Molecular Plant Breeding 2024, Vol.15, No.5, 220-232 http://genbreedpublisher.com/index.php/mpb 221 This study analyzes the impact of nucleotide polymorphism on crop traits involves examining how genetic variations influence phenotypic characteristics and overall crop performance. Specific genetic loci have been linked to ear traits that determine maize yield, with some regions showing pleiotropic effects on multiple traits. Additionally, the introgression of adaptive alleles from wild relatives has been shown to enhance the adaptability of maize to different environmental conditions. Understanding these genetic influences is crucial for developing breeding strategies aimed at improving crop traits and ensuring food security. The study of nucleotide polymorphism in maize provides valuable insights into the genetic factors that influence crop traits, explores the historical and current genetic diversity of maize, researchers can develop strategies to enhance its yield, adaptability, and overall performance, thereby supporting global food production and sustainability. 2 Definition and Overview of Nucleotide Polymorphism 2.1 Basic concept of nucleotide polymorphism (SNPs) Nucleotide polymorphisms, particularly single nucleotide polymorphisms (SNPs), are the most common form of genetic variation within a species. SNPs represent a single base pair change in the DNA sequence and can occur throughout the genome. These variations can be found in both coding and non-coding regions of the genome and may or may not affect the function of genes. SNPs are highly abundant and evenly distributed across the genomes of many organisms, making them ideal markers for genetic studies (Rafalski, 2002; Duran et al., 2020; Morgil et al., 2020). The discovery and application of SNPs have been significantly advanced by next-generation sequencing technologies, which allow for the rapid and cost-effective identification of these polymorphisms (Ganal et al., 2009; Morgil et al., 2020). SNPs can be used in various applications, including genetic mapping, population structure analysis, and marker-assisted breeding, due to their high resolution and low mutation rate (Ganal et al., 2009; Duran et al., 2020). 2.2 Distribution and characteristics of nucleotide polymorphisms in plants In plants, SNPs are distributed throughout the genome and are particularly useful for studying genetic diversity and crop improvement. The distribution of SNPs can vary between species and even within different populations of the same species. For example, in maize, SNPs are abundant and evenly distributed, making them valuable for genetic research and breeding programs (Yan et al., 2010). The identification of SNPs in plants has been facilitated by the availability of extensive genomic resources, such as expressed sequence tags (ESTs) and whole-genome sequences (Rafalski, 2002; Duran et al., 2020). These resources allow for the direct readout of SNP haplotypes, which can provide more informative analyses than individual SNPs alone. Additionally, SNPs can be used to identify regions of the genome associated with specific phenotypes, aiding in the selection of desirable traits in breeding programs (Figure 1) (Rafalski, 2002; Morgil et al., 2020). 2.3 Characteristics of nucleotide polymorphism in the maize genome The maize genome is characterized by a high level of nucleotide polymorphism, which has been extensively studied using SNP markers. Maize exhibits a high degree of intraspecific nucleotide diversity, making it an excellent model for genetic studies (Rafalski, 2002; Yan et al., 2010). SNPs in maize are not only abundant but also evenly distributed across the genome, which facilitates their use in high-throughput genotyping platforms such as the GoldenGate assay. This assay allows for the simultaneous genotyping of thousands of SNP markers, providing a comprehensive view of genetic variation in maize populations (Yan et al., 2010). In addition to SNPs, other types of nucleotide polymorphisms, such as insertions and deletions (indels), are also prevalent in the maize genome. These indels can serve as highly informative genetic markers and can be used for genetic mapping and diagnostics (Bhattramakki et al., 2002). The presence of large-scale structural variations, such as chromosomal inversions, further adds to the complexity of the maize genome. For instance, a megabase-scale inversion polymorphism has been identified on chromosome 1 of maize, which captures over 700 genes and shows evidence of adaptive evolution. This inversion is present in the wild ancestors of maize but is absent in domesticated varieties, highlighting the impact of structural variations on the genetic makeup of maize (Fang et al., 2012).
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