Application of Next-Generation Sequencing (NGS) Technologies for Efficient Breeding, Quality Assurance and Testing of Seeds
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Authors
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BONY DE KUMAR
Yale Center for Genome Analysis, Yale University, New Haven, CT, USA, 06516
Author
Keywords:
Next-generation sequencing, Seed quality assurance, Genomic technologiesAbstract
Seed constitutes the foundational resource for global agriculture and food security. The availability of high-quality, genetically pure, and pathogen-free seed is indispensable for ensuring sustainable crop productivity and resilient farming systems. Traditional seed testing approaches—such as morphological characterization, protein or isozyme profiling, and PCR-based molecular assays—continue to provide valuable information but often lack the resolution, scalability, and diagnostic breadth required to address modern seed industry challenges.Next-generation sequencing (NGS) has transformed our ability to interrogate seed biology by enabling high-resolution analysis of seed genomes, transcriptomes, epigenomes, and microbiomes within a single technological framework. This review summarizes the evolution of sequencing platforms, clarifies key terminology, and delineates how advanced sequencing technologies are increasingly integrated into seed research, seed technology innovation, and quality assurance programs. The transition from first-generation Sanger sequencing to second-generation high-throughput sequencing dramatically reduced sequencing cost while exponentially increasing data output. Illumina sequencing, as the dominant short-read system, provided reliable and costefficient genome-wide genotyping solutions. The advent of third-generation long-read platforms, including PacBio and Oxford Nanopore technologies, has enabled accurate resolution of repetitive regions, structural variants, and complex polyploid genomes—characteristics that are highly relevant to many modern cultivated crops. Integrating complementary sequencing approaches with massively parallel data acquisition has deepened our understanding of plant genetic architecture and the molecular determinants of yield performance, stress resilience (biotic and abiotic), seed vigor, and post-harvest quality. Emerging technologies—such as advanced nanopore chemistries, spatially resolved and in situ sequencing, and microscopy-coupled nucleic acid profiling—promise to further accelerate discovery and operational deployment. Collectively, these innovations are reshaping the seed sector, providing unprecedented opportunities for precision breeding, rigorous genetic purity testing, comprehensive phytosanitary certification, and the development of next-generation seed quality standards.
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