaf tissues subjected to drought stress. A total of 879 lncRNAs were identified, out of which 209 (leaf control, root control), 198 (leaf treated, root treated), 115 (leaf control, leaf treated) and 194 (root control, root treated) were differentially expressed. Two lncRNAs were found as potential target mimics of three miRNAs from the miRBase database. Gene ontology study revealed that drought-responsive lncRNAs are involved in biological processes like ‘metabolic process’ and ‘cellular process’, molecular functions like ‘binding’ and ‘catalytic activities’ and cellular components like ‘cell’, ‘cell part’ and ‘membrane part’. LncRNA-miRNA-mRNA network shows that it plays a vital role in the stress-responsive mechanism through their activities in hormone signal transduction, response to stress, response to auxin and transcription factor activity. Only four lncRNAs were found to get a match with the lncRNAs present in the plant lncRNA database CANTATAdb, which shows its poorly conserved nature among species. This information has been cataloged in the pearl millet drought-responsive long non-coding RNA database (PMDlncRDB). The discovered lncRNAs can be used in the improvement of important traits, as well as CISPR-Cas technology, in the editing of ncRNAs in plants for trait improvement. Such a study will increase our understanding of the expression behavior of lncRNAs, as well as its underlying mechanisms under drought stress in pearl millet.

Among several important wheat foliar diseases, Stripe rust (YR), Leaf rust (LR), and Stem rust (SR) have always been an issue of concern to the farmers and wheat breeders. Evolution of virulent pathotypes of these rusts has posed frequent threats to an epidemic. Pyramiding rust-resistant genes are the most economical and environment-friendly approach in postponing this inevitable threat. To achieve durable long term resistance against the three rusts, an attempt in this study was made searching for novel sources of resistant alleles in a panel of 483 spring wheat genotypes. This is a unique and comprehensive study where evaluation of a diverse panel comprising wheat germplasm from various categories and adapted to different wheat agro-climatic zones was challenged with 18 pathotypes of the three rusts with simultaneous screening in field conditions. The panel was genotyped using 35K SNP array and evaluated for each rust at two locations for two consecutive crop seasons. High heritability estimates of disease response were observed between environments for each rust type. A significant effect of population structure in the panel was visible in the disease response. Using a compressed mixed linear model approach, 25 genomic regions were found associated with resistance for at least two rusts. Out of these, seven were associated with all the three rusts on chromosome groups 1 and 6 along with 2B. For resistance against YR, LR, and SR, there were 16, 18, and 27 QTL (quantitative trait loci) identified respectively, associated at least in two out of four environments. Several of these regions got annotated with resistance associated genes viz. NB-LRR, E3-ubiquitin protein ligase, ABC transporter protein, etc. Alien introgressed (on 1B and 3D) and pleiotropic (on 7D) resistance genes were captured in seedling and adult plant disease responses, respectively. The present study demonstrates the use of genome-wide association for identification of a large number of favorable alleles for leaf, stripe, and stem rust resistance for broadening the genetic base. Quick conversion of these QTL into user-friendly markers will accelerate the deployment of these resistance loci in wheat breeding programs.

Next-generation sequencing (NGS) based virome analyses of mRNA and sRNA have recently become a routine approach for reliable detection of plant viruses and viroids. In the present study we identified the viral/viroidal spectrum of several Indian grapevine cultivars and reconstructed their whole genomes using the publically available mRNAome and sRNAome datasets. Twenty three viruses and viroids (including two variants of grapevine leafroll associated virus 4) were identified from two tissues (fruit peels and young leaves) of three cultivars among which nine unique grapevine viruses and viroids were identified for the first time in India. Irrespective of the assemblers and tissues used, the mRNA based approach identified more acellular pathogens than the sRNA based approach across cultivars. Further, the mRNAome was on par with the whole transcriptome in viral identification. Through de novo assembly of transcriptomes followed by mapping against reference genome, we reconstructed 19 complete/near complete genomes of identified viruses and viroids. The reconstructed viral genomes included four larger RNA genomes (>13 kb), a DNA genome (RG grapevine geminivirus A), a divergent genome (RG grapevine virus B) and a genome for which no reference is available (RG grapevine virus L). A large number of SNPs detected in this study ascertained the quasispecies nature of viruses. Detection of three recombination events and phylogenetic analyses using reconstructed genomes suggested the possible introduction of viruses and viroids into India from several continents through the planting material. The whole genome sequences generated in this study can serve as a resource for reliable indexing of grapevine viruses and viroids in quarantine stations and certification programs.

