CRISPR-based innovations in seed development and quality enhancement: A comprehensive review

Introduction 1.1 Background and Importance of Seed Quality

Seeds are the fundamental unit of agricultural production and play a decisive role in determining crop establishment, productivity, and food security. High-quality seeds contribute significantly to improved germination, uniform plant growth, enhanced stress tolerance, and higher yield potential in both field and horticultural crops. Seed quality is generally evaluated through several critical parameters, including viability, vigor, genetic and physical purity, dormancy behavior, and germination capacity, all of which directly influence crop performance under diverse environmental conditions (Ali et al., 2023; Hasan et al., 2023). In recent years, increasing global demand for nutritious and resilient crops has intensified the need for advanced seed improvement strategies capable of addressing both productivity and quality concerns. Conventional seed enhancement methods, although valuable, often require long breeding cycles and may lack precision in modifying complex seed-related traits (Shivani et al., 2025). Furthermore, environmental stresses such as drought, salinity, heat, and emerging pests negatively affect seed development and storage longevity, thereby threatening sustainable agricultural systems (Farooq & Nadeem, 2022) [2,11,29,49] .

Need for Advanced Breeding Technologies

Traditional breeding approaches have contributed substantially to crop improvement; however, they are constrained by limited genetic variability, time-consuming selection processes, and linkage drag associated with undesirable traits. Similarly, transgenic technologies have faced regulatory, biosafety, and public acceptance challenges in many countries (Ricroch et al., 2022) [27] . The growing impacts of climate change, rapid population expansion, shrinking arable land, and increasing food insecurity demand innovative breeding technologies capable of generating climate-resilient and nutritionally superior seeds within shorter timeframes (Gao, 2021; Ahmed & Fatima, 2025). Precision breeding tools have therefore emerged as promising alternatives for targeted modification of genes associated with seed quality and crop adaptability [8,44] .

Emergence of CRISPR Technology

Among modern genome-editing technologies, the CRISPR-Cas system has revolutionized plant biotechnology because of its simplicity, efficiency, accuracy, and cost-effectiveness.

CRISPR enables precise editing of target genes involved in seed development, nutrient accumulation, dormancy regulation, and stress tolerance (Chen et al., 2022; Tuncel et al., 2025). Compared with earlier genome-editing platforms such as TALENs and zinc-finger nucleases (ZFNs), CRISPR systems are easier to design, highly multiplexable, and more adaptable across diverse crop species (Gupta et al., 2022; Yin et al., 2021). Consequently, CRISPR-based approaches are increasingly being integrated into seed biotechnology for developing high-yielding and quality-enhanced crop varieties [5, 33, 10, 40] .

Objectives and Scope of the Review

This review comprehensively examines recent advances in CRISPR-mediated seed biotechnology with particular emphasis on seed development and quality enhancement. It highlights the applications of CRISPR technologies in improving seed vigor, germination, dormancy regulation, nutritional quality, storage properties, and resistance to environmental stresses across major crop species (Khan et al., 2025; Islam et al., 2023). The review also discusses emerging trends, challenges, biosafety considerations, and future prospects of CRISPR-driven innovations for sustainable agriculture and global food security [14,51] .

Fundamentals of CRISPR-Cas Systems 2.1 Historical Development of CRISPR

The CRISPR-Cas system has emerged as one of the most transformative genome-editing technologies in modern plant biotechnology. Initially discovered as unusual repetitive DNA sequences in bacterial genomes during the late 1980s, CRISPR was later recognized as a natural adaptive immune mechanism that protects bacteria and archaea from invading viruses and foreign genetic elements. Subsequent studies revealed that CRISPR-associated (Cas) proteins function alongside guide RNAs to identify and cleave target nucleic acids with remarkable precision (Jaganathan et al., 2021) [12] . The adaptation of this microbial defense system for genome engineering revolutionized crop improvement research because it enabled precise, rapid, and cost-effective modification of plant genomes compared with conventional breeding and earlier gene-editing platforms such as zinc finger nucleases and TALENs (Gao, 2021; Yin et al., 2021) [8, 40] . Since the development of CRISPR-Cas9 as a programmable editing tool, researchers have expanded the technology into advanced platforms capable of targeted mutagenesis, gene insertion, transcriptional regulation, and epigenetic modification in crops (Zhang et al., 2021) [41] .

