eChapter Name: Single Nucleotide Polymorphisms (SNPs) and Their Applications in Fingerprinting of Crop Varieties
9789372197969
eBook Name: RECENT ADVANCES IN CROP VARIETY IDENTIFICATION USING DNA TECHNOLOGY
Introduction
The distinctions that differentiate one genotype from another are encoded in their hereditary material i.e., DNA (deoxyribonucleic acid). DNA is packaged into chromosomal pairs, with one strand of genetic material derived from each parent. The genes that govern a plant’s traits are situated on distinct portions of each chromosome (King and Stansfield, 1990). Depending on the context, a genetic marker may be defined as: (a) a chromosomal landmark that facilitates the tracing of a specific DNA region; (b) a distinct DNA segment with a known genomic position; or (c) a gene whose phenotypic expression is easily observable, and used to identify an individual and used as a probe to spot a nucleus, chromosomes, or locus. Molecular markers are distinguishable DNA sequences located at specific loci within the genome, inherited according to the established principles of inheritance from one generation to the subsequent generation. The presence of several molecular approaches, along with their distinct concepts and procedures, necessitates meticulous evaluation when selecting one or more marker types or loci (King and Stansfield, 1990). Various molecular markers have been described, based on mode of transmission, mode of gene action and method of analysis. Single nucleotide polymorphisms (SNPs) are variations in DNA sequences characterized by a single nucleotide (A, T, C, or G) that differs among individuals, serving as biological markers for the identification of genes linked to phenotypes. The genome sequences in public domain from various organisms have facilitated the examination of sequence variations among individuals, among cultivars, and among subspecies. These investigations demonstrated that single nucleotide polymorphisms (SNPs) are prevalent and dispersed across the genome across numerous species, including plants (Drenkard et al., 2000; Nasu et al., 2002).The prevalence of SNPs polymorphisms in plant genomes renders the SNP marker system a valuable marker technology for mapping, marker-assisted breeding, and map-based cloning (Rafalski, 2002a; Batley et al., 2003).A single nucleotide polymorphic (SNP) marker is a single base alteration in a DNA sequence, with a typical alternative of two possible nucleotides at a specific position. In recent years, numerous SNP genotyping methodologies have been established, utilizing diverse techniques for allelic discrimination and detection platforms (Rafalski, 2002b; Vignal et al., 2002; Sobrino et al., 2005; Tost and Gut, 2005).At now, SNPs are preferred for DNA fingerprinting, investigations of genetic diversity and association studies, phylogenetic linkages, studies of evolutionary history of species and population, genome-wide association mapping, and genomic selection. Single nucleotide polymorphisms (SNPs) are the most prevalent and reliable markers, suitable for automated high-throughput genotyping, highly reproducible, and capable of identifying variants, therefore superseding older markers due to their high throughput, efficiency, and cost-effectiveness (Alkan et al, 2011; Amdadul et al, 2016; Close et al., 2009; Muñoz-Amatriaín et al, 2014; Li et al., 2020; Qiuetal., 2012). The swift advancement and use of NGS technology have led to the creation and application of diverse reduced-representation genome sequencing methods for SNP genotyping. The methodologies encompass GBS (Elshire et al., 2011),