Abstract Background Soybean (Glycine max L. Merril) crop is major source of edible oil and protein for human and animals besides its various industrial uses including biofuels. Phytoplasma induced floral bud distortion syndrome (FBD), also known as witches’ broom syndrome (WBS) has been one of the major biotic stresses adversely affecting its productivity. Transcriptomic approach can be used for knowledge discovery of this disease manifestation by morpho-physiological key pathways. Results We report transcriptomic study using Illumina HiSeq NGS data of FBD in soybean, revealing 17,454 differentially expressed genes, 5561 transcription factors, 139 pathways and 176,029 genic region putative markers single sequence repeats, single nucleotide polymorphism and Insertion Deletion. Roles of PmbA, Zn-dependent protease, SAP family and auxin responsive system are described revealing mechanism of flower bud distortion having abnormalities in pollen, stigma development. Validation of 10 randomly selected genes was done by qPCR. Our findings describe the basic mechanism of FBD disease, right from sensing of phytoplasma infection by host plant triggering molecular signalling leading to mobilization of carbohydrate and protein, phyllody, abnormal pollen development, improved colonization of insect in host plants to spread the disease. Study reveals how phytoplasma hijacks metabolic machinery of soybean manifesting FBD. Conclusions This is the first report of transcriptomic signature of FBD or WBS disease of soybean revealing morphological and metabolic changes which attracts insect for spread of disease. All the genic region putative markers may be used as genomic resource for variety improvement and new agro-chemical development for disease control to enhance soybean productivity.

The genus Musa is one of three genera in the family Musaceae, which includes bananas and plantains, which are monocotyledonous plants. Bananas have valuable nutritional content of vitamin C, B6, minerals, and dietary fiber and are a rich food energy source, given that carbohydrates account for 22%–32% of fruit weight. Molecular markers are valuable for crop improvement and population genetics studies. The availability of whole-genome sequence and in silico approaches has revolutionized bulk marker discovery. We describe an online web genomic resource, BanSatDB (http://webtom.cabgrid.res.in/bansatdb/) having the highest number (>341,000) of putative STR markers from Musa genera so far, represented by three species: M. acuminata (110,000), M. balbisiana (107,000), and M. itinerans (124,000) from 11 chromosomes of each species. BanSatDB has also been populated with 580 validated STR markers from the published literature. It is based on a three-tier architecture using MySQL, PHP and Apache. The markers can be retrieved by use of multiple search parameters including chromosome number(s), microsatellite types (simple or compound), repeat nucleotides (1–6), copy number, microsatellite length, pattern of repeat motif, and chromosome location. These markers can be used for Distinctness, Uniformity and Stability (DUS) tests of variety identification and for marker assisted selection (MAS) in variety improvement and management. These STRs have also proved to be helpful in classification of Musa germplasm to distinguish individual accessions and in the development of a standardized procedure for genotyping. These markers can also be used in gene discovery and QTL mapping. The database represents a source of markers for developing and implementing new approaches for molecular breeding, which are required to enhance banana productivity. Keywords: Musaceae, Musa, Banana, Microsatellite, Short tandem repeat (STR), Primers