Components and Mechanism

The CRISPR-Cas system mainly consists of a guide RNA (gRNA) and a Cas nuclease. The gRNA directs the nuclease toward a complementary DNA sequence, enabling sequencespecific editing (Khatodia et al., 2021). Cas9 remains the most widely used nuclease because of its high editing efficiency and versatility in plants. However, newer nucleases such as Cas12a (Cpf1) and Cas13 have broadened genome-editing applications due to their unique PAM requirements and RNA-targeting capabilities ( [53, 5, 48, 54] .

Types of CRISPR Systems

Among different CRISPR platforms, CRISPR-Cas9 is the most extensively utilized system in seed trait engineering due to its simplicity and efficiency in targeted genome modification (Gupta et al., 2022). CRISPR-Cas12a/Cpf1 offers additional advantages such as staggered DNA cleavage and multiplex editing, making it valuable for complex trait improvement in crops (Wang et al., 2022). Furthermore, base-editing systems facilitate precise nucleotide conversion for improving seed nutritional quality, protein composition, and stress tolerance without introducing foreign DNA (Kaur & Saini, 2024). Prime editing represents a next-generation advancement that enables highly accurate insertions, deletions, and substitutions with reduced off-target effects, thereby expanding possibilities for precision breeding (Das et al., 2025) [10,36,13,6] .

Delivery Methods in Plants

Efficient delivery of CRISPR reagents into plant cells is essential for successful genome editing. Agrobacteriummediated transformation is widely used because of its stable gene integration and high transformation efficiency in many crops (Ricroch et al., 2022) [27,15,22,33] . [8,5,10,33] .

Seed Development: Biological and Genetic Basis

Seed Formation and Development

Seed formation begins immediately after double fertilization, where one sperm nucleus fuses with the egg cell to form the embryo while the second fuses with polar nuclei to generate the endosperm. Embryogenesis is a critical developmental phase that establishes the basic body plan of the future plant, including shoot and root meristems. This process is regulated by complex gene networks involving transcription factors, signaling molecules, and epigenetic regulators (Pramanik et al., 2021). Studies have shown that CRISPR-mediated editing of developmental genes can precisely alter embryo architecture, thereby improving seed viability and crop establishment (Wang et al., 2023) [22,37] . [34,28,16,31,26,6,44] .

Genetic Regulation of Seed Traits

Seed traits such as size, weight, dormancy, and germination are controlled by multiple quantitative trait loci and regulatory genes. Seed size and weight are major determinants of crop yield and market value. Genes involved in cell proliferation, hormonal signaling, and nutrient transport significantly influence these characteristics (Liu et al., 2021). CRISPR/Cas-mediated editing of yield-associated genes has demonstrated substantial improvements in grain weight and seed biomass in rice, wheat, and maize (Ahmad et al., 2024; Chandra & Patel, 2023) [1] . Seed dormancy is an adaptive trait that prevents premature germination under unfavorable conditions. However, excessive dormancy may reduce crop uniformity and germination efficiency. Hormonal balance, particularly between abscisic acid (ABA) and gibberellins (GA), plays a key role in dormancy regulation (Devi & Choudhary, 2024). Genome editing of dormancy-related genes has enabled the development of varieties with optimized germination behavior and improved field emergence (Ali et al., 2023). Germination control genes regulate water uptake, enzymatic activation, and metabolic reprogramming during seed sprouting. Manipulation of these genes through CRISPR technology has improved seed vigor, accelerated germination, and enhanced tolerance to abiotic stress conditions such as salinity and drought (Farooq & Nadeem, 2022; Hasan et al., 2023) [17,1,46,7,2,11] .

Molecular Pathways Influencing Seed Quality

Seed quality is strongly influenced by hormonal signaling pathways and stress-responsive molecular mechanisms. Among plant hormones, ABA regulates seed maturation, dormancy, and desiccation tolerance, whereas GA promotes germination and embryo growth. Auxins contribute to cell division, seed enlargement, and nutrient allocation during early development (Yang et al., 2022) Consequently, integrating molecular biology with genome editing technologies is transforming seed science and paving the way for sustainable crop improvement and global food security [39,45,53,50,29] . [8, 40, 33 59, 27, 45] .

