Triticeae Genomics and Genetics, 2024, Vol.15, No.1, 56-65 http://cropscipublisher.com/index.php/tgg 59 Nucleotide diversity refers to the variation at the nucleotide level within a population. It is a measure of genetic variation and is crucial for understanding the evolutionary processes and genetic health of a species. Nucleotide diversity is typically quantified using metrics such as the average number of nucleotide differences per site between two DNA sequences chosen randomly from the population. This measure helps in identifying regions of the genome that are under selection and those that are neutral (Russell et al., 2011). 2.2 Development and application of genome sequencing technology Genomic sequencing technology refers to the technique of sequencing the entire genome of an organism. With the continuous development of sequencing technology, from the first generation sequencing technology to the second and third generation sequencing technology, the throughput, accuracy, and speed of sequencing have been greatly improved, enabling a deeper understanding of the genome structure, function, and evolutionary process of organisms. The application of genome sequencing technology is very extensive, including research on human genetic diseases, animal and plant genes, genomic medicine, drug development, and other fields. The advent of genome sequencing technologies has revolutionized the study of nucleotide diversity. High-throughput sequencing methods, such as RNA sequencing, allow for the comprehensive analysis of genetic variation across the entire genome. These technologies enable the identification of single nucleotide polymorphisms (SNPs) and other genetic markers at an unprecedented scale and resolution. For instance, deep transcriptome sequencing has been used to explore sequence variations in transcribed sequences of barley, revealing tens of thousands of SNPs and their genome-wide distribution (Takahagi et al., 2016). This approach is particularly useful for species with large and complex genomes, such as barley (Takahagi et al., 2016). 2.3 Detection and analysis of single nucleotide polymorphism (SNP) Single nucleotide polymorphism (SNP) refers to the genetic marker formed by the variation of a single nucleotide in the genome. This variation is widely present in the human genome, with an average of 1 SNP per 500~1 000 base pairs. SNPs have significant implications in human genetic diseases, differences in drug response, and human evolution. SNPs are the most common type of genetic variation among individuals of a species. They are single base-pair changes in the DNA sequence and serve as valuable markers for genetic studies. The detection and analysis of SNPs involve sequencing DNA from multiple individuals and comparing the sequences to identify variations. In barley, SNP platforms have been employed to assess the evolution and domestication processes. For example, a study using an oligonucleotide pool assay SNP platform analyzed over 1 000 SNPs in geographically matched samples of landrace and wild barley, providing insights into the genetic differentiation and hybridization events in barley populations (Russell et al., 2011). Another study sequenced alleles at multiple loci in barley, identifying numerous SNPs and using them to construct phylogenetic trees and analyze genetic relationships. 2.4 Application of molecular markers in nucleotide diversity research Molecular markers refer to DNA sequence variations that can be stably inherited and easily detected. In the study of nucleotide diversity, molecular markers are widely used in population genetic structure analysis, phylogenetic identification, gene mapping, and other aspects. Common molecular markers include restriction fragment length polymorphism (RFLP), randomly amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and SNP. These markers have different characteristics and applicability, and suitable marker types can be selected based on specific research objectives and conditions. Molecular markers, such as SNPs, are essential tools in nucleotide diversity research. They enable the identification of genetic variations associated with important traits and the study of evolutionary relationships. In barley, molecular markers have been used to investigate the genetic basis of domestication and adaptation. For instance, SNP data have been utilized to differentiate between landrace and wild barley, identify regions of the genome under selection, and suggest possible hybridization events that contribute to the continued adaptation of barley under cultivation (Russell et al., 2011). Additionally, the use of SNP markers has facilitated the study of
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