Karnal bunt (KB) of wheat (Triticum aestivum L.), known as partial bunt has its origin in Karnal, India and is caused by Tilletia indica (Ti). Its incidence had grown drastically since late 1960s from northwestern India to northern India in early 1970s. It is a seed, air and soil borne pathogen mainly affecting common wheat, durum wheat, triticale and other related species. The seeds become inedible, inviable and infertile with the precedence of trimethylamine secreted by teliospores in the infected seeds. Initially the causal pathogen was named Tilletia indica but was later renamed Neovossia indica. The black powdered smelly spores remain viable for years in soil, wheat straw and farmyard manure as primary sources of inoculum. The losses reported were as high as 40% in India and also the cumulative reduction of national farm income in USA was USD 5.3 billion due to KB. The present review utilizes information from literature of the past 100 years, since 1909, to provide a comprehensive and updated understanding of KB, its causal pathogen, biology, epidemiology, pathogenesis, etc. Next generation sequencing (NGS) is gaining popularity in revolutionizing KB genomics for understanding and improving agronomic traits like yield, disease tolerance and disease resistance. Genetic resistance is the best way to manage KB, which may be achieved through detection of genes/quantitative trait loci (QTLs). The genome-wide association studies can be applied to reveal the association mapping panel for understanding and obtaining the KB resistance locus on the wheat genome, which can be crossed with elite wheat cultivars globally for a diverse wheat breeding program. The review discusses the current NGS-based genomic studies, assembly, annotations, resistant QTLs, GWAS, technology landscape of diagnostics and management of KB. The compiled exhaustive information can be beneficial to the wheat breeders for better understanding of incidence of disease in endeavor of quality production of the crop.

Abstract 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.

Black pepper (Piper nigrum L.) (2n= 52; Piperaceae), is a perennial, trailing woody flowering vine having global importance with widespread dietary, medicinal, and preservative uses. It is one of the highly traded high cost spice germplasms cultivated for its fruit. Unlike model species, the whole genome sequence information and genomic resources of black pepper are still unavailable in public domain. Crop production is highly affected by abiotic and biotic stresses. Hence transcriptome profiling has permitted a significant enhancement in discovery and expression profiling of genes and functional genomic studies in black pepper. Stress responsive transcriptomic data of various black pepper genotypes were obtained from public domain (SRA database, NCBI) for the de novo transcriptome assembly, identification of transcription factors and mining of putative simple sequence repeat markers. De novo transcriptome assembly was done with SOAP denovo-trans assembler, which generated 53690 transcripts. A total of 14005 transcription factors with BLAST and 39685 without BLAST hits were identified. A total of 4770 putative SSR markers were identified using de novo transcriptome assembly. Myeloblastosis (MYB) related proteins, Basic helix-loop-helix (BHLH), NAC, WRKY and ERF transcriptional factors found in this study are reported to be associated with plant tolerance against stress condition. These SSR markers can be valuable and facilitate advancements in genetic and molecular studies in the endeavour of better productivity of P. nigrum germplasm, especially in the era of rising abiotic stress.

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 (-log10P ≥ 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 ∼38 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.

Identification and diversity analysis of fungi is greatly challenging. Though internal transcribed spacer (ITS), region-based DNA fingerprinting works as a “gold standard” for most of the fungal species group, it cannot differentiate between all the groups and cryptic species. Therefore, it is of paramount importance to find an alternative approach for strain differentiation. Availability of whole genome sequence data of nearly 2000 fungal species are a promising solution to such requirement. We present whole genome sequence-based world’s largest microsatellite database, FungSatDB having >19M loci obtained from >1900 fungal species/strains using >4000 assemblies across globe. Genotyping efficacy of FungSatDB has been evaluated by both in-silico and in-vitro PCR. By in silico PCR, 66 strains of 8 countries representing four continents were successfully differentiated. Genotyping efficacy was also evaluated by in vitro PCR in four fungal species. This approach overcomes limitation of ITS in species, strain signature, and diversity analysis. It can accelerate fungal genomic research endeavors in agriculture, industrial, and environmental management.

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.