CRISPR Applications in

Enhancement of Seed Size and Yield

One of the most significant applications of CRISPR technology is the enhancement of seed size and grain yield through targeted editing of yield-related genes. [17,1,5,42,57,31] . [7,2,11,4] .

Improvement of Seed

Hybrid Seed Production

Hybrid seed production has benefited substantially from CRISPR-assisted breeding strategies. The technology has been widely used to develop male sterility and fertility restoration systems, which are essential for efficient hybrid seed production. [15,46,12,44] .

Seed Longevity and Storage Potential

Seed longevity is a major factor influencing seed quality during storage and distribution. CRISPR technology has enabled targeted editing of genes associated with oxidative stress responses, cellular repair mechanisms, and seed aging processes. Modifications in antioxidant-related pathways have shown potential in reducing seed deterioration and improving storage life (Raza et al., 2023). Enhanced regulation of reactive oxygen species and protective metabolites through genome editing can maintain seed viability and vigor over extended storage periods (Farooq & Nadeem, 2022). Such innovations are particularly valuable for seed banks, germplasm conservation, and sustainable agricultural systems where long-term seed preservation is essential [26,49] .

Development of Climate-Resilient Seeds

The development of climate-resilient seeds is one of the most promising applications of CRISPR-based seed biotechnology. Genome editing has been extensively used to enhance tolerance against drought, salinity, heat, and cold stress by targeting stress-responsive genes and regulatory networks (Das et al., 2025). In rice, wheat, and maize, CRISPR-mediated editing of transcription factors and signaling pathways has improved water-use efficiency and osmotic adjustment under drought conditions (Khatodia et al., 2021). Similarly, salinity tolerance has been enhanced through modifications in ion transport and stress-responsive genes, leading to better seed germination and plant establishment in saline soils (Farooq & Nadeem, 2022). Heatand cold-tolerant seed varieties have also been developed through precise editing of temperature-responsive genes, thereby ensuring stable productivity under extreme climatic fluctuations (Prakash & Reddy, 2025; Ghosh et al., 2026). Collectively, these innovations highlight the immense potential of CRISPR technology in developing resilient seed systems for future sustainable agriculture [6,53,49,50] .

CRISPR-Based Seed Quality Enhancement

CRISPR/Cas-mediated genome editing has emerged as a transformative approach for improving seed quality traits in major food and oilseed crops. Unlike conventional breeding, which is often time-consuming and limited by genetic variability, CRISPR technology enables precise modification of target genes associated with nutritional composition, disease resistance, processing quality, and seed storage characteristics (Gao, 2021; Gupta et al., 2022). Recent advances in genome engineering have accelerated the development of nutritionally superior and climate-resilient crop varieties with enhanced consumer and industrial value (Tuncel et al., 2025; Tyagi & Sharma, 2026) [8,10,33,59] .

Nutritional Biofortification

One of the most significant applications of CRISPR technology in seed improvement is nutritional biofortification. Genome editing has been widely used to enhance seed protein quality by modifying genes involved in amino acid biosynthesis and seed storage proteins. In legumes and cereals, CRISPR-mediated editing has improved lysine content, digestibility, and overall protein balance, thereby addressing protein malnutrition in developing regions . These developments demonstrate the potential of CRISPR technology to support global nutritional security and functional food production [28,34,3,13,20,55,19,31] . [12,11,18,42,24,54,14 ] .

Disease and Pest

Reduction of Anti-Nutritional Factors:

Another important area of seed quality enhancement involves reducing anti-nutritional compounds and allergenic proteins.

CRISPR technology has been successfully used to eliminate toxic metabolites and allergenic seed proteins that negatively affect human health and nutrient absorption (Liu et al., 2021; Yang et al., 2022). Low-phytate crop varieties developed through targeted gene editing exhibit improved mineral bioavailability because phytate normally binds essential micronutrients such as iron and zinc (Jha et al., 2021). Likewise, editing gluten-related genes in wheat has shown promise for developing low-gluten products suitable for individuals with gluten intolerance and celiac disease (Tyagi et al., 2024). Such innovations not only improve nutritional quality but also expand the market potential of edited crops in health-conscious consumer sectors [18,39,52,34] .

