Bioscience Methods 2024, Vol.15, No.5, 226-236 http://bioscipublisher.com/index.php/bm 227 recent advancements, This study provides information and guidance for future research and breeding strategies to enhance maize productivity and sustainability. 2 Types of Genetic Markers and Their Applications in Maize Breeding 2.1 Simple sequence repeats (SSR) markers Simple sequence repeats (SSRs), also known as microsatellites, are short, tandemly repeated DNA sequences that are highly polymorphic and distributed throughout the genome. They are co-dominant markers, meaning they can distinguish between homozygous and heterozygous states, which is particularly useful in breeding programs. SSRs are easy to score, highly abundant, and provide high-resolution genome coverage. For instance, a study identified 264 658 SSRs across 17 maize genomes, with an average marker density of one SSR every 15.48 kb, highlighting their abundance and utility in genetic studies (Xu et al., 2013). Additionally, SSR markers exhibit high levels of polymorphism, which is beneficial for assessing genetic diversity and relatedness among maize lines (Hamblin et al., 2007). SSRs have been extensively used in maize breeding for various applications, including genetic diversity analysis, germplasm characterization, and marker-assisted selection. They are particularly effective in clustering germplasm into populations and measuring genetic distances based on allele-sharing (Hamblin et al., 2007). SSR markers have also been employed to map quantitative trait loci (QTLs) and to assist in the selection of desirable traits in breeding programs. For example, SSR markers have been used to estimate genetic diversity among maize inbred lines, providing valuable information for breeding strategies (Shehata et al., 2009). Moreover, SSRs have been integrated into high-density genetic linkage maps, facilitating the identification of genomic regions associated with important agronomic traits (Daware et al., 2016). 2.2 Single nucleotide polymorphisms (SNPs) Single nucleotide polymorphisms (SNPs) are single base-pair variations in the DNA sequence that occur throughout the genome. SNPs are the most abundant type of genetic variation and can be detected using high-throughput genotyping technologies. They offer several technical advantages, including higher data repeatability, lower levels of missing data, and the ability to detect expected alleles in hybrids and DNA pools. For instance, SNP marker data showed more than a fourfold lower level of missing data compared to SSRs and higher repeatability rates (Jones et al., 2007). These characteristics make SNPs highly suitable for large-scale genotyping and genetic studies. SNPs have been increasingly used in hybrid maize development due to their high density and the ability to provide detailed genetic information. They are particularly useful in assessing genetic diversity and relatedness among maize lines, which is crucial for hybrid breeding. Although SSRs performed better at clustering germplasm into populations, SNPs can compensate for their lower polymorphism by increasing the number of loci analyzed (Hamblin et al., 2007). SNP markers have been successfully used to genotype maize inbreds and hybrids, providing valuable insights into the genetic makeup and aiding in the selection of parent lines for hybrid development (Jones et al., 2007). 2.3 Other molecular markers Other molecular markers, such as random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP), have also been used in maize breeding. RAPD markers are based on the amplification of random DNA segments, while AFLP markers involve the selective amplification of restriction fragments. These markers are generally dominant, meaning they cannot distinguish between homozygous and heterozygous states. However, they are useful for generating a large number of markers quickly and can be applied to a wide range of species without prior sequence information. RAPD and AFLP markers have been used in specific breeding scenarios where rapid and cost-effective genotyping is required. They are particularly useful in early-stage breeding programs for preliminary genetic mapping and diversity studies. For example, RAPD markers have been employed to assess genetic diversity in maize germplasm collections, providing initial insights into the genetic structure of the populations. AFLP
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