Molecular Plant Breeding 2024, Vol.15, No.5, 220-232 http://genbreedpublisher.com/index.php/mpb 223 genetic material to create new allele combinations. In maize, the rate of single nucleotide substitutions has been estimated using data from the domestication locus teosinte branched1 (tb1). This locus, a major target of human selection during maize domestication, shows that polymorphism in the region is consistent with new mutations following fixation for a small number of haplotypes during domestication (Clark et al., 2005). The estimated nucleotide substitution rates for the tb1 intergenic region are approximately 2.9×10-8 and 3.3×10-8 substitutions per site per year, highlighting the role of mutation in generating genetic diversity. Recombination also plays a crucial role in shaping genetic diversity in maize. Genome-wide studies have mapped recombination events across the maize genome, revealing substantial variation in recombination frequency and distribution among different populations. These studies identified 143 recombination hot regions and showed that intragenic recombination events are associated with variation in gene expression and agronomic traits, suggesting that recombination contributes significantly to phenotypic diversity (Pan et al., 2016). Additionally, the correlation between sequence diversity and recombination rates indicates that recombination can break down linkage disequilibrium among single nucleotide polymorphisms (SNPs), further promoting genetic variation (Tenaillon et al., 2001; Tenaillon et al., 2002). 3.2 Gene flow and natural selection Gene flow and natural selection are critical processes influencing nucleotide polymorphism in maize. Gene flow, the transfer of genetic material between populations, introduces new alleles and increases genetic diversity. In maize, gene flow from wild relatives such as teosinte has contributed to the genetic makeup of domesticated maize. This exchange of genetic material has facilitated the adaptation of maize to diverse environments and agricultural practices. Natural selection acts on genetic variation, favoring alleles that confer a selective advantage. In maize, patterns of polymorphism along chromosome 1 show that natural selection shapes genetic diversity. For instance, regions with high gene density and frequent crossing-over exhibit lower levels of nucleotide variability, suggesting that selection on linked variation reduces genetic diversity in these areas (Flowers et al., 2012). Additionally, chromosomal inversions, which suppress recombination, have been identified in wild maize ancestors. These inversions capture locally adapted alleles and show evidence of adaptive evolution, including associations with environmental variables and phenotypic traits (Fang et al., 2012). 3.3 Influence of artificial selection on polymorphism Artificial selection has profoundly influenced nucleotide polymorphism in maize. During domestication, humans selected for desirable traits, leading to rapid phenotypic evolution. Analysis of single-nucleotide polymorphisms in maize genes indicates that 2 to 4% of these genes experienced artificial selection, affecting approximately 1 200 genes throughout the maize genome (Wright et al., 2005). These selected genes are often clustered near quantitative trait loci that contribute to phenotypic differences between maize and its wild ancestor, teosinte. Recent studies have also identified genomic regions that underwent positive artificial selection during maize improvement. For example, a gene-oriented haplotype comparison revealed over 1 100 genomic regions selected during the improvement of temperate and tropical maize germplasm. These regions include regulatory genes and key genes with visible mutant phenotypes, highlighting the role of artificial selection in shaping the maize genome (He et al., 2017). Furthermore, selection for specific traits, such as starch metabolism, has led to low genetic diversity in critical genes involved in these pathways, suggesting that artificial selection can significantly reduce genetic variation in targeted loci (Whitt et al., 2002). The interplay between gene mutation, recombination, gene flow, natural selection, and artificial selection has created a complex landscape of nucleotide polymorphism in maize. Understanding these mechanisms provides valuable insights into the genetic basis of crop traits and informs strategies for future maize breeding and improvement.
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