Improvement in Seed Processing and Industrial Traits

CRISPR applications are increasingly being extended to seed processing and industrial quality traits. Editing genes associated with seed senescence and oxidative degradation has improved seed longevity and shelf life during storage (Raza et al., 2023). In cereals and pulses, genome editing has enhanced milling efficiency, cooking quality, starch composition, and seed texture, thereby improving industrial processing performance (Li et al., 2023; Yadav et al., 2024). Furthermore, manipulation of genes controlling seed coat thickness, hardness, and pigmentation has contributed to better seed handling, improved appearance, and increased resistance to mechanical damage (Wang et al., 2023; Chandra & Patel, 2023). Collectively, these advancements highlight the broad potential of CRISPR technology in developing high-quality seeds that meet the evolving demands of agriculture, food industries, and consumers [26,16,38,37,46] . Collectively, these integrated technologies enhance the efficiency, accuracy, and sustainability of next-generation crop breeding and seed improvement programs.

Major Crop-Specific Case Studies 6.1 Rice Yield Enhancement and Blast Resistance

Rice has emerged as one of the most extensively studied crops for CRISPR/Cas-mediated seed improvement and trait enhancement. Researchers have successfully edited genes associated with grain yield, panicle architecture, and disease resistance to develop superior rice cultivars with improved productivity and resilience. Editing of yield-related genes such as Gn1a, DEP1, and GS3 has contributed to enhanced grain number, seed size, and overall yield performance. In addition, CRISPR/Cas9-mediated modification of susceptibility genes has significantly improved resistance against rice blast disease caused by Magnaporthe oryzae, thereby reducing yield losses and dependence on chemical fungicides. Recent studies also demonstrated successful development of herbicide-resistant and stress-tolerant rice lines through homology-directed repair and multiplex genome editing approaches. These innovations indicate that CRISPR technology can accelerate precision breeding in rice while maintaining desirable seed quality traits, nutritional value, and environmental adaptability (Gao, [8,32,36,1,33] . [8,12] Herbicide resistance HDR-based CRISPR/Cas9 editing Development of herbicide-tolerant rice lines Sun et al. (2021) [32] Stress [16,34] Low-gluten wheat Gluten gene modification Reduced allergenic potential [12, 53] Seed longevity Precision genome editing Improved storage and seed viability Raza et al. (2023) [26]

Maize Stress Tolerance and Nutritional Traits

Maize has benefited considerably from CRISPR-mediated interventions aimed at improving abiotic stress tolerance, nutrient content, and seed quality traits. Genome editing strategies have targeted genes associated with drought tolerance, heat stress adaptation, and nitrogen-use efficiency to enhance maize productivity under changing climatic conditions. In addition, biofortification efforts have focused on increasing provitamin A, essential amino acids, and micronutrient accumulation in maize kernels. CRISPR/Cas technology has also enabled modification of starch biosynthesis pathways, improving industrial and nutritional quality. These approaches are increasingly important for ensuring food security and sustainable crop production in stress-prone environments. Recent advances in base editing and multiplex gene editing further support rapid improvement of complex seed traits in maize breeding programs.

Soybean Oil Quality and Protein Enhancement

Soybean is a major oilseed and protein crop where CRISPR technology has shown remarkable potential in improving seed composition and nutritional quality. Genome editing has been widely used to modify fatty acid biosynthesis pathways, leading to increased oleic acid content and reduced undesirable fatty acids, thereby improving oil stability and nutritional value. Researchers have also targeted genes [5,11] associated with seed protein accumulation to enhance amino acid composition and overall protein quality. Such modifications are particularly important for food, feed, and industrial applications. Furthermore, CRISPR-based editing has contributed to improved stress tolerance and seed storage characteristics in soybean. These advancements demonstrate the potential of precision breeding to develop high-value soybean cultivars with superior seed traits and better market acceptance [28,52] Stress resilience CRISPR/Cas-mediated editing Improved adaptability and seed quality Rahman & Karim (2023) [57] Nutraceutical [37] Canola Oil composition Enhanced edible oil quality Mahapatra & Roy (2024); Pandey et al.

