eChapter Name: Harnessing Next Generation Sequencing for Precision DNA Fingerprinting in Varietal Screening: An Overview
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eBook Name: RECENT ADVANCES IN CROP VARIETY IDENTIFICATION USING DNA TECHNOLOGY
Introduction
Crop improvement is critical for tackling global food security challenges caused by population growth, resource scarcity, and climate change (Singha and Singha, 2024). Traditional breeding techniques, such as Sanger sequencing, have been around for a long, but their accuracy, speed, and usefulness are typically limited. Sanger sequencing is useful for small-scale inquiries, but its laborintensive procedures and limited throughput make it unsuitable for large-scale genome analysis. Molecular marker-based breeding strategies have proven to be effective tools for addressing these difficulties by increasing plant growth and overall quality (Bohar et al., 2020). In this respect, molecular markers like as single nucleotide polymorphisms (SNPs), insertions/deletions (indels), simple sequence repeats (SSRs), and structural variations (SVs) are expected to be useful for future breeding operations (Panahi et al., 2024). The discovery and characterization of these molecular markers is strongly reliant on advances in sequencing technology, namely next generation sequencing (NGS). Furthermore, NGS technologies have shown to be crucial for functional genomics, allowing for large-scale transcriptome and whole genome sequencing across plant taxa (Singh et al., 2024). These vast databases give a comprehensive picture of gene expression and genetic variation, making it easier to identify functional markers linked with certain features (Figure 1). The integration of NGS and bioinformatics technologies has simplified the study of these datasets, enabling more efficient discovery of markers and improving the use of marker-assisted selection (MAS) in breeding programs (Panahi et al., 2024).
The development of high-throughput genotyping technology has enabled substantial SNP-based research, which has improved our understanding of genetic diversity, population structure, and disease association (Yirgu et al., 2023). With the progress of genotyping by sequencing (GBS), SNPs have emerged as the most extensively utilized DNA markers in the twenty-first century (Thomson, 2014). SNP markers have significantly advanced plant breeding across a variety of crops, including tomato (Peterson et al., 2012), maize (Junta et al., 2020), rice (Razak et al., 2020), wheat (Wei et al., 2011), soybean (Kim et al., 2010), oil palm (Maryanto et al., 2020), cassava (Karim et al., 2020), and taro (Helmkampf et al., 2018). Overall, SNP markers have emerged as critical tools for genetic improvement and precision breeding across a wide range of crop species. SNPs initially trailed behind SSRs in DNA fingerprinting because they have fewer polymorphisms