Molecular Plant Breeding 2024, Vol.15, No.6, 340-350 http://genbreedpublisher.com/index.php/mpb 342 contaminating crops with mycotoxins. Identifying stable QTLs for resistance traits enables breeders to incorporate these loci into breeding programs, thereby improving the selection efficiency for disease-resistant varieties. For instance, studies have identified multiple QTLs associated with resistance to Fusarium ear rot (FER) and Gibberella ear rot (GER), which can be used to develop maize varieties with enhanced resistance (Figure 1) (Ding et al., 2008; Wu et al., 2020; Zhou et al., 2021; Akohoue and Miedaner, 2022; Yuan et al., 2022). Figure 1 Original QTL reported from SNP-based mapping studies for Fusarium ear rot (FER) and Gibberella ear rot (GER) (Adopted from Akohoue and Miedaner, 2022) Image caption (A), distribution of QTL for FER across chromosomes; (B), phenotypic variance explained (PVE) by QTL for FER; (C), distribution of QTL for GER across chromosomes; (D), phenotypic variance explained by QTL for GER. DON, deoxynivalenol accumulation; FUM , fumonisin accumulation; HC, husk coverage; KDD, kernel dry-down rate; KR, kernel resistance; SR, silk resistance (Adopted from Akohoue and Miedaner, 2022) 3.3 Application of SNP markers in QTL mapping for disease resistance Single nucleotide polymorphisms (SNPs) are the most abundant type of genetic variation in the genome and serve as valuable markers in QTL mapping. SNP markers provide high-resolution mapping, which is essential for identifying precise genomic regions associated with disease resistance. For example, SNP-based QTL mapping has been used to identify loci associated with resistance to Fusarium and Gibberella ear rots in maize. These markers facilitate the integration of QTLs into genomics-assisted breeding programs, enabling the development of maize varieties with improved resistance to these diseases (Ding et al., 2008; Chen et al., 2016; Lanubile et al., 2017; Giomi et al., 2021; Akohoue and Miedaner, 2022; Yuan et al., 2022; Zhou and Jiang, 2024). 4 SNP Markers in Maize Genomics 4.1 Overview of single nucleotide polymorphisms (SNPs) Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation among individuals of a species (Rafalski, 2002; Zhu et al., 2003). In maize, SNPs are valuable markers for genetic studies due to their abundance and stable inheritance patterns. They represent a single base-pair change in the DNA sequence and can be used to track the inheritance of genes associated with important traits, such as disease resistance and yield improvement. 4.2 Advantages of SNP markers in maize genetic studies SNP markers offer several advantages in maize genetic studies. SNPs are densely distributed across the maize genome, providing high-resolution mapping of genetic traits (Lanubile et al., 2017; Akohoue and Miedaner, 2022). And SNPs are stable and reproducible, making them reliable markers for genetic mapping and breeding programs (Zhou et al., 2021; Yuan et al., 2022). Advances in genotyping technologies have made SNP detection cost-effective, facilitating large-scale genetic studies (Gaikpa and Miedaner, 2019). SNP markers are instrumental
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