(2026) [19,21] Horticultural

Challenges and Limitations

Despite remarkable progress in CRISPR-mediated seed engineering, several scientific and practical limitations continue to restrict its broader application. One of the major technical challenges is inconsistent editing efficiency across crop species and genotypes, particularly in polyploid and recalcitrant crops where precise editing remains difficult (Chen et al., 2022). Off-target mutations, although reduced through improved editing platforms, still represent a concern for genomic stability and biosafety (Yin et al., 2021). In many crops, low transformation and regeneration efficiency further limit the successful production of edited plants, especially in legumes and horticultural species (Wang et al., 2023). Regulatory uncertainties across countries also slow commercialization and international acceptance of geneedited seeds. Additionally, the high costs associated with laboratory infrastructure, sequencing technologies, regulatory approvals, and product commercialization create barriers for research institutions in developing nations (Khan et al., 2025). These limitations highlight the need for more efficient, affordable, and universally accepted genomeediting strategies.

Future Perspectives and Research Directions

Future developments in CRISPR technology are expected to revolutionize seed biotechnology through the emergence of next-generation genome-editing tools such as base editing, prime editing, multiplex editing, and CRISPR-associated transposases, which offer greater precision and flexibility in crop improvement (Mishra et al., 2022; Tuncel et al., 2025). The concept of de novo domestication using CRISPR has also opened new opportunities for converting wild plant species into climate-resilient crops with superior nutritional and agronomic traits (Zsögön et al., 2021). Researchers are increasingly focusing on climate-smart seed systems capable of tolerating drought, salinity, heat, and emerging pests under changing climatic conditions (Das et al., 2025). Another promising direction involves the genome editing of orphan crops and underutilized species that are important for regional food security but have historically received limited research attention (Tyagi & Sharma, 2026). Integration of CRISPR technology with microbiome engineering, seed coating innovations, and digital breeding platforms may further enhance seed quality and agricultural sustainability (Biswal et al., 2026; Singh et al., 2026). Overall, CRISPR-based seed innovations hold immense potential to support sustainable agriculture, improve nutritional security, and strengthen global food systems in the coming decades. [ 36,42,44,45,46,47,50,51,59] Conclusion CRISPR-based genome editing has transformed the field of seed biotechnology by providing highly precise, efficient, and flexible tools for improving seed development and quality traits in crop plants. The technology has significantly accelerated modern breeding programs by enabling targeted manipulation of genes associated with seed size, germination, dormancy, nutrient composition, stress tolerance, disease resistance, and storage longevity. Compared with conventional breeding methods, CRISPR systems offer faster and more accurate genetic improvement without extensive linkage drag or prolonged selection cycles. Applications in major crops such as rice, wheat, maize, soybean, and several horticultural species clearly demonstrate the enormous potential of CRISPR-mediated breeding for enhancing agricultural productivity, nutritional quality, and climate resilience. The review further highlights the growing integration of CRISPR with advanced scientific approaches including artificial intelligence, multi-omics technologies, nanobiotechnology, and precision agriculture. These innovations are improving editing efficiency, target specificity, and large-scale breeding applications, thereby opening new opportunities for sustainable crop improvement. Emerging genome-editing platforms such as base editing, prime editing, and multiplex CRISPR systems are expected to further expand the possibilities for precise and complex trait engineering in seeds. Despite these promising advancements, several challenges remain, including regulatory inconsistencies, biosafety concerns, off-target mutations, limited transformation efficiency in certain crops, and unequal access to advanced technologies. Addressing these issues through transparent regulatory frameworks, improved biosafety assessment, public awareness, and inclusive innovation policies will be essential for responsible and equitable adoption of CRISPRbased seed technologies. Overall, CRISPR-driven innovations represent a major breakthrough in next-generation agriculture and seed science. With continued research, technological refinement, and global collaboration, CRISPR technology has the potential to

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