Molecular Plant Breeding 2024, Vol.15, No.5, 220-232 http://genbreedpublisher.com/index.php/mpb 224 4 Distribution Patterns of Nucleotide Polymorphism in Maize 4.1 Genome-wide distribution of SNPs Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic variation in the maize genome, and their distribution is widespread across the genome. Studies have shown that maize exhibits a high level of nucleotide diversity, with an average of one SNP every 104 base pairs (bp) between two randomly sampled sequences (Tenaillon et al., 2001). This level of diversity is higher than that observed in humans or Drosophila melanogaster. The distribution of SNPs is not uniform, with some regions exhibiting higher diversity than others. For instance, a study using RNA-sequencing (RNA-seq) identified 351 710 polymorphic loci distributed throughout the maize genome, covering 22 830 annotated genes (Hansey et al., 2012). This extensive distribution of SNPs across the genome facilitates their use in genome-wide association studies (GWAS) and marker-assisted selection in breeding programs. The development of high-throughput genotyping platforms, such as the maize 55K SNP array, has further enhanced our ability to map SNPs across the genome. This array includes 55 229 SNPs evenly distributed across the genome, with a significant portion located in exonic and intronic regions (Figure 2) (Xu et al., 2017). Such comprehensive coverage ensures that SNP markers can be effectively used for various genetic analyses, including the identification of genomic regions associated with important agronomic traits. Figure 2 a: Inferred population structure for 593 diverse maize inbred lines with different total number of populations (k = 2 to 8); b: Maximum likelihood phylogenetic tree for 593maize inbred lines (Adopted from Xu et al., 2017) Image caption: a: Each vertical line represents one sample. Membership coefficients (Q values) were summarized from 20 replications performed by fastSTRUCTURE. b: Major population groups were determined by population structure (Adopted from Xu et al., 2017) 4.2 Differences in polymorphism between and within genes The level of nucleotide polymorphism in maize varies significantly between and within genes. In a study examining 21 loci along chromosome 1, it was found that sequence diversity was heterogeneous among loci, with no clear pattern of diversity along the genetic map (Tenaillon et al., 2001). This heterogeneity is influenced by several factors, including recombination rates and selection pressures. For example, recombination rates were found to be correlated with sequence diversity (r=0.65), suggesting that regions with higher recombination rates tend to have higher levels of polymorphism (Tenaillon et al., 2001). RNA-seq studies have also revealed differences in polymorphism within genes. For instance, transcript abundance analysis across 21 maize inbred lines showed that while the total number of genes expressed was relatively
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