Molecular Plant Breeding 2025, Vol.16, No.1, 24-34 http://genbreedpublisher.com/index.php/mpb 26 height across multiple environments, highlighting the genetic variation present in tropical maize populations (Sibov et al., 2004). Additionally, the integration of high-density SNP markers through genotyping-by-sequencing (GBS) has facilitated the construction of detailed genetic linkage maps, enabling the identification of numerous QTLs associated with yield traits (Su et al., 2017). This genetic diversity is crucial for the development of robust maize varieties that can adapt to mechanized farming practices, ultimately leading to improved crop performance and yield stability. 4 SNP Markers and Their Application in Gene Mapping 4.1 Overview of single nucleotide polymorphisms (SNPs) as genetic markers Single nucleotide polymorphisms (SNPs) are the most frequent type of genetic variation found within genomes. They occur when a single nucleotide in the genome sequence is altered. SNPs are abundant and evenly distributed across the genomes of most plant species, making them ideal markers for genetic research. Their high frequency and distribution allow for detailed genetic mapping and association studies, which are crucial for understanding the genetic basis of complex traits in crops like maize (Rafalski, 2002; Jones et al., 2009; Yan et al., 2010). 4.2 Methods for SNP marker identification and validation The identification and validation of SNP markers involve several steps, starting from sequencing and SNP discovery to marker design and validation. Various high-throughput platforms and technologies have been developed to facilitate this process. Sequencing-by-synthesis technologies, such as Illumina sequencing, enable efficient genome-wide SNP discovery by reducing genome complexity and focusing on informative regions. Complexity reduction of polymorphic sequences (CRoPS) reduces the complexity of the genome, allowing for the identification of informative SNPs between genetically distinct lines (Mammadov et al., 2010). GoldenGate assay allows for the rapid and simultaneous genotyping of up to a million SNP markers, providing high accuracy and low error rates (Yan et al., 2010). KASP SNP markers developed from RNA-Seq data, these markers are used for automatic genotyping and are highly polymorphic, making them valuable for map-based cloning and marker-assisted selection (Chen et al., 2021). Validation of SNP markers typically involves in silico analysis and experimental validation using platforms like the Illumina GoldenGate assay, which ensures the accuracy and polymorphism of the identified SNPs (Mammadov et al., 2010; Chen et al., 2021). 4.3 Case studies of successful SNP mapping in maize Several studies have demonstrated the successful application of SNP markers in maize gene mapping. Researchers mined 1 088 loci sequenced across 60 public inbreds used in maize breeding, identifying SNPs that were amenable to marker design. These SNPs were mapped on the IBM2 high-resolution genetic map, showing high colinearity with the genetic nested association map (Jones et al., 2009). A custom GoldenGate assay containing 1 536 SNPs was developed and used to genotype two recombinant inbred line populations and a panel of diverse inbred lines. This study successfully integrated SNP markers with previously mapped simple sequence repeat markers to construct a high-density linkage map (Yan et al., 2010). Using the DArTseq method, researchers identified 49 911 polymorphisms, including 16 459 SNP markers, which were associated with various morphological traits in maize. This method allowed for the identification of markers linked to important agronomic traits, facilitating marker-assisted selection (Tomkowiak et al., 2021). These case studies highlight the effectiveness of SNP markers in genetic mapping and their potential to enhance maize breeding programs by enabling the precise identification of genes associated with desirable traits. 5 Breeding Strategies for Mechanical Adaptation 5.1 Traditional breeding methods for enhancing mechanization-friendly traits Traditional breeding methods have long been employed to enhance mechanization-friendly traits in maize. These methods primarily rely on phenotypic selection, where plants exhibiting desirable traits are selected and bred over multiple generations. This approach, while effective, is often time-consuming and labor-intensive. Traditional breeding has been successful in improving traits such as plant height, ear placement, and stalk strength, which are crucial for mechanical harvesting. However, the process is limited by the genetic variability present in the breeding population and the environmental influence on phenotypic expression.
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