Sarika Jaiswal

Cucumber is a globally significant vegetable crop whose production and market value are affected by fruit quality and resilience to diverse environmental stressors. Despite the identification of numerous Quantitative Trait Loci (QTL) over the last two decades, their direct application in breeding has been hindered by inconsistent genomic positions and broad confidence intervals. In this study, we conducted a comprehensive Meta-QTL (mQTL) analysis by integrating 647 initial QTLs from 40 independent studies published between 2003 and 2024. Using a high-density consensus map containing 9,299 markers, we projected 531 QTLs, identifying 38 robust mQTLs associated with fruit quality, biotic and abiotic stress tolerance. The identified mQTLs exhibited a significant reduction in the average confidence interval (CI) by 5.3-fold, compared to the average CI of the original QTLs and phenotypic variance explained values reaching up to 49.81% (mQTL 6.8). Our results identifying specific genomic hotspots on chromosomes 1, 3, 5, and 6 that harbor high-confidence candidate genes responsible for stress tolerance and fruit quality. Comparative analysis with seven independent genome-wide association studies validated 16 mQTL regions, confirming their stability across diverse genetic backgrounds. Biotic stress resilience was linked to immune regulators such as LRK10L2 and MLO-like protein 12, while abiotic stress tolerance was anchored by genes like NCED5 (cold), ClpB1 (heat), and MYB44-like (waterlogging). Furthermore, we identified key drivers of fruit quality, including Expansin-A4 and CNR2 for dimensions, CsWOX9 for epidermal spine initiation, and Hd3a for flowering phenology. Transcriptomic profiling provided robust expression support for these prioritized candidate genes within the target mQTL intervals. The markers linked to these genes serve as robust tools for marker-assisted selection and fine mapping, offering precise targets for the development of climate-resilient, high-quality cucumber cultivars.

The family Cyprinidae represents the most taxonomically diverse group of freshwater fishes, encompassing over 3 000 species of ecological and economic importance in aquaculture, conservation, and ecological monitoring. Simple sequence repeats (SSRs), also known as microsatellites, are highly informative molecular markers widely used for genetic diversity analysis, population structure assessment, and marker-assisted breeding. However, comprehensive genome-wide SSR resources for cyprinids remain limited. Existing databases, such as FishMicrosat, provide restricted taxonomic coverage and lack standardized chromosome-level datasets suitable for comparative genomic analyses. To address this gap, we developed CypriSSR, a genome-wide SSR database encompassing 11 representative cyprinid species. Chromosome-level genome assemblies were retrieved from NCBI. SSR loci were identified using MISA, and primer pairs were designed using Primer3. In total, over 7.8 million SSR loci were identified. Mononucleotide repeats were the most abundant class (39–53%), followed by dinucleotide and trinucleotide motifs. SSRs were predominantly distributed in genic regions (54%–71% across species), suggesting potential functional roles. Each database entry includes repeat type, genomic coordinates, primer sequences, melting temperatures, and predicted PCR product sizes. The CypriSSR web interface enables flexible querying of SSR markers based on species, chromosome, motif class, and genomic location, and supports sequence similarity searches through an integrated BLAST module along with data export options. CypriSSR provides a comprehensive and standardized multi-species microsatellite resource for cyprinid genomes and supports applications in population genetics, molecular breeding, and conservation genomics. Database URL: http://46.202.167.198/fishssr/

Fruits are integral to agriculture and receive considerable attention due to their multifold health and nutritional benefits, particularly in the post-pandemic era. The wide range of climatic conditions gives rise to a myriad of fruits grown in different agro-climatic zones; however, fruits grown in tropical and subtropical zones deserve particular attention by virtue of their bountiful nutritional compounds and contribution to substantial growth in the economic sector. Nevertheless, their production is severely affected by their perishable and delicate nature, often limited by various biotic and abiotic factors that result in pre- and post-harvest losses. Scientific advancements have catalyzed efforts to augment the production of tropical and subtropical fruits through genetic and genomic interventions, resulting in the development of numerous advanced genomic resources. These innovations present new opportunities to address key challenges in fruit production, including the mitigation of anti-nutritional factors, improvement of sensory attributes, extension of both pre- and post-harvest shelf-life, chilling sensitivities, and ancillary crop improvements. This review provides a comprehensive synthesis of the genetic and genomic resources available for influential tropical and subtropical fruits, with an emphasis on their potential impact in the context of market acceptability and economic feasibility. These include whole-genome sequencing, which provides insights into domestication and adaptation processes; quantitative traits facilitating the identification of loci associated with desirable traits; functional genomics, enabling biotechnological interventions; the miRNA repertoire for precise trait modulation; and the integration of these resources with CRISPR/Cas9 for tailoring trait modification and recovery. Furthermore, the review highlights the role of web-based platforms that enhance stakeholder engagement and marketing strategies, thereby accelerating the translational potential of research and development in this field. Moreover, the inclusion of single-cell approaches for uncovering cellular heterogeneity, along with multi-omics strategies for dissecting complex traits, is critically discussed. Collectively, these genomic resources are poised to drive transformative changes in the production and utilization of tropical and subtropical fruits, contributing to global nutritional security and sustainable horticultural practices.

