Molecular Plant Breeding 2024, Vol.15, No.5, 220-232 http://genbreedpublisher.com/index.php/mpb 222 Figure 1 A common workflow schema for in silico SNP mining (Adopted from Morgil et al., 2020) Image caption: According to the input data type, the steps and the algorithms change. If the data set is de novo assembly output, clustering step is needed. If the data set is based on a reference mapped output, mapping step is required. In order to mine possible SNPs, after clustering and mapping steps, alignment, variant calling, annotation, and diversity analysis should be applied, respectively (Adopted from Morgil et al., 2020) The study of nucleotide polymorphisms in maize provides valuable insights into the genetic diversity and evolutionary history of this important crop. The identification and characterization of these polymorphisms are crucial for understanding the genetic basis of phenotypic traits and for the development of improved maize varieties through marker-assisted breeding (Rafalski, 2002; Yan et al., 2010; Morgil et al., 2020). 3 Mechanisms of Nucleotide Polymorphism Formation in Maize 3.1 Gene mutation and recombination Gene mutation and recombination are fundamental mechanisms driving nucleotide polymorphism in maize. Mutations introduce new genetic variations by altering the DNA sequence, while recombination shuffles existing
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