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)–CRISPR associated protein (CRISPR-Cas) has emerged and evolved as a revolutionary genome editing technology, transforming research across diverse biological disciplines. Over the past decade, this technology has unveiled numerous opportunities for precise genome manipulation. However, the processes of discovering Cas proteins, repurposing them as editing tools, selecting appropriate candidate tool from the CRISPR-toolbox, designing experiments, and analyzing data are often complex and require careful consideration. To support researchers at every stage of CRISPR experimentation, a wide array of web resources has been developed. In this article, we provide a comprehensive overview of standalone and web-based tools that assist in the identification of CRISPR-Cas systems and the design of guide RNAs (gRNAs). We also highlight tools for evaluating gRNA efficiency, predicting CRISPR-Cas9 mutation profiles, as well as tools for base editing and prime editing, and the analysis and visualization of experimental results. Additionally, we introduce CRISPR–Gateway for Accessing Tools and Resources (CRISPR-GATE), an all-inclusive web repository that consolidates publicly available tools for genome editing research. This repository offers a categorized and user-friendly interface, allowing researchers to quickly access relevant tools based on their specific needs. CRISPR-GATE aims to streamline the search for CRISPR resources, facilitating both education and accelerating innovation. The web repository can be accessed from https://crispr-gate.daasbioinfromaticsteam.in/.

The genomic diversity among Indian horse and pony breeds was investigated to under-stand how their unique traits, shaped by different environments, might help improve their health and performance. A cost-effective genetic analysis method of the genome-based ddRAD approach was used to identify admixture. The investigators identified 322732 variants, of which 298782 were SNPs and 23950 were Indels across horses and ponies. In the thoroughbred horses, 149134 genetic variants were observed, of which 161002 were SNPs. 1631 positive selection signatures were found common among all horse breeds. 700 selection signatures were enumerated to 306 genes. SLC4A10, CADM1, AUST2, and LOC733058 genes contained more than 10 selection signatures. Many of these selection signatures were linked to important functions, such as brain development (via genes GRM8 and GRIK3), muscle strength (VDR), and tendon durability (TNC)—all of which contribute to horses’ athletic abilities. Genes such as ANK2, BCL2, and RYR2 possess pos-itive selection signatures and play central roles in managing calcium movement and heart function. These genes may help horses maintain lower heart rates during intense activity, enhancing their stamina and performance. This study offered insights to enhance horse welfare and performance globally, benefiting communities reliant on these animals.

To decipher the molecular mechanism behind submergence tolerance in a typical rice genotype (var. Kumrogarh), leaf transcriptome analysis was performed on submerged plant tissue with 7 and 14 days of induced submergence, followed by cataloguing the differentially expressed transcripts. Subsequent bioinformatics analysis identified 5,267 differentially expressed genes (DEGs), of which 2,657 were upregulated and 2,610 were downregulated in four comparative combinations: T7–C7, T14–T7, T14–T7, and C14–C7. A group of 41 co-expressed genes was found across all sets, while 1427, 558 and 83 transcripts were uniquely expressed in the T7–C7, T14–T7, and C14–C7 combinations, respectively. Constructed Ven diagram showed that 1428, 65, and 44 transcripts were commonly expressed in the paired combinations “T7–C7” and “T14–T7”, “C14–C7” and “T7–C7”, and “C14–C7” and “T14–T7”. Gene ontology study functionally categorized the DEGs into molecular functions, biological processes, and cellular components. Additionally, nine transcription factor families were identified, including MYB, WRKY, bZIP, bHLH, SET domain, NAC domain, C2H2 zinc finger, E2F, and HSF, along with a set of differentially regulated signalling genes. Twelve genes related to submergence adaptation were selected for final validation through quantitative real-time PCR-based expression analysis, which demonstrated a strong association with a coefficient (R² = 0.716) after aligning with the RNA-Seq data. Derived results showed upregulation of gibberellin receptor GID1L2 (LOC_Os02g35940.1), ethylene-responsive element-binding protein (LOC_Os06g08360.1), glyceraldehyde-3-phosphate dehydrogenase (LOC_Os04g38600.1), decarboxylase (LOC_Os08g04540.1), sucrose synthase (LOC_Os03g22120.1), aldehyde dehydrogenase (LOC_Os12g07810.1), endonuclease/exonuclease/phosphatase family domain-containing protein (LOC_Os01g08780.1), polygalacturonase inhibitor 1 precursor (LOC_Os07g38130.1), transmembrane amino acid transporter protein (LOC_Os01g41420.1), and SAM-dependent carboxyl methyltransferase (LOC_Os02g48770.1). This study provides a comprehensive profile of leaf transcriptomics in a traditionally tall-type rice landrace containing both submergence-tolerant Sub1 and SK alleles, highlighting an area of research that remains largely unexplored. These remarkable findings have driven this investigation to decipher the interplay among these key genetic factors by hypothesizing a model leading to the development of a genetic network associated with improved survival under prolonged deep submergence of such a unique